• Journal of Microbiology and Biotechnology
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• v.33 no.3
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• pp.410-418
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• 2023

Bacilysin is a dipeptide antibiotic composed of L-alanine and L-anticapsin produced by certain strains of Bacillus subtilis. Bacilysin is gaining increasing attention in industrial agriculture and pharmaceutical industries due to its potent antagonistic effects on various bacterial, fungal, and algal pathogens. However, its use in industrial applications is hindered by its low production in the native producer. The biosynthesis of bacilysin is mainly based on the bacABCDEF operon. Examination of the sequence surrounding the upstream of the bac operon did not reveal a clear, strong ribosome binding site (RBS). Therefore, in this study, we aimed to investigate the impact of RBS as a potential route to improve bacilysin production. For this, the 5' untranslated region (5'UTR) of the bac operon was edited using the CRISPR/Cas9 approach by introducing a strong ribosome binding sequence carrying the canonical Shine-Dalgarno sequence (TAAGGAGG) with an 8 nt spacing from the AUG start codon. Strong RBS substitution resulted in a 2.87-fold increase in bacilysin production without affecting growth. Strong RBS substitution also improved the mRNA stability of the bac operon. All these data revealed that extensive RBS engineering is a promising key option for enhancing bacilysin production in its native producers.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.3
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• pp.143-148
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• 2015

In some pathogenic bacteria, there are RNA thermometers, which regulate the production of virulence associated factors or heat shock proteins depending on temperature changes. Like a riboswitches, RNA thermometers are located in the 5'-untranslated region and involved translational gene regulatory mechanism. RNA thermometers block the ribosome-binding site and start codon area under the $37^{\circ}C$ within their secondary structure. After bacterial infection, increased the temperature in the host causes conformations changes of RNA, and the ribosome-binding site is exposed for translational initiation. Because structural differences between open and closed forms of RNA thermometers are mainly mediated by base pairing changes, NMR spectroscopy is a very useful method to study these thermodynamically changing RNA structure. In this review, we briefly provide a fundamental function of RNA thermometers, and also suggest a proper NMR experiments for studying RNA thermometers.

• Journal of Microbiology and Biotechnology
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• v.25 no.7
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• pp.963-977
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• 2015

The well-characterized gram-positive bacterium Bacillus subtilis is an outstanding industrial candidate for protein expression owing to its single membrane and high capacity of secretion, simplifying the downstream processing of secretory proteins. During the last few years, there has been continuous progress in the illustration of secretion mechanisms and application of this robust host in various fields of life science, such as enzyme production, feed additives, and food and pharmaceutical industries. Here, we review the developments of Bacillus subtilis as a highly promising expression system illuminating strong chemical- and temperatureinducible and other types of promoters, strategies for ribosome-binding-site utilization, and the novel approach of signal peptide selection. Furthermore, we outline the main steps of the Sec pathway and the relevant elements as well as their interactions. In addition, we introduce the latest discoveries of Tat-related complex structures and functions and the countless applications of this full-folded protein secretion pathway. This review also lists some of the current understandings of ATP-binding cassette transporters. According to the extensive knowledge on the genetic modification strategies and molecular biology of Bacillus subtilis, we propose some suggestions and strategies for improving the yield of intended productions. We expect this to promote striking future developments in the optimization and application of this bacterium.

• International Journal of Industrial Entomology and Biomaterials
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• v.6 no.1
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• pp.81-85
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• 2003

To verify importance of the intervening sequence between the ribosome binding site (RBS) and the initiation codon for expression of Bacillus thuringiensis $\delta$-endotoxin, the pProMu, containing SphI and NcoIsites between RBS and the initiation codon of the cry1Ac gene, and the deletion derivatives of pProMu were constructed and transformed into the B. thuringiensis subsp. kurstaki $Cry^{-B}$ strain. The pProMu-ΔSphIhad identical six bases of intervening sequence to pProAc though the arrangement of sequence was different. Other mutants containing pProMu had 1 or 10 or 14 bases between RBS and the initiation codon. Among deletion mutants, only ProMu-ΔSphI/CB only produced 130 kDa typical bipyramidal crystals like those seen for ProAc/CB. However, ProMu/CB, $ProMu-{\Delta}NcoI$, and ProMu-ΔSphI＋NcoIdid not produce Cry1Ac crystals. In conclusion, the results suggest that 6-base intervening sequence was important for expression of cry1-type class gene. Furthermore, spacing effect of the intervening sequences may play an important role in expression of individual crystal proteins in B. thuringiensis without doubt.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.35-40
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• 2005

Interaction of twelve erythromycin A analogues with 50S ribosomal subunit were studied employing AutoDock 3.0.5. Results showed that all active macrolides bound at the same binding site with erythromycin A in contrast to the inactive analogues which bound at location slightly different than erythromycin A. The binding site showed consistency with the X-ray data from the perspectives of hydrogen bonding and hydrophobic interactions formed by erythromycins, roxithromycin, azithromycin, cethromycin and telithromycin with the ribosome. The inactive derivatives of erythromycin A anhydride showed higher binding free energy, while 5-desosaminyl erythronolides A and B even though having quiet similar values of binding free energy with the active analogues, docked at binding sites which are quiet different than the active analogues. These results suggest the molecular docking technique can be used in predicting the binding of erythromycin A analogues to their ribosomal target.

• Molecules and Cells
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• v.20 no.1
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• pp.1-16
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• 2005

The peptidyl transferase center (PTC) is located in a protein free environment, thus confirming that the ribosome is a ribozyme. This arched void has dimensions suitable for accommodating the 3'ends of the A-and the P-site tRNAs, and is situated within a universal sizable symmetry-related region that connects all ribosomal functional centers involved in amino-acid polymerization. The linkage between the elaborate PTC architecture and the A-site tRNA position revealed that the A-to P-site passage of the tRNA 3'end is performed by a rotatory motion, which leads to stereochemistry suitable for peptide bond formation and for substrate mediated catalysis, thus suggesting that the PTC evolved by genefusion. Adjacent to the PTC is the entrance of the protein exit tunnel, shown to play active roles in sequence-specific gating of nascent chains and in responding to cellular signals. This tunnel also provides a site that may be exploited for local co-translational folding and seems to assist in nascent chain trafficking into the hydrophobic space formed by the first bacterial chaperone, the trigger factor. Many antibiotics target ribosomes. Although the ribosome is highly conserved, subtle sequence and/or conformational variations enable drug selectivity, thus facilitating clinical usage. Comparisons of high-resolution structures of complexes of antibiotics bound to ribosomes from eubacteria resembling pathogens, to an archaeon that shares properties with eukaryotes and to its mutant that allows antibiotics binding, demonstrated the unambiguous difference between mere binding and therapeutical effectiveness. The observed variability in antibiotics inhibitory modes, accompanied by the elucidation of the structural basis to antibiotics mechanism justifies expectations for structural based improved properties of existing compounds as well as for the development of novel drugs.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.3
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• pp.109-113
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• 2017

The hepatitis C virus (HCV) internal ribosome entry site (IRES) is an RNA structure located in the 5'-UTR of the HCV RNA genome. The HCV IRES consists of four domains I, II, III, and IV, where domains II - IV are recognized by 40S ribosomal subunit and the domain III is bound to eukaryotic initiation factor 3 (eIF3) for translation initiation. Here, we have characterized the tertiary interaction between an L-/K- rich peptide and the HCV IRES domain IV. To probe the peptide binding interface in RNA, we synthesized $^{13}C$- and $^{15}N$-double labeled RNA and the binding site was identified by using the chemical shift perturbation (CSP) NMR methods. Our results showed that the peptide binds to the upper stem of the IRES domain IV, indicating that the tertiary interaction between the IRES domain IV and the peptide would disrupt the initiation of translation of HCV mRNA by blocking the start codon exposure. This study will provide an insight into the new peptide-based anti-viral drug design targeting HCV IRES RNA.

• Journal of Microbiology and Biotechnology
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• v.28 no.12
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• pp.2046-2056
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• 2018

Phospholipase D has great commercial value due to its transphosphatidylation products that can be used in the food and medicine industries. In order to construct a strain for use in the production of PLD, we employed a series of combinatorial strategies to increase PLD expression in Bacillus subtilis WB600. These strategies included screening of signal peptides, selection of different plasmids, and optimization of the sequences of the ribosome-binding site (RBS) and the spacer region. We found that using the signal peptide amyE results in the highest extracellular PLD activity (11.3 U/ml) and in a PLD expression level 5.27-fold higher than when the endogenous signal peptide is used. Furthermore, the strain harboring the recombinant expression plasmid pMA0911-PLD-amyE-his produced PLD with activity enhanced by 69.03% (19.1 U/ml). We then used the online tool \RBS Calculator v2.0 to optimize the sequences of the RBS and the spacer. Using the optimized sequences resulted in an increase in the enzyme activity by about 26.7% (24.2 U/ml). In addition, we found through a transfer experiment that the retention rate of the recombinant plasmid after 5 generations was still 100%. The final product, phosphatidylserine (PS), was successfully detected, with transphosphatidylation selectivity at 74.6%. This is similar to the values for the original producer.

• Korean Journal of Microbiology
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• v.24 no.3
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• pp.236-242
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• 1986

The nucleotide sequence of the genetic control site of Bacillus subtilis gene for $(1-4)-{\beta}-D-glucan$ endoglucanase (cellulase) was determined according to the procedures of the dideoxy chain termination method(Sanger et. al., 1977). The deduced amino acid sequence of this enzyme has a hydrophobic signal peptide at the $NH_2$ terminus similar to those found in fifteen other extracellualr enzymes from Bacillus species. This is followed by a sequence resembling the Bacillus ribosome binding site 14 nucleotide before the first codon of the gene. The presumptive promoter sequence was located 92 base pairs upstream fromthe initiation codon. The homology region in signal sequences was striking when comparing all the signal sequences of sixteen extracellular enzymes from Bacillus species so far compiled.

• Archives of Pharmacal Research
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• v.29 no.12
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• pp.1154-1157
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• 2006

The ermK gene from Bacillus lichenformis encodes an inducible rRNA methylase that confers resistance to the macrolide-lincosamide-streptogramin B antibiotics. The ermK mRNA leader sequence has a total length of 357 nucleotides and encodes a 14-amino acid leader peptide together with its ribosome binding site. The secondary structure of ermK leader mRNA and a leader peptide sequence have been reported as the elements that control expression. In this study, the contribution of specific leader peptide amino acid residues to induction of ermK was studied using the PCR-based megaprimer mutation method. ermK methylases with altered leader peptide codons were translationally fused to E. coli ${\beta}-galactosidase$ reporter gene. The deletion of the codons for Thr-2 through Ser-4 reduced inducibility by erythromycin, whereas that for Thr-2 and His-3 was not. The replacement of the individual codons for Ser-4, Met-5 and Arg-6 with termination codon led to loss of inducibility, but stop mutation of codon Phe-9 restored inducibility by erythromycin. Collectively, these findings suggest that the codons for residue 4, 5 and 6 comprise the critical region for induction. The stop mutation at Leu-7 expressed constitutively ermK gene. Thus, ribosome stalling at codon 7 appears to be important for ermK induction.