• Journal of Life Science
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• v.13 no.5
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• pp.596-603
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• 2003

Cells respond to an accumulation of unfolded proteins in the endoplasmic reticulum (ER) by increasing transcription of genes encoding molecular chaperones and folding enzymes. The information is transmitted from the ER lumen to the nucleus by intracellular signaling pathway, called the unfolded protein response (UPR). To obtain genes related to UPR from B. mori, the cDNA library was constructed with mRNA isolated from Bm5 cell lines in which N-glycosylation was inhibited by tunicamycin treatment. From the cDNA library, we selected 40 clones that differentially expressed when cells were treated with tunicamycin. Among these clones, we have isolated ATFC gene showing similarity with Hac1p, encoding a bZIP transcription factor of 5. cerevisiae. Basic-leucine zipper (bZIP) domain in amino acid sequences of ATFC shared homology with yeast Hac1p. Also, ATFC is up-regulated by accumulation of unfolded proteins in the ER through the treatment of ER stress drugs. Therefore we suggest that ATFC represents a major component of the putative transcription factor responsible for the UPR leading to the induction of ER-localized stress proteins.

• Journal of Microbiology and Biotechnology
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• v.20 no.2
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• pp.301-310
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• 2010

Bacillus subtilis strains produce a broad spectrum of bioactive peptides. The lipopeptide surfactin belongs to one well-known class, which includes amphiphilic membrane-active biosurfactants and peptide antibiotics. Both the srfA promoter and the ComP-ComA signal transduction system are an important part of the factor that results in the production of surfactin. Bs-M49, obtained by means of low-energy ion implantation in wild-type Bs-916, produced significantly lower levels of surfactin, and had no obvious effects against R. solani. Occasionally, we found strain Bs-M49 decreased spore formation and the development of competence. Blast comparison of the sequences from Bs-916 and M49 indicate that there is no difference in the srfA operon promoter PsrfA, but there are differences in the coding sequence of the comA gene. These differences result in three missense mutations within the M49 ComA protein. RT-PCR analyses results showed that the expression levels of selected genes involved in competence and sporulation in both the wild-type Bs-916 and mutant M49 strains were significantly different. When we integrated the comA ORF into the chromosome of M49 at the amyE locus, M49 restored hemolytic activity and antifungal activity. Then, HPLC analyses results also showed the comA-complemented strain had a similar ability to produce surf actin with wild-type strain Bs-916. These data suggested that the mutation of three key amino acids in ComA greatly affected the biological activity of Bacillus subtilis. ComA protein 3D structure prediction and motif search prediction indicated that ComA has two obvious motifs common to response regulator proteins, which are the N-terminal response regulator receiver motif and the C-terminal helix-turn-helix motif. The three residues in the ComA N-terminal portion may be involved in phosphorylation activation mechanism. These structural prediction results implicate that three mutated residues in the ComA protein may play an important role in the formation of a salt-bridge to the phosphoryl group keeping active conformation to subsequent regulation of the expression of downstream genes.

• Journal of Sericultural and Entomological Science
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• v.52 no.2
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• pp.102-109
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• 2014

We constructed the fibroin H-chain expression system to produce enhanced yellow fluorescent proteins (EYFP) in the silk of transgenic silkworm. Fluorescent silk could be made by fusing EYFP cDNA to the heavy chain gene and injecting it into a silkworm. The EYFP fusion protein, each with N- and C-terminal sequences of the fibroin H-chain, was designed to be secreted into the lumen of the posterior silk glands. The expression of the EYFP/H-chain fusion gene was regulated by the fibroin H-chain promoter. The yellow fluorescence proving that the fusion protein was present in the silk. Accordingly, we suggest that the EYFP fluorescence silk will enable the production of novel biomaterial based on the transgenic silk.

• Journal of Microbiology and Biotechnology
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• v.34 no.5
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• pp.1146-1153
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• 2024

The increasing economic losses associated with growth retardation caused by Enterocytozoon hepatopenaei (EHP), a microsporidian parasite infecting penaeid shrimp, require effective monitoring. The internal transcribed spacer (ITS)-1 region, the non-coding region of ribosomal clusters between 18S and 5.8S rRNA genes, is widely used in phylogenetic studies due to its high variability. In this study, the ITS-1 region sequence (~600-bp) of EHP was first identified, and primers for a polymerase chain reaction (PCR) assay targeting that sequence were designed. A newly developed nested-PCR method successfully detected the EHP in various shrimp (Penaeus vannamei and P. monodon) and related samples, including water and feces collected from Indonesia, Thailand, South Korea, India, and Malaysia. The primers did not cross-react with other hosts and pathogens, and this PCR assay is more sensitive than existing PCR detection methods targeting the small subunit ribosomal RNA (SSU rRNA) and spore wall protein (SWP) genes. Phylogenetic analysis based on the ITS-1 sequences indicated that the Indonesian strain was distinct (86.2% nucleotide sequence identity) from other strains collected from Thailand and South Korea, and also showed the internal diversity among Thailand (N = 7, divided into four branches) and South Korean (N = 5, divided into two branches) samples. The results revealed the ability of the ITS-1 region to determine the genetic diversity of EHP from different geographical origins.

• Journal of KIISE:Databases
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• v.31 no.5
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• pp.468-478
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• 2004

It is essential in various application areas of data mining and bioinformatics to effectively retrieve the occurrences of interesting patterns from sequence databases. For example, let's consider a network event management system that records the types and timestamp values of events occurred in a specific network component(ex. router). The typical query to find out the temporal casual relationships among the network events is as fellows: 'Find all occurrences of CiscoDCDLinkUp that are fellowed by MLMStatusUP that are subsequently followed by TCPConnectionClose, under the constraint that the interval between the first two events is not larger than 20 seconds, and the interval between the first and third events is not larger than 40 secondsTCPConnectionClose. This paper proposes an indexing method that enables to efficiently answer such a query. Unlike the previous methods that rely on inefficient sequential scan methods or data structures not easily supported by DBMSs, the proposed method uses a multi-dimensional spatial index, which is proven to be efficient both in storage and search, to find the answers quickly without false dismissals. Given a sliding window W, the input to a multi-dimensional spatial index is a n-dimensional vector whose i-th element is the interval between the first event of W and the first occurrence of the event type Ei in W. Here, n is the number of event types that can be occurred in the system of interest. The problem of‘dimensionality curse’may happen when n is large. Therefore, we use the dimension selection or event type grouping to avoid this problem. The experimental results reveal that our proposed technique can be a few orders of magnitude faster than the sequential scan and ISO-Depth index methods.hods.

• ALGAE
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• v.32 no.4
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• pp.359-377
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• 2017

Pyropia haitanensis (T. J. Chang et B. F. Zheng) N. Kikuchi et M. Miyata is one of the most commercially useful macroalgae cultivated in southeastern China. In red algae, the biosynthesis of terpenoids through 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway can produce a direct influence on the synthesis of many biologically important metabolites. In this study, two genes of cDNAs, 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and 1-deoxy-D-xylulose-5-phosphate reductase (DXR), which encoding the first two rate-limiting enzymes among MEP pathway were cloned from P. haitanensis. The cDNAs of P. haitanensis DXS (PhDXS) and DXR (PhDXR) both contained complete open reading frames encoding polypeptides of 764 and 426 amino acids residues, separately. The expression analysis showed that PhDXS was significant differently expressed between leafy thallus and conchocelis as PhDXR been non-significant. Additionally, expression of PhDXR and its downstream gene geranylgeranyl diphosphate synthase were both inhibited by fosmidomycin significantly. Meanwhile, we constructed types of phylogenetic trees through different algae and higher plants DXS and DXR encoding amino acid sequences, as a result we found tree clustering consequences basically in line with the "Cavalier-Smith endosymbiotic theory." Whereupon, we speculated that in red algae, there existed only complete MEP pathway to meet needs of terpenoids synthesis for themselves; Terpenoids synthesis of red algae derivatives through mevalonate pathway came from two or more times endosymbiosis of heterotrophic eukaryotic parasitifer. This study demonstrated that PhDXS and PhDXR could play significant roles in terpenoids biosynthesis at molecular levels. Meanwhile, as nuclear genes among MEP pathway, PhDXS and PhDXR could provide a new way of thinking to research the problem of chromalveolata biological evolution.

• Journal of Microbiology and Biotechnology
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• v.33 no.7
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• pp.909-914
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• 2023

While searching for the bacteria which are responsible for degradation of pesticide in soybean field soil, a novel bacterial strain, designated 5-5^T, was isolated. The cells of the strain were Gram-staining-positive, aerobic and non-motile rods. Growth occurred at 10-42℃ (optimum, 30℃), pH 5.5-9.0 (optimum, pH 7.0-7.5), and 0-2% (w/v) NaCl (optimum, 1%). The predominant fatty acids were C_15:0 anteiso, C_17:0 anteiso, and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The predominant menaquinone was MK-9 (H₂). Diphosphatidylglycerol, glycolipids, phosphatidylinositol, and phosphatidylglycerol were the major polar lipids. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain 5-5^T is a member of the genus Sinomonas and its closest relative is Sinomonas humi MUSC 117^T, sharing a genetic similarity of 98.4%. The draft genome of strain 5-5^T was 4,727,205 bp long with an N50 contig of 4,464,284 bp. Genomic DNA G+C content of strain 5-5^T was68.0 mol%. The average nucleotide identity (ANI) values between strain 5-5^T and its closest strains S. humi MUSC 117^T and S. susongensis A31^T were 87.0, and 84.3 % respectively. In silico DNA-DNA hybridization values between strain 5-5^T and its closest strains S. humi MUSC 117^T and S. susongensis A31^T were 32.5% and 27.9% respectively. Based on the ANI and in silico DNA-DNA hybridization analyses, the 5-5^T strain was considered as novel species belonging to the genus Sinomonas. On the basis of the results from phenotypic, genotypic and chemotaxonomic analyses, strain 5-5^T represents a novel speciesof the genus Sinomonas, for which the name Sinomonas terrae sp. nov. is proposed. The type strain is 5-5^T (=KCTC 49650^T =NBRC 115790^T).

• Korean Journal of Microbiology
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• v.54 no.1
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• pp.60-68
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• 2018

A cold-active and alkaline serine protease (Pro21717) was partially purified from the Antarctic marine bacterium Pseudoalteromonas arctica PAMC 21717. On a zymogram gel containing skim milk, Pro21717 produced two distinct clear-zones of approximately 37 kDa (low intensity) and 74 kDa (high intensity). These were found to have identical N-terminal sequences, suggesting they arose from an identical precursor and that the 37 kDa protease might homodimerize to the more active 74 kDa form of the protein. Pro21717 displayed proteolytic activity at $0-40^{\circ}C$ (optimal temperature of $40^{\circ}C$) and maintained this activity at pH 5.0-10.0 (optimal pH of 9.0). Notably, relative activities of 30% and 45% were observed at $0^{\circ}C$ and $10^{\circ}C$, respectively, in comparison to the 100% activity observed at $40^{\circ}C$, and this enzyme showed a broad substrate range against synthetic peptides with a preference for proline in the cleavage reaction. Pro21717 activity was enhanced by $Cu^{2+}$ and remained stable in the presence of detergent surfactants (linear alkylbenzene sulfonate and sodium dodecyl sulfate) and other chemical components ($Na_2SO_4$ and metal ions, such as $Ba^{2+}$, $Mg^{2+}$, $Ca^{2+}$, $Zn^{2+}$, $Fe^{2+}$, $K^+$, and $Na^{2+}$), which are often included in commercial detergent formulations. These data indicate that the psychrophilic Pro21717 has properties comparable to the well-characterized mesophilic subtilisin Carlsberg, which is commercially produced by Novozymes as the trademark Alcalase. Thus it has the potential to be used as a new additive enzyme in laundry detergents that must work well in cold tap water below $15^{\circ}C$.

• Research in Plant Disease
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• v.27 no.1
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• pp.1-7
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• 2021

In August 2020, necrotic ringspots on leaves were observed on 20 from 143 Plantago asiatica plants in open fields in Eumseong, Chungcheongbuk-do. Eight symptomatic Plantago asiatica plants were subjected to investigation on viral infection by reverse transcription and polymerase chain reaction. Impatiens necrotic spot virus, tomato spotted wilt virus and cucumber mosaic virus were detected from the symptomatic plants. Two impatiens necrotic spot virus (INSV) isolates ('INSV-plantain kr1' and '-plantain kr5') were sequenced and analyzed by comparing L genomic segment, nucleoprotein (N) gene and non-structural protein S (NSs) gene sequences. The nucleotide sequence of 'INSV-plantain kr1' isolate (MW114834) was most closely related to that of a 'Phalaenopsis' isolate (GQ336991) from China in the L genomic segment. 'INSV-plantain kr1' and '-plantain kr5' isolates shared the highest identities with those from 'Pepe' isolate (LC384872) and 'J' isolate (AB109100) in the NSs gene, respectively, and with that from 'YSMi-SH' isolate (FN400773) in the N gene. Phylogenetic analysis based on L genomic segment grouped the INSV-plantain kr1 isolate together with isolates from Korea (LC384870), China (GU112505, GQ336991), and Italy (DQ425094). This is the first report on INSV in P. asiatica from Korea.

• Journal of Animal Science and Technology
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• v.45 no.6
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• pp.911-916
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• 2003

The mitochondrial DNA(mtDNA) D-loop region was amplified from Duroc(Sus scrofa) by polymerase chain reaction(PCR). The oligonucleotide primer used to amplify the Sus scrofa mtDNA D-loop region was designed using tRNA-Pro and tRNA-Phe sequence in mtDNA regions highly conserved in many other animal species. There were 1,145 base pairs(bp) in the D-loop region. The middle of the region contained 10 tandem repeat of an 10-bp Sus scrofa-specific sequence, TACACGTGCG. We designed primers for PCR-mediated single stranded conformation polymorphism(SSCP) analysis that amplified a 345 bp fragment, which contained the most variable region according to our sequencing data. SSCP analysis of denatured amplification products was carried out by polyacrylamide(8%) gel electrophoresis followed by ethidium bromide staining. The SSCP analysis identified two band patterns(A and B) and comparision of these two nucleotide sequences identified 21 base substitutions. These results show that SSCP analysis of the D-loop region is useful for detecting the genetic polymorphism.