• Genomics & Informatics
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• 제20권2호
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• pp.24.1-24.8
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• 2022

Hypomyelinating leukodystrophy type 2 (HLD2), is an inherited genetic disease of the central nervous system caused by recessive mutations in the gap junction protein gamma 2 (GJC2/GJA12). HLD2 is characterized by nystagmus, developmental delay, motor impairments, ataxia, severe speech problem, and hypomyelination in the brain. The GJC2 sequence encodes connexin 47 protein (Cx47). Connexins are a group of membrane proteins that oligomerize to construct gap junctions protein. In the present study, a novel missense mutation gene c.760G>A (p.Val254Met) was identified in a patient with HLD2 by performing whole exome sequencing. Following the discovery of the new mutation in the proband, we used Sanger sequencing to analyze his affected sibling and parents. Sanger sequencing verified homozygosity of the mutation in the proband and his affected sibling. The autosomal recessive inheritance pattern was confirmed since Sanger sequencing revealed both healthy parents were heterozygous for the mutation. PolyPhen2, SIFT, PROVEAN, and CADD were used to evaluate the function prediction scores of detected mutations. Cx47 is essential for oligodendrocyte function, including adequate myelination and myelin maintenance in humans. Novel mutation p.Val254Met is located in the second extracellular domain of Cx47, both extracellular loops are highly conserved and probably induce intramolecular disulfide interactions. This novel mutation in the Cx47 gene causes oligodendrocyte dysfunction and HLD2 disorder.

• 한국컴퓨터정보학회논문지
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• 제14권1호
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• pp.73-80
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• 2009

GPCR(Gprotein-coupled receptors) 패밀리(family)는 세포막 단백질로서, 외부 신호를 세포막을 경유하여 세포 내로 전달하는 신호전달 기전에서 중요한 역할을 담당한다. 그러나 GPCR마다 다양하고 복잡한 조절기전을 보이며 매우 특이적인 신호전달 기전을 가지는 것으로 알려져 있다. GPCR의 구조적인 특징과 패밀리 및 서브패밀리 등은 기능별로 잘 알려져 있는데 과거 GPCR을 찾아내는 연구 중에 가장 기본이 되는 일이 주어진 단백질 서열로부터 GPCR을 분류하는 일이다. 이미 발견된 GPCR들을 가지고 수학적인 모델을 이용하여 보다 정확하게 분류하는 연구가 주로 진행되어 왔다. 본 논문에서는 단백질의 기능이 입체적 구조에 의해 결정되는 점에 착안하여 두 GPCR의 아미노산 서열의 유사도가 낮은 경우에 그 2차 구조의 서열을 비교함으로써 기존의 발견된 GPCR의 데이터베이스에서 동일한 기능을 가졌을 것으로 추정되는 미지의 GPCR을 검출하는 방법을 제안한다.

• 제어로봇시스템학회논문지
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• 제12권10호
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• pp.1044-1049
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• 2006

Multiple sequence alignment is a method to compare two or more DNA or protein sequences. Most of multiple sequence alignment tools rely on pairwise alignment and Smith-Waterman algorithm to generate an alignment hierarchy. Therefore, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST and CDD (Conserved Domain Database)search were combined with a clustering tool. Our clustering and annotating tool consists of constructing suffix tree, overlapping common subsequences, clustering gene sequences and annotating gene clusters by BLAST and CDD search. The system was successfully evaluated with 36 gene sequences in the pentose phosphate pathway, clustering 10 clusters, finding out representative common subsequences, and finally identifying functional domains by searching CDD database.

• Mycobiology
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• 제50권4호
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• pp.254-257
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• 2022

Wolfiporia cocos is a wood-decay brown rot fungus belonging to the family Polyporaceae. While the fungus grows, the sclerotium body of the strain, dubbed Bokryeong in Korean, is formed around the roots of conifer trees. The dried sclerotium has been widely used as a key component of many medicinal recipes in East Asia. Wolfiporia cocos strain KMCC03342 is the reference strain registered and maintained by the Korea Seed and Variety Service for commercial uses. Here, we present the first draft genome sequence of W. cocos KMCC03342 using a hybrid assembly technique combining both short- and long-read sequences. The genome has a total length of 55.5 Mb comprised of 343 contigs with N50 of 332 kb and 95.8% BUSCO completeness. The GC ratio was 52.2%. We predicted 14,296 protein-coding gene models based on ab initio gene prediction and evidence-based annotation procedure using RNAseq data. The annotated genome was predicted to have 19 terpene biosynthesis gene clusters, which was the same number as the previously sequenced W. cocos strain MD-104 genome but higher than Chinese W. cocos strains. The genome sequence and the predicted gene clusters allow us to study biosynthetic pathways for the active ingredients of W. cocos.

• KSII Transactions on Internet and Information Systems (TIIS)
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• 제6권11호
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• pp.2784-2799
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• 2012

Biological data have been increased exponentially in recent years, and analyzing these data using data mining tools has become one of the major issues in the bioinformatics research community. This paper focuses on the protein construction process in higher organisms where the deoxyribonucleic acid, or DNA, sequence is filtered. In the process, "unmeaningful" DNA sub-sequences (called introns) are removed, and their meaningful counterparts (called exons) are retained. Accurate recognition of the boundaries between these two classes of sub-sequences, however, is known to be a difficult problem. Conventional approaches for recognizing these boundaries have sought for solely enhancing machine learning techniques, while inherent nature of the data themselves has been overlooked. In this paper we present an approach which makes use of the data attributes inherent to species in order to increase the accuracy of the boundary recognition. For experimentation, we have taken the data sets for four different species from the University of California Santa Cruz (UCSC) data repository, divided the data sets based on the species types, then trained a preprocessed version of the data sets on neural network(NN)-based and support vector machine(SVM)-based classifiers. As a result, we have observed that each species has its own specific features related to the splice sites, and that it implies there are related distances among species. To conclude, dividing the training data set based on species would increase the accuracy of predicting splicing junction and propose new insight to the biological research.

• 한국자기공명학회논문지
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• 제17권1호
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• pp.54-58
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• 2013

SAV0506 is an 87 residue hypothetical protein from Staphylococcus aureus strain Mu50 and also predicted to have similar function to ribosome associated heat shock protein, Hsp 15. Hsp15 is thought to be involved in the repair mechanism of erroneously produced 50S ribosome subunit. In this report, we present the sequence specific backbone resonance assignment of SAV0506. About 82.5% of all resonances could be assigned unambiguously. By analyzing deviations of the $C{\alpha}$ and $C{\beta}$ chemical shift values, we could predict the secondary structure of SAV0506. This study is an essential step towards the structural characterization of SAV0506.

• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2010년도 추계학술발표대회
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• pp.197-200
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• 2010

단백질의 서열 정보와 기능 정보의 양이 증가함에 따라 컴퓨터 실험을 통한 단백질의 기능 예측이 가능해졌으며 정확성이 높은 예측 시스템을 개발하려는 여러 연구가 시도되고 있다. 대표적인 방법으로 서열 유사도를 기반으로 기능 예측을 하는 시스템이 제안되었으나 단백질 중에는 서열이 유사하지만 기능이 다르거나 또는 서열은 다름에도 불구하고 기능이 같은 단백질이 존재하기 때문에 서열의 유사도 만을 이용해서는 단백질의 기능 예측을 어렵다. 이러한 유사도 방법의 단점을 극복하기 위해 단백질 서열로부터 추출한 특징을 기반으로 분류하는 방법도 제안되었다. 본 논문에서는 이러한 기존 방법들의 장점을 얻기 위하여 서열 유사도 방법과 특징 기반 방법을 융합한 단백질 기능 예측 시스템을 제안하고 예측 정확성 분석을 위한 실험을 실시하였다. 실험의 결과에 따르면 제안된 융합시스템이 서열 유사도만을 이용한 방법과 특징 기반 방법보다 좋은 예측 정확률을 갖는 것으로 분석되었다.

• Journal of Microbiology and Biotechnology
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• 제20권2호
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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.

• Genomics & Informatics
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• 제20권4호
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• pp.45.1-45.7
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• 2022

Food security will be affected by climate change worldwide, particularly in the developing world, where the most important food products originate from plants. Plants are often exposed to environmental stresses that may affect their growth, development, yield, and food quality. Auxin is a hormone that plays a critical role in improving plants' tolerance of environmental conditions. Auxin controls the expression of many stress-responsive genes in plants by interacting with specific cis-regulatory elements called auxin-responsive elements (AuxREs). In this work, we performed an in silico prediction of AuxREs in promoters of five auxin-responsive genes in Zea mays. We applied a data fusion approach based on the combined use of Dempster-Shafer evidence theory and fuzzy sets. Auxin has a direct impact on cell membrane proteins. The short-term auxin response may be represented by the regulation of transmembrane gene expression. The detection of an AuxRE in the promoter of prolyl oligopeptidase (POP) in Z. mays and the 3-fold overexpression of this gene under auxin treatment for 30 min indicated the role of POP in maize auxin response. POP is regulated by auxin to perform stress adaptation. In addition, the detection of two AuxRE TGTCTC motifs in the upstream sequence of the bx1 gene suggests that bx1 can be regulated by auxin. Auxin may also be involved in the regulation of dehydration-responsive element-binding and some members of the protein kinase superfamily.

• BMB Reports
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• 제39권5호
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• pp.560-570
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• 2006

Mistletoe (Viscum album) lectins, which are classified as a type II ribosome-inactivating protein (RIP) due to their unique biological function and the potential medical and therapeutic application in cancer cells, receive a rising attention. The heterodimeric glycoproteins contain the A-chain with catalytic activity and the B-chain with sugar binding properties. In recent years, studies involving the lectins from the white berry European mistletoe (Viscum album) and the yellow berry Korean mistletoe (Viscum album coloratum) have been described. However, the detailed mechanism in exerting unique cytotoxic effect on cancer cells still remains unclear. Here, we aim to understand and define the molecular basis and biological effects of the type II RIPs, through the studies of the recombinant Korean mistletoe lectin. To this end, we expressed, purified the recombinant Korean mistletoe lectin (rKML), and investigated its molecular characteristics in vitro, its cytotoxicity and ability to induce apoptotic cell death in cancer cells. To gain structural basis for its catalytic activity and sugar binding properties, we performed homology modeling studies based on the high degree of sequence identity and conserved secondary structure prediction between Korean and European, Himalayan mistletoe lectins, and Ricin.