• Mycobiology
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• 제46권4호
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• pp.349-360
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• 2018

Whole-genome sequencing of Flammulina ononidis, a wood-rotting basidiomycete, was performed to identify genes associated with carbohydrate-active enzymes (CAZymes). A total of 12,586 gene structures with an average length of 2009 bp were predicted by the AUGUSTUS tool from a total 35,524,258 bp length of de novo genome assembly (49.76% GC). Orthologous analysis with other fungal species revealed that 7051 groups contained at least one F. ononidis gene. In addition, 11,252 (89.5%) of 12,586 genes for F. ononidis proteins had orthologs among the Dikarya, and F. ononidis contained 8 species-specific genes, of which 5 genes were paralogous. CAZyme prediction revealed 524 CAZyme genes, including 228 for glycoside hydrolases, 21 for polysaccharide lyases, 87 for glycosyltransferases, 61 for carbohydrate esterases, 87 with auxiliary activities, and 40 for carbohydrate-binding modules in the F. ononidis genome. This genome information including CAZyme repertoire will be useful to understand lignocellulolytic machinery of this white rot fungus F. ononidis.

• 한국미생물·생명공학회지
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• 제46권3호
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• pp.300-312
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• 2018

Whole-genome sequencing of the wood-rotting fungus, Flammulina fennae, was carried out to identify carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) of short reads by next-generation sequencing revealed a total genome length of 32,423,623 base pairs (39% GC). A total of 11,591 gene models in the assembled genome sequence of F. fennae were predicted by ab initio gene prediction using the AUGUSTUS tool. In a genome-wide comparison, 6,715 orthologous groups shared at least one gene with F. fennae and 10,667 (92%) of 11,591 genes for F. fennae proteins had orthologs among the Dikarya. Additionally, F. fennae contained 23 species-specific genes, of which 16 were paralogous. CAZyme identification and annotation revealed 513 CAZymes, including 82 auxiliary activities, 220 glycoside hydrolases, 85 glycosyltransferases, 20 polysaccharide lyases, 57 carbohydrate esterases, and 45 carbohydrate binding-modules in the F. fennae genome. The genome information of F. fennae increases the understanding of this basidiomycete fungus. CAZyme gene information will be useful for detailed studies of lignocellulosic biomass degradation for biotechnological and industrial applications.

• 생명과학회지
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• 제18권11호
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• pp.1617-1624
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• 2008

키틴과 그 탈아세틸화된 형태인 키토산은 지구 상에 가장 풍부하게 존재하는 바이오매스의 하나이다. 키틴과 키토산은 항균활성, 면역증강, 중금속 흡착 등 다양한 생리활성을 보이고 있으며 식품, 의약품, 환경산업 등에서 다양하게 응용되고 있다. 이러한 키틴/키토산을 가수분해하는 효소들과 그 3차구조, 유전자들이 세균, 고세균, 진핵생물등 모든 생물종에서 보고되어 왔다. 탄수화물을 가수분해하는 효소들은 그 아미노산 서열에 따라 CAZy (Carbohydrate Active Enzymes) 데이터베이스에 분류되었는데 흥미롭게도 최근까지 키틴가수분해효소와 키토산가수분해효소들은 14개의 glycosyl hydrolase (GH) family들로 분류되어 있다(GH2, GH5, GH7, GH8, GH18, GH19, GH20, GH46, GH48, GH73, GH75, GH80, GH84, GH85). 본 총설에서는 새로운 유전자원를 찾기위한 한 방편으로서 최근에 새롭게 분류된 glycosyl hydrolase family의 분류법에 따라 각각의 GH family에 속하는 키틴/키토산가수분해효소의 종류 및 구조, 그리고 그 효소적 특징에 대하여 논하고자 한다.

• International Journal of Industrial Entomology and Biomaterials
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• 제18권2호
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• pp.91-95
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• 2009

The presence of considerable amount of enzymes of TCA cycle isocitrate dehydrogenase (ICDH-NADP+, EC1.1.1.42), $\alpha$-ketogluterate dehydrogenase ($\alpha$-KGD, EC1.2.4.2) and malate dehydrogenase (MDH, EC1.1.1.37) in fresh control and in vitro starved adult Isoparorchis hypselobagri establish the functional TCA cycle in this fluke. The major metabolic end products are pyruvate, lactate, oxaloacetate and malate. The ratio of oxaloacetate/malate assess that oxaloacetate is reduced to malate and in this fluke the reverse TCA cycle is active. The pyruvate/lactate ratio shows pyruvate is reduced to lactate and the fluke is homolactate farmenters.

• Journal of Microbiology and Biotechnology
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• 제29권8호
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• pp.1255-1265
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• 2019

To investigate the diversity of gastrointestinal microflora and lignocellulose-degrading enzymes in wild Asian elephants, three of these animals living in the same group were selected for study from the Wild Elephant Valley in the Xishuangbanna Nature Reserve of Yunnan Province, China. Fresh fecal samples from the three wild Asian elephants were analyzed by metagenomic sequencing to study the diversity of their gastrointestinal microbes and cellulolytic enzymes. There were a high abundance of Firmicutes and a higher abundance of hemicellulose-degrading hydrolases than cellulose-degrading hydrolases in the wild Asian elephants. Furthermore, there were a high abundance and a rich diversity of carbohydrate active enzymes (CAZymes) obtained from the gene set annotation of the three samples, with the majority of them showing low identity with the CAZy database entry. About half of the CAZymes had no species source at the phylum or genus level. These indicated that the wild Asian elephants might possess greater ability to digest hemicellulose than cellulose to provide energy, and moreover, the gastrointestinal tracts of these pachyderms might be a potential source of novel efficient lignocellulose-degrading enzymes. Therefore, the exploitation and utilization of these enzyme resources could help us to alleviate the current energy crisis and ensure food security.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.2-2
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• pp.59-61
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• 2003

Organic compounds play an important role in the area of pharmaceutical, agrochemical, and other materials, which possess useful biological activities. Generally, such biological activities are come from the interaction of the organic compounds with the receptors in biological system, such as enzymes. Such receptors are composed of the chiral building blocks such as amino acid or carbohydrate, which means the biological active sites of receptors are chiral. (omiited)

• 한국식품과학회지
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• 제48권6호
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• pp.542-547
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• 2016

The thermal properties of ramie leaf ${\beta}$-amylase (RBA) were examined to develop a novel process for enzyme purification. The thermostability of RBA extract prepared from ramie leaf powder was examined at various temperatures. RBA activity decreased slightly, whereas other carbohydrate-active enzymes, such as $\small{D}$-enzyme, were rapidly inactivated during 30 min incubation at $60^{\circ}C$. When the heat-treated extract was incubated with various substrates, maltose was produced exclusively as the major product, whereas the untreated crude extract produced maltose and other maltooligosaccharides. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, fewer protein bands were observed for the heat-treated extract than the untreated extract, indicating that the thermostable RBA was partially purified and other thermolabile enzymes were eliminated. Thus, the treatment of the RBA extract at $60^{\circ}C$ for 30 min resulted in 5.4-fold purification with a recovery yield of 90%.

• Journal of Animal Science and Technology
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• 제62권2호
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• pp.121-140
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• 2020

Anaerobic fungi habitat in the gastrointestinal tract of foregut fermenters or hindgut fermenters and degrade fibrous plant biomass through the hydrolysis reactions with a wide variety of cellulolytic enzymes and physical penetration through fiber matrix with their rhizoids. To date, seventeen genera have been described in family Neocallimasticaceae, class Neocallimastigomycetes, phylum Neocallimastigomycota and one genus has been described in phylum Neocallimastigomycota. In National Center for Biotechnology Information (NCBI) database (DB), 23,830 nucleotide sequences and 59,512 protein sequences have been deposited and most of them were originated from Piromyces, Neocallimastix and Anaeromyces. Most of protein sequences (44,025) were acquired with PacBio next generation sequencing system. The whole genome sequences of Anaeromyces robustus, Neocallimastix californiae, Pecoramyces ruminantium, Piromyces finnis and Piromyces sp. E2 are available in Joint Genome Institute (JGI) database. According to the results of protein prediction, average Isoelectric points (pIs) were ranged from 5.88 (Anaeromyces) to 6.57 (Piromyces) and average molecular weights were ranged from 38.7 kDa (Orpinomyces) to 56.6 kDa (Piromyces). In Carbohydrate-Active enZYmes (CAZY) database, glycoside hydrolases (36), carbohydrate binding module (11), carbohydrate esterases (8), glycosyltransferase (5) and polysaccharide lyases (3) from anaerobic fungi were registered. During four decades, 1,031 research articles about anaerobic fungi were published and 444 and 719 articles were available in PubMed (PM) and PubMed Central (PMC) DB.

• Journal of Microbiology and Biotechnology
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• 제28권12호
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• pp.2036-2045
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• 2018

An endo-${\beta}$-1,4-glucanase gene, cel5L, was cloned using the shot-gun method from Bacillus sp.. The gene, which contained a predicted signal peptide, encoded a protein of 496 amino acid residues, and the molecular mass of the mature Cel5L was estimated to be 51.8 kDa. Cel5L contained a catalytic domain of glycoside hydrolase (GH) family 5 and a carbohydrate-binding module family 3 (CBM_3). Chromatography using HiTrap Q and CHT-II resulted in the isolation of two truncated forms corresponding to 50 (Cel5L-p50) and 35 kDa (Cel5L-p35, CBM_3-deleted form). Both enzymes were optimally active at pH 4.5 and $55^{\circ}C$, but had different half-lives of 4.0 and 22.8 min, respectively, at $70^{\circ}C$. The relative activities of Cel5L-p50 and Cel5L-p35 for barley ${\beta}$-glucan were 377.0 and 246.7%, respectively, compared to those for carboxymethyl-cellulose. The affinity and hydrolysis rate of pNPC by Cel5L-p35 were 1.7 and 3.3 times higher, respectively, than those by Cel5L-p50. Additions of each to a commercial enzyme set increased saccharification of pretreated rice straw powder by 17.5 and 21.0%, respectively. These results suggest CBM_3 is significantly contributing to thermostability, and to affinity and substrate specificity for small substrates, and that these two enzymes could be used as additives to enhance enzymatic saccharification.

• Journal of Microbiology and Biotechnology
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• 제31권1호
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• pp.154-162
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• 2021

L-5-methyltetrahydrofolate (5-MTHF) is one of the biological active forms of folate, which is widely used as a nutraceutical. However, low yield and serious pollution associated with the chemical synthesis of 5-MTHF hampers its sustainable supply. In this study, 5-MTHF production was improved by engineering the 5-MTHF biosynthesis pathway and NADPH supply in Lactococcus lactis for developing a green and sustainable biosynthesis approach. Specifically, overexpressing the key rate-limiting enzyme methylenetetrahydrofolate reductase led to intracellular 5-MTHF accumulation, reaching 18 ㎍/l. Next, 5-MTHF synthesis was further enhanced by combinatorial overexpression of 5-MTHF synthesis pathway enzymes with methylenetetrahydrofolate reductase, resulting in 1.7-fold enhancement. The folate supply pathway was strengthened by expressing folE encoding GTP cyclohydrolase I, which increased 5-MTHF production 2.4-fold to 72 ㎍/l. Furthermore, glucose-6-phosphate dehydrogenase was overexpressed to improve the redox cofactor NADPH supply for 5-MTHF biosynthesis, which led to a 60% increase in intracellular NADPH and a 35% increase in 5-MTHF production (97 ㎍/l). To reduce formation of the by-product 5-formyltetrahydrofolate, overexpression of 5-formyltetrahydrofolate cyclo-ligase converted 5-formyltetrahydrofolate to 5,10-methyltetrahydrofolate, which enhanced the 5-MTHF titer to 132 ㎍/l. Finally, combinatorial addition of folate precursors to the fermentation medium boosted 5-MTHF production, reaching 300 ㎍/l. To the best of our knowledge, this titer is the highest achieved by L. lactis. This study lays the foundation for further engineering of L. lactis for efficient 5-MTHF biosynthesis.