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Novel Insights into Agar Metabolism in Marine Heterotrophic Bacteria
파티라자 무디얀셀라게 둘리브 파티라자(Pathiraja Mudiyanselage Duleepa Pathiraja ),최인걸(In-Geol Choi) 고려대학교 생명자원연구소 2022 생명자원연구 Vol.30 No.-
대형 홍조류는 해양 생태계에서 해양 종속영양세균을 위한 풍부한 서식지를 제공하며, 한천은 대형 홍조류를 이루는 주요 구조적 다당류이다. 한천을 단일 탄소원으로 사용할 수 있는 해양 한천분해세균은 개방된 연안 해역에서 해양 초식 동물의 내장에 이르기까지 다양한 해양 환경에 분포한다. 한천분해세균에서의 한천의 해중합은 탄수화물 활성 효소(CAZymes)의 조합을 통해 이루어 진다. 한천분해세균의 유전체 구조에 대한 다양한 연구에서 이러한 탄수화물 활성 효소를 암호화하고 있는 유전자가 다당류 이용유전자좌(PUL)를 이루고 있음이 밝혀졌다. 한천 가수분해 효소(agarases)는 다음과 같이 분류되어질 수 있다. β-한천분해효소(GH16, GH50, GH86 및 GH118), α-한천분해효소(GH96), 네오아가로바이오스 가수분해효소(GH117) 및 한천분해 β-갈락토시데이스(GH2). 서로 다른 GH 계열에 속한 한천 가수분해효소들은 분자수준 기능, 구조 요소 및 촉매 메커니즘에 있어 고유한 특성을 나타낸다. 한천의 주요 성분 중 하나인 L-AHG는 희귀한 단당류이며, 그 대사 경로는 해양 한천분해세균에서만 발견되어 있다. 한천분해 시스템에 대한 최근의 연구들은 해양 종속영양세균이 가진 한천분해 경로의 보편적인 한천분해 효소 레퍼토리와 이의 진화를 보여주는 서열분석 데이터에 초점을 맞추고 있다. 또한, 올리고당의 수송 메커니즘과 PUL 유전자의 전사 조절을 이해하는 데에도 점점 더 많은 관심이 기울어지고 있다. 이 리뷰에서 우리는 한천 분해와 관련된 해양 종속영양세균의 유전체 구조에서부터 한천 분해의 대사 과정, 한천 가수분해 효소의 구조 및 기능 분석까지의 포괄적인 개요를 다룰 것이다. Agar is a key structural polysaccharide of red macroalgae which provides a rich habitat for marine heterotrophic bacteria in marine ecosystems. Marine agarolytic bacteria, that can use agar as the sole carbon source, are distributed in diverse marine environments from open coastal waters to the gut of marine herbivores. Agarolytic bacteria employ a combination of carbohydrate-active enzymes (CAZymes) for the depolymerization of agar. Extensive studies on the genomic architecture of the agarolytic bacteria suggested that genes encoding these CAZymes are arranged in polysaccharide utilization loci (PUL). Agar hydrolyzing enzymes (agarases) are categorized into; β-agarase (GH16, GH50, GH86, and GH118), α-agarase (GH96), neoagarooligosaccharide hydrolase (GH117), and agarolytic β-galactosidase (GH2). The molecular functionality, structural elements, and catalytic mechanisms of agarases belonging to different GH families show unique characteristics. L-AHG, one of the main constituents in agar, is a rare monosaccharide and its metabolic pathway is exclusively found in marine agarolytic bacteria. Recent trends in the agarolytic systems are mostly focused on the sequence data to visualize the universal agarolytic enzyme repertoire and the evolution of the agarolytic pathway in marine heterotrophic bacteria. In addition, increasing attention is paid to understanding the oligosaccharide transport mechanisms and transcriptional regulation of genes in PUL. In this review, we will cover a comprehensive overview of genomic architecture, structural and functional analysis of agar hydrolyzing enzymes, and agar metabolism in marine heterotrophic bacteria.
Effect of Probiotic-Fortified Infant Formula on Infant Gut Health and Microbiota Modulation
어주영,이철상,문성호,전주영,Duleepa Pathiraja,박병혁,신민재,이재영,김상종,노영배,김윤한,최인걸,김세헌 한국축산식품학회 2023 한국축산식품학회지 Vol.43 No.4
Compared to infant formula, breast milk is the best source of nutrition for infants; it not only improves the neonatal intestinal function, but also regulates the immune system and gut microbiota composition. However, probiotic-fortified infant formula may further enhance the infant gut environment by overcoming the limitations of traditional infant formula. We investigated the probiotic formula administration for one month by comparing 118 Korean infants into the following three groups: infants in each group fed with breast milk (50), probiotic formula (35), or placebo formula-fed group (33). Probiotic formula improved stool consistency and defecation frequency compared to placebo formula-fed group. The probiotic formula helped maintaining the level of secretory immunoglobulin A (sIgA), which had remarkably decreased over time in placebo formula-fed infants (compared to weeks 0 and 4). Moreover, probiotic formula decreased the acidity of stool and considerably increased the butyrate concentration. Furthermore, the fecal microbiota of each group was evaluated at weeks 0 and 4. The microbial composition was distinct between each groups, and the abundance of healthpromoting bacteria increased in the probiotic formula compared to the placebo formulafed group. In summary, supplementation of probiotic infant formula can help optimize the infant gut environment, microbial composition, and metabolic activity of the microbiota, mimicking those of breast milk.
김보근,Ziayo Meng,Xiaoyue Xu,Seungwoo Baek,Duleepa Pathiraja,최인걸,오세종 한국축산학회 2023 한국축산학회지 Vol.65 No.1
Lactic acid bacteria (LAB) have been reported to possess various beneficial properties and are commonly used as probiotics. LAB play a crucial role in milk fermentation, industrial lactic acid fermentation, and health and medicine. Limosilactobacillus fermentum isolated from fermented dairy and food products is considered as ‘Generally Recognized as Safe’ by FDA. Limosilactobacillus fermentum plays an important role in modulation of the intestinal microbiota, enhancing the host immune system and improving feed digestibility. We isolated a probiotic candidate that was identified and named Limosilactobacillus fermentum JNU532. In a previous report, cell-free culture of L. fermentum JNU532 exhibited anti-melanogenic and antioxidant activities. In this study, we present the complete genome assembly of the bacterial strain JNU532. The final genome consists of one circular chromosome (2,077,416 base pairs) with a guanine + cytosine (GC) ratio of 51.5%.
김보근,Kiyeop Kim,Xiaoyue Xu,Hyunju Lee,Duleepa Pathiraja,Dong June Park,최인걸,오세종 한국축산학회 2023 한국축산학회지 Vol.65 No.6
In this study, we report the complete genome sequence of Lactiplantibacillus plantarum L55, a probiotic strain of lactic acid bacteria isolated from kimchi. The genome consists of one circular chromosome (2,077,416 base pair [bp]) with a guanine cytosine (GC) content of 44.5%, and two circular plasmid sequences (54,267 and 19,592 bp, respectively). We also conducted a comprehensive analysis of the genome, which identified the presence of functional genes, genomic islands, and antibiotic-resistance genes. The genome sequence data presented in this study provide insights into the genetic basis of L. plantarum L55, which could be beneficial for the future development of probiotic applications.
이아로,Cao Son Trinh,이원제,김민서,이혜리,Duleepa Pathiraja,최인철,정남현,최창현,이병천,이호정 한국응용생명화학회 2020 Applied Biological Chemistry (Appl Biol Chem) Vol.63 No.1
Aegilops tauschii (Ae. tauschii) is a diploid (2n = 2x = 14) wild grass species, which has been reported as the progenitor of hexaploid wheat (Triticum aestivum) with D-genome. In this study, 68 Ae. tauschii accessions with diverse geographical backgrounds were investigated for their resistance to infection by the leaf rust fungi Puccinia triticina. Two Ae. tauschii accessions that exhibited hyper-resistance to leaf rust at both seedling and adult stages were identified. Utilizing two susceptible Ae. tauschii ecotypes and keumkang, a common Korean wheat cultivar known to be susceptible to leaf rust, as the negative control, further investigations were conducted for understanding the mechanism underlying immunity to leaf rust disease of these two resistant accessions. Resistant accessions displayed the increased β-1,3-glucanase activity to prevent fungal penetration and the better peroxidase activity to cope with leaf rustinduced oxidative stress. Moreover, transcriptional analyses reveal the important role of the LRR receptor-like serine/ threonine-protein kinase FLS2 (lrr) to the disease resistance of the two ecotypes. Ae. tauschii is a remarkable genetic source, especially for abiotic and biotic stress resistance genes, as the plant is known for its wide-ranging geographical habitat and adaptability to different environments. This, combined with the fact that Ae. tauschii and wheat share a close evolutionary relationship, is indicative of the immense benefit of using Ae. tauschii as a material for improving the quality of synthetic wheat. Our aim was to identify and evaluate the strongest Ae. tauschii contenders for breeding leaf rust-resistant synthetic wheat.
Complete genome sequence of candidate probiotic Limosilactobacillus fermentum KUFM407
( Bogun Kim ),( Ji Yu Heo ),( Xiaoyue Xu ),( Hyunju Lee ),( Duleepa Pathiraja ),( Jae-young Kim ),( Yi Hyun Choi ),( In-geol Choi ),( Sae Hun Kim ) 한국축산학회 2024 한국축산학회지 Vol.66 No.4
It has been reported that the administration of Limosilactobacillus fermentum alleviates diseases such as osteoporosis and colitis. In this study, we report the complete genome sequence of Limosilactobacillus fermentum KUFM407, a probiotic strain of LAB isolated from Korean traditional fermented food, Kimchi. Whole genome sequencing of L. fermentum KUFM407 was performed on the Illumina MiSeq and Oxford Nanopore MinION platform. The genome consisted of one circular chromosome (2,077,616 base pair [bp]) with a guanine cytosine (GC) content of 51.5% and one circular plasmid sequence (13,931 bp). Genome annotation identified 1,932 protein-coding genes, 15 rRNAs, and 58 tRNAs in the assembly. The function annotation of the predicted proteins revealed genes involved in the biosynthesis of bacteriocin and fatty acids. The complete genome of L. fermentum KUFM407 could provide valuable information for the development of new probiotic food and health supplements.
Olfactory receptor 544 reduces adiposity by steering fuel preference toward fats
Wu, Chunyan,Hwang, Su Hyeon,Jia, Yaoyao,Choi, Joobong,Kim, Yeon-Ji,Choi, Dahee,Pathiraja, Duleepa,Choi, In-Geol,Koo, Seung-Hoi,Lee, Sung-Joon American Society for Clinical Investigation 2017 The Journal of clinical investigation Vol.127 No.11