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Complete genome sequence of Sphingobium sp. strain PAMC 28499 reveals a potential for degrading pectin with comparative genomics approach

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Title
Complete genome sequence of Sphingobium sp. strain PAMC 28499 reveals a potential for degrading pectin with comparative genomics approach
Other Titles
고산지대 빙하 샘플에서 발견된 미생물 (Sphingobium sp. strain PAMC 28499) 의 유전체 분석을 통해 이 미생물이 유용한 펙틴 분해 효소를 가지고 있다는 사실 규명
Authors
Han, So-Ra
Jang, Sung-Min
Chi, Young Min
Kim, Byeollee
Jung, Sang-Hee
Lee, Yung Mi
Uetake, Jun
Lee, Jun Hyuck
Park, Hyun
Oh, Tae-Jin
Subject
Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity
Keywords
Carbohydrate active enzyme; Comparative genomics; Genome sequencing; Pectin degradation; Sphingobium sp.
Issue Date
2020-07
Citation
Han, So-Ra, et al. 2020. "Complete genome sequence of Sphingobium sp. strain PAMC 28499 reveals a potential for degrading pectin with comparative genomics approach". GENES & GENOMICS, 42(9): 1087-1096.
Abstract
Background: Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry. Objective: In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region. Methods: Genome sequencingwas performed using PacBio sequel single-molecule real-time (SMRT) sequencing technology. The predicted gene sequences were functionally annotated and gene prediction was carried out using the program NCBI nonredundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes). Results: The genome sequence has 64.5% GC content, 4432 coding protein coding genes, 61 tRNAs, and 12 rRNA operons. Its genome encodes a simple set of metabolic pathways relevant to pectin and its predicted degradation protein an unusual distribution of CAZymes with extracellular esterases and pectate lyases. CAZyme annotation analyses revealed 165 genes related to carbohydrate active, and especially we have found GH1, GH2, GH3, GH38, GH35, GH51, GH51, GH53, GH106, GH146, CE12, PL1 and PL11 such as known pectin degradation genes from Sphingobium yanoikuiae. These results conirmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway. Conclusion: In this study, isolated and sequenced the complete genome of Spingobium sp. PAMC 28499. Also, this strain has comparative genome analysis. Through the complete genome we can predict how this strain can store and produce energy in extreme environment. It can also provide bioengineered data by inding new genes that degradation the pectin.
URI
https://repository.kopri.re.kr/handle/201206/11885
DOI
http://dx.doi.org/10.1007/s13258-020-00976-y
Appears in Collections  
2020-2020, Development of potential candidates as antibiotics based on polar genetic resources (20-20) / Lee, Jun Hyuck (PM20030)
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