Evidence map›Paper›PMID 32737807›Full record

ArticleGenes & genomics2020

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

So-Ra Han, Sung-Min Jang, Young Min Chi, Byeollee Kim, Sang-Hee Jung, Yung Mi Lee, Jun Uetake, Jun Hyuck Lee, Hyun Park, Tae-Jin Oh

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Article in Genes & genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

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5citing papers in PubMed
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3 · Its place in the literature

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5 citing papers in PubMed.

  1. Review
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  3. Complete Genome Analysis ofMicroorganisms · 2023
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5 · Who and what money

Authors and funding

10 authors.

So-Ra HanDepartment of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea.
Sung-Min JangDivision of Biotechnology, Korea University, Seoul, 02841, Korea.
Young Min ChiDivision of Biotechnology, Korea University, Seoul, 02841, Korea.
Byeollee KimDepartment of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea.
Sang-Hee JungDepartment of Dental Hygiene, Gangneung Yeongdong University, Gangneung, Korea.
Yung Mi LeeDepartment of Polar Sciences, Korea Polar Research Institute, Incheon, Korea.
Jun UetakeDepartment of Atmospheric Science, Colorado State University, 200 West Lake Street, 1371 Campus Delivery, Fort Collins, CO, 80523-1371, USA.
Jun Hyuck LeeUnit of Research for Practical Application, Korea Polar Research Institute, Incheon, Korea.
Hyun ParkDivision of Biotechnology, Korea University, Seoul, 02841, Korea. hpark@korea.ac.kr.ORCID 0000-0002-8055-2010
Tae-Jin OhDepartment of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea. tjoh3782@sunmoon.ac.kr.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundSpingobium 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.

objectiveIn this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region.

methodsGenome sequencing was 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 non-redundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes).

resultsThe 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 confirmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway.

conclusionIn 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 finding new genes that degradation the pectin.

Indexed as

Base CompositionBase SequenceChromosome MappingGenome, BacterialGenomicsPectinsPhylogenyPolysaccharide-LyasesSphingomonadaceaeSphingomonasUgandaWhole Genome Sequencingpectate lyasePectinsPolysaccharide-LyasesCarbohydrate active enzymeComparative genomicsGenome sequencingPectin degradationSphingobium sp.

Identifiers

PMID32737807

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