Genome-Wide Identification and Functional Characterization of β-Agarases in Vibrio astriarenae Strain HN897

Frontiers in Microbiology
Yupeng LiuZhe Zhao

Abstract

The genus Vibrio is a genetically and metabolically versatile group of heterotrophic bacteria that are important contributors to carbon cycling within marine and estuarine ecosystems. HN897, a Vibrio strain isolated from the coastal seawater of South China, was shown to be agarolytic and capable of catabolizing D-galactose. Herein, we used Illumina and PacBio sequencing to assemble the whole genome sequence for the strain HN897, which was comprised of two circular chromosomes (Vas1 and Vas2). Genome-wide phylogenetic analysis with 140 other Vibrio sequences firmly placed the strain HN897 into the Marisflavi clade, with Vibrio astriarenae strain C7 being the closest relative. Of all types of carbohydrate-active enzyme classes, glycoside hydrolases (GH) were the most common in the HN897 genome. These included eight GHs identified as putative β-agarases belonging to GH16 and GH50 families in equal proportions. Synteny analysis showed that GH16 and GH50 genes were tandemly arrayed on two different chromosomes consistent with gene duplication. Gene knockout and complementation studies and phenotypic assays confirmed that Vas1_1339, a GH16_16 subfamily gene, exhibits an agarolytic phenotype of the strain. Collectively, these findings...Continue Reading

References

Jan 26, 1990·European Journal of Biochemistry·T AokiM Kitamikado
Feb 4, 1994·Journal of Molecular Biology·A KroghD Haussler
Mar 1, 1996·Journal of Bacteriology·D L MiltonH Wolf-Watz
May 15, 1999·Nucleic Acids Research·A L DelcherS L Salzberg
Sep 9, 2004·Microbiology and Molecular Biology Reviews : MMBR·Fabiano L ThompsonJean Swings
May 5, 2006·Applied and Environmental Microbiology·Nathan A EkborgSteven W Hutcheson
Mar 3, 2007·Bioinformatics·Jason S Papadopoulos, Richa Agarwala
Mar 6, 2007·Applied and Environmental Microbiology·Wei-wei Zhang, Li Sun
Mar 7, 2007·Applied Microbiology and Biotechnology·Jinhua DongToshiyoshi Araki
Oct 16, 2007·Applied and Environmental Microbiology·Dana E HuntMartin F Polz
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Federico M LauroRicardo Cavicchioli
Dec 22, 2009·Journal of Bacteriology·Milana FraibergRaphael Lamed
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Apr 13, 2010·International Journal of Systematic and Evolutionary Microbiology·Hong WangXiao-Hua Zhang
Oct 12, 2010·International Journal of Systematic and Evolutionary Microbiology·Shih-Yi SheuWen-Ming Chen
Aug 9, 2011·Applied and Environmental Microbiology·Li LiaoMin Wu
Nov 1, 2011·International Journal of Systematic and Evolutionary Microbiology·Zhao-Ming GaoYu-Zhong Zhang
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Apr 25, 2012·Applied Microbiology and Biotechnology·Won-Jae ChiSoon-Kwang Hong
Sep 12, 2012·Systematic and Applied Microbiology·Teresa LucenaMaría J Pujalte
Sep 20, 2012·Applied Microbiology and Biotechnology·Wei XieZhong Hu
Oct 3, 2012·PloS One·Andrew TrittAaron E Darling
Dec 12, 2012·Journal of Microbiology and Biotechnology·Dong-Geun LeeSang-Hyeon Lee
Feb 16, 2013·Molecular Biology and Evolution·Marnix H MedemaRainer Breitling
Aug 8, 2013·The Journal of Biological Chemistry·Benjamin PluvinageAlisdair B Boraston
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
Jan 28, 2014·Applied Microbiology and Biotechnology·Won-Jae ChiSoon-Kwang Hong
Apr 23, 2014·Nucleic Acids Research·Xavier Robert, Patrice Gouet
Jul 20, 2014·Applied and Environmental Microbiology·Chan Hyoung LeeKyoung Heon Kim
May 30, 2015·Antonie van Leeuwenhoek·Adrián González-CastilloBruno Gomez-Gil

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Citations

Jun 6, 2021·Microbiological Research·Min LiuZhe Zhao

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Datasets Mentioned

BETA
CP047475
CP047476

Methods Mentioned

BETA
gene knockouts
PCR

Software Mentioned

SPSS
Ion PGM
InterProScan
GView Server
CheckM
iTOL
SOAPec
tBLASTx
COBALT ( Constraint - based Multiple Alignment Tool )
MultiGeneBLAST

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