Isolation and Characterization of a Novel Agar-Degrading Marine Bacterium, Gayadomonas joobiniege gen, nov, sp. nov., from the Southern Sea, Korea

Chi, Won Jae; Park, Jae-Seon; Kwak, Min Jung; Kim, Jihyun F.; Chang, Yong Keun; Hong, Soon Kwang

doi:10.4014/jmb.1308.08007

Cited by 18 publications

(7 citation statements)

References 38 publications

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“…Likewise, Glaciecola agarilytica dominated an agar-degrading community ( Wietz et al, 2015 ) in accordance with the agarolytic phenotype reported for this bacterium ( Yong et al, 2007 ). Several other genera within the Alteromonadaceae family have been connected with agarolytic activities such as Agarivorans ( Kim et al, 2016 ), Gayadomonas ( Chi et al, 2013 ), and Catenovulum ( Yan et al, 2011 ), however, little is known about the responsible enzymatic systems within these taxa. Paraglaciecola hydrolytica S66 T represents a newly isolated Gammaproteobacterium of the Alteromonadaceae family, which has the ability to degrade both agar and carrageenan ( Bech et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus

et al. 2018

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Marine microbes are a rich source of enzymes for the degradation of diverse polysaccharides. Paraglaciecola hydrolytica S66T is a marine bacterium capable of hydrolyzing polysaccharides found in the cell wall of red macroalgae. In this study, we applied an approach combining genomic mining with functional analysis to uncover the potential of this bacterium to produce enzymes for the hydrolysis of complex marine polysaccharides. A special feature of P. hydrolytica S66T is the presence of a large genomic region harboring an array of carbohydrate-active enzymes (CAZymes) notably agarases and carrageenases. Based on a first functional characterization combined with a comparative sequence analysis, we confirmed the enzymatic activities of several enzymes required for red algal polysaccharide degradation by the bacterium. In particular, we report for the first time, the discovery of novel enzyme activities targeting furcellaran, a hybrid carrageenan containing both β-carrageenan and κ/β-carrageenan motifs. Some of these enzymes represent a new subfamily within the CAZy classification. From the combined analyses, we propose models for the complete degradation of agar and κ/β-type carrageenan by P. hydrolytica S66T. The novel enzymes described here may find value in new bio-based industries and advance our understanding of the mechanisms responsible for recycling of red algal polysaccharides in marine ecosystems.

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Section: Introductionmentioning

confidence: 99%

A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus

et al. 2018

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“…A Novel Agarase (AgaJ5) of G. joobiniege G7 There are 12 putative agarase genes in G. joobiniege, a marine bacterium with strong agar-degrading ability [30]. Among them, we have characterized two novel β-agarases, AgaJ9 and AgaJ11 [3,27].…”

Section: Resultsmentioning

confidence: 99%

“…The 16S rRNA gene sequence of G. joobiniege G7 shows 95.5% similarity with that of Catenovulum agarivorans YM01 [30,31]. The whole-genome sequence revealed 12 putative agarase genes belonging to GH16, GH39, GH42, and GH86 [30,31]. Among them, two β-agarases were biochemically characterized.…”

Section: Introductionmentioning

confidence: 98%

“…Gayadomonas joobiniege G7 is a rod-shaped, aerobic, nonmotile, and non-pigmented gram-negative marine bacterium that was isolated from a seawater sample from Gaya Island, and has strong agar-degrading activity [30]. The 16S rRNA gene sequence of G. joobiniege G7 shows 95.5% similarity with that of Catenovulum agarivorans YM01 [30,31]. The whole-genome sequence revealed 12 putative agarase genes belonging to GH16, GH39, GH42, and GH86 [30,31].…”

Section: Introductionmentioning

confidence: 99%

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Biochemical Characterization of a Novel GH86 ��-Agarase Producing Neoagarohexaose from Gayadomonas joobiniege G7

Lee

Jung

Chi

et al. 2018

Journal of Microbiology and Biotechnology

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A novel β-agarase, AgaJ5, was identified from an agar-degrading marine bacterium, G7. It belongs to the glycoside hydrolase family 86 and is composed of 805 amino acids with a 30-amino-acid signal peptide. Zymogram analysis showed that purified AgaJ5 has agarase activity. The optimum temperature and pH for AgaJ5 activity were determined to be 30°C and 4.5, respectively. AgaJ5 was an acidic β-agarase that had strong activity at a narrow pH range of 4.5-5.5, and was a cold-adapted enzyme, retaining 40% of enzymatic activity at 10°C. AgaJ5 required monovalent ions such as Na and K for its maximum activity, but its activity was severely inhibited by several metal ions. The and of AgaJ5 for agarose were 8.9 mg/ml and 188.6 U/mg, respectively. Notably, thin-layer chromatography, mass spectrometry, and agarose-liquefication analyses revealed that AgaJ5 was an endo-type β-agarase producing neoagarohexaose as the final main product of agarose hydrolysis. Therefore, these results suggest that AgaJ5 from G7 is a novel endo-type neoagarohexaose-producing β-agarase having specific biochemical features that may be useful for industrial applications.

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“…Agar oligosaccharides (AOS) produced by agarase has a good application prospect. Agar, a marine polysaccharide producing from red algae, is widely used in food industry, pharmaceutical industry and biological engineering ( Won-Jae et al, 2013 ). As the main component of agar, agarose is composed of 3,6-anhydro-L-galactose (L-AHG) and D -galactose (D-Gal) bonded alternately by α-1,3 and β-1,4 linkages ( Araki, 1956 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomic and Secretomic Analysis Provide Insights Into Unique Agar Degradation Function of Marine Bacterium Vibrio fluvialis A8 Through Horizontal Gene Transfer

et al. 2020

Front. Microbiol.

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Agarose-oligosaccharide production from agar degradation by agarase exhibits lots of advantages and good application prospects. In this study, a novel agar-degrading bacterium Vibrio sp. A8 was isolated from a red algae in the South China Sea. The whole genome sequencing with comparative genomic and secretomic analysis were used to better understand its genetic components about agar degradation. This strain exhibited good agarase production in artificial seawater after culture optimization. The complete genome (4.88 Mb) of this strain comprised two circular chromosomes (3.19 and 1.69 Mb) containing 4,572 protein-coding genes, 108 tRNA genes and 31 rRNA genes. This strain was identified as Vibrio fluvialis A8 by comparative genomic analysis based on genome phylogenetic tree and average nucleotide identity (ANI) similarity. Different from other 20 similar strains including three strains of the same species, V. fluvialis A8 possessed unique agar degradation ability with four β-agarases (GH50) and one α-1,3-L-NA2 hydrolase (GH117) due to the horizontal gene transfer. Secretomic analysis showed that only β-agarase (gene 3152) was abundantly expressed in the secretome of V. fluvialis A8. This agarase had a good substrate specificity and wide work conditions in complex environments, suggesting its potential application for agarose-oligosaccharide production.

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Isolation and Characterization of a Novel Agar-Degrading Marine Bacterium, Gayadomonas joobiniege gen, nov, sp. nov., from the Southern Sea, Korea

Cited by 18 publications

References 38 publications

A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus

A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus

Biochemical Characterization of a Novel GH86 ��-Agarase Producing Neoagarohexaose from Gayadomonas joobiniege G7

Comparative Genomic and Secretomic Analysis Provide Insights Into Unique Agar Degradation Function of Marine Bacterium Vibrio fluvialis A8 Through Horizontal Gene Transfer

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