Dataset Information

Genome sequence of a high agarase-producing strain Flammeovirga sp. SJP92.

ABSTRACT: Flammeovirga sp. SJP92 is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated strain that belongs to the family Flammeovirgaceae of the class Cytophagia. The strain was isolated from the intestine of abalone, which produces many extracellular agarases and exhibits efficient degradation activities on various polysaccharides, especially agarose. Here we present the high-quality draft genome of Flammeovirga sp. SJP92, together with its phenotypic characteristics. The genome sequence is 8, 534, 834 bp, which comprised with one chromosome and no plasmid. It contained 6, 291 protein-coding and 99 RNA genes, including 93 tRNA, 5 rRNA and 1 ncRNA genes.

SUBMITTER: Dong Q

PROVIDER: S-EPMC5267422 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Genome sequence of a high agarase-producing strain Flammeovirga sp. SJP92.

Dong Qi Q Ruan Lingwei L Shi Hong H

Standards in genomic sciences 20170126

Flammeovirga sp. SJP92 is a Gram-negative, aerobic, rod-shaped, non-motile and non-flagellated strain that belongs to the family Flammeovirgaceae of the class Cytophagia. The strain was isolated from the intestine of abalone, which produces many extracellular agarases and exhibits efficient degradation activities on various polysaccharides, especially agarose. Here we present the high-quality draft genome of Flammeovirga sp. SJP92, together with its phenotypic charact ...[more]

PMID: 28138357

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Project description:Exo-type agarases release disaccharide units (3,6-anhydro-l-galactopyranose-?-1,3-d-galactose) from the agarose chain and, in combination with endo-type agarases, play important roles in the processive degradation of agarose. Several exo-agarases have been identified. However, their substrate-degrading patterns and corresponding mechanisms are still unclear because of a lack of proper technologies for sugar chain analysis. Herein, we report the novel properties of AgaO, a disaccharide-producing agarase identified from the genus Flammeovirga AgaO is a 705-amino-acid protein that is unique to strain MY04. It shares sequence identities of less than 40% with reported GH50 ?-agarases. Recombinant AgaO (rAgaO) yields disaccharides as the sole final product when degrading agarose and associated oligosaccharides. Its smallest substrate is a neoagarotetraose, and its disaccharide/agarose conversion ratio is 0.5. Using fluorescence labeling and two-stage mass spectrometry analysis, we demonstrate that the disaccharide products are neoagarobiose products instead of agarobiose products, as verified by (13)C nuclear magnetic resonance spectrum analysis. Therefore, we provide a useful oligosaccharide sequencing method to determine the patterns of enzyme cleavage of glycosidic bonds. Moreover, AgaO produces neoagarobiose products by gradually cleaving the units from the nonreducing end of fluorescently labeled sugar chains, and so our method represents a novel biochemical visualization of the exolytic pattern of an agarase. Various truncated AgaO proteins lost their disaccharide-producing capabilities, indicating a strict structure-function relationship for the whole enzyme. This study provides insights into the novel catalytic mechanism and enzymatic properties of an exo-type ?-agarase for the benefit of potential future applications.Exo-type agarases can degrade agarose to yield disaccharides almost exclusively, and therefore, they are important tools for disaccharide preparation. However, their enzymatic mechanisms and agarose degradation patterns are still unclear due to the lack of proper technologies for sugar chain analysis. In this study, AgaO was identified as an exo-type agarase of agarose-degrading Flammeovirga bacteria, representing a novel branch of glycoside hydrolase family 50. Using fluorescence labeling, high-performance liquid chromatography, and mass spectrum analysis technologies, we provide a useful oligosaccharide sequencing method to determine the patterns of enzyme cleavage of glycosidic bonds. We also demonstrate that AgaO produces neoagarobiose by gradually cleaving disaccharides from the nonreducing end of fluorescently labeled sugars. This study will benefit future enzyme applications and oligosaccharide studies.

Dataset Information

Genome sequence of a high agarase-producing strain Flammeovirga sp. SJP92.

Publications

Genome sequence of a high agarase-producing strain <i>Flammeovirga</i> sp. SJP92.

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