New insight into the mode of action of a GH74 xyloglucanase on tamarind seed xyloglucan: Action pattern and cleavage site

Chen, Mingrui; Ropartz, David; Mac-Béar, Jessica; Bonnin, Estelle; Lahaye, Marc

doi:10.1016/j.carres.2022.108661

Cited by 3 publications

(1 citation statement)

References 34 publications

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“…Besides, GH74 family is generally considered as xyloglucanase e.g. endo-b-1,4-glucanases (Chen et al, 2022).…”

Section: Figurementioning

confidence: 99%

Characterization of Maribacter polysaccharolyticus sp. nov., Maribacter huludaoensis sp. nov., and Maribacter zhoushanensis sp. nov. and illumination of the distinct adaptative strategies of the genus Maribacter

Gao,

Ying,

Dong

et al. 2023

Front. Mar. Sci.

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Polysaccharides are complex carbohydrates and are abundant in the marine environment. Microbes degrade and utilize them using Carbohydrate-active enzymes (CAZymes), which mediate polysaccharides into the marine carbon cycle. With the continued supply of polysaccharides from the marine environment, tidal flats are also abundant in polysaccharides, resulting in an abundance of marine polysaccharide degrading strains. In this study, three novel strains, designated as D37T, M208T, and SA7T, were isolated from the intertidal sediment samples located in Zhoushan, Zhejiang and Huludao, Liaoning, PR China. The phylogenetic trees using the 16S rRNA gene and genome sequences showed that the three novel strains belonged to the genus Maribacter. The highest 16S rRNA gene sequence similarities between the three novel strains and other strains of the genus Maribacter were 98.7%, 99.2%, and 98.8%, respectively, while the ANI, AAI, and dDDH values between the three strains and the other strains of the genus Maribacter were 70-86%, 67-91%, and 17-30%, respectively, supporting their affiliation as novel species. Combined with other phenotypic and genotypic characterization in this study, three novel species are proposed as Maribacter polysaccharolyticus sp. nov., Maribacter huludaoensis sp. nov., and Maribacter zhoushanensis sp. nov., respectively, for the three strains. Furthermore, we compared all available genomes of Maribacter representatives and found that Maribacter strains could be divided into two groups (A and B). The two groups are different in genome size and G + C content and gene densities of CAZyme, peptidase, and sulfatase. Group A possesses more CAZymes which are related to degrading laminarin, fucoidan, mannan, xylose, and xylan. This result suggests that the two groups may have different niche adaptation strategies. Our study contributes to a better understanding of the role of marine flavobacteria in biogeochemical cycles and niche specialization.

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“…Besides, GH74 family is generally considered as xyloglucanase e.g. endo-b-1,4-glucanases (Chen et al, 2022).…”

Section: Figurementioning

confidence: 99%

Characterization of Maribacter polysaccharolyticus sp. nov., Maribacter huludaoensis sp. nov., and Maribacter zhoushanensis sp. nov. and illumination of the distinct adaptative strategies of the genus Maribacter

Gao,

Ying,

Dong

et al. 2023

Front. Mar. Sci.

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Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2021–2022

Harvey

2024

Mass Spectrometry Reviews

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The use of matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well‐established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo‐ and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.

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Molecular mechanisms of processive glycoside hydrolases underline catalytic pragmatism

Hrmová

Schwerdt

2023

Biochemical Society Transactions

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Processive and distributive catalysis defines the conversion continuum, thus underpinning the transformation of oligo- and polymeric substrates by enzymes. Distributive catalysis follows an association–transformation–dissociation pattern during the formation of enzyme–reactant complexes, whereas during processive catalysis, enzymes partner with substrates and complete multiple catalytic events before dissociation from an enzyme–substrate complex. Here, we focus on processive catalysis in glycoside hydrolases (GHs), which ensures efficient conversions of substrates with high precision, and has the advantage over distributive catalysis in efficiency. The work presented here examines a recent discovery of substrate-product-assisted processive catalysis in the GH3 family enzymes with enclosed pocket-shaped active sites. We detail how GH3 β-d-glucan glucohydrolases exploit a transiently formed lateral pocket for product displacement and reactants sliding (or translocation motion) through the catalytic site without dissociation, including movements during nanoscale binding/unbinding and sliding. The phylogenetic tree of putative 550 Archaean, bacterial, fungal, Viridiplantae, and Metazoan GH3 entries resolved seven lineages that corresponded to major substrate specificity groups. This analysis indicates that two tryptophan residues in plant β-d-glucan glucohydrolases that delineate the catalytic pocket, and infer broad specificity, high catalytic efficiency, and substrate-product-assisted processivity, have evolved through a complex evolutionary process, including horizontal transfer and neo-functionalisation. We conclude that the definition of thermodynamic and mechano-structural properties of processive enzymes is fundamentally important for theoretical and practical applications in bioengineering applicable in various biotechnologies.

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New insight into the mode of action of a GH74 xyloglucanase on tamarind seed xyloglucan: Action pattern and cleavage site

Cited by 3 publications

References 34 publications

Characterization of Maribacter polysaccharolyticus sp. nov., Maribacter huludaoensis sp. nov., and Maribacter zhoushanensis sp. nov. and illumination of the distinct adaptative strategies of the genus Maribacter

Characterization of Maribacter polysaccharolyticus sp. nov., Maribacter huludaoensis sp. nov., and Maribacter zhoushanensis sp. nov. and illumination of the distinct adaptative strategies of the genus Maribacter

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2021–2022

Molecular mechanisms of processive glycoside hydrolases underline catalytic pragmatism

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