Carbohydrate Esterases: An Overview

Armendáriz-Ruiz, Mariana; Rodríguez-González, Jorge Alberto; Camacho-Ruíz, Rosa María; Mateos-Díaz, Juan Carlos

doi:10.1007/978-1-4939-8672-9_2

Cited by 22 publications

(17 citation statements)

References 135 publications

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“…Bacteria use CEHs to demolish cell walls and membrane structures for food uptake [7], and to infect hosts [8][9][10]. The functional diversity of CEHs is mediated by substrate specificities on various biomolecules, such as carbohydrates [11], lipids [12], polypeptides [13,14], nucleic acids [15] and other small molecules [16]. Their catalytic reaction is followed by the cooperation of catalytic residues including a classical Ser-His-Asp triad and substrate-binding residues.…”

Section: Introductionmentioning

confidence: 99%

Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application

Kim

2019

Crystals

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Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from 52 genera and metagenome have been reported. In this review, we categorize these structures based on catalytic machinery, structure and substrate specificity to provide a comprehensive understanding of the bacterial CEHs. CEHs use Ser, Asp or water as a nucleophile to drive diverse catalytic machinery. The α/β/α sandwich architecture is most frequently found in CEHs, but 3-solenoid, β-barrel, up-down bundle, α/β/β/α 4-layer sandwich, 6 or 7 propeller and α/β barrel architectures are also found in these CEHs. Most are substrate-specific to various esters with types of head group and lengths of the acyl chain, but some CEHs exhibit peptidase or lactamase activities. CEHs are widely used in industrial applications, and are the objects of research in structure- or mutation-based protein engineering. Structural studies of CEHs are still necessary for understanding their biological roles, identifying their structure-based functions and structure-based engineering and their potential industrial applications.

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Section: Introductionmentioning

confidence: 99%

Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application

Kim

2019

Crystals

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“…CAZy is also a Carbohydrate-Active enZYmes Database [35], a specialized database of carbohydrate enzymes, which includes a family of related enzymes that catalyze the degradation, modification, and biosynthesis of carbohydrates. CAZy's are divided into five main categories: Glycoside Hydrolase (GH) [36], Glycosyl Transferase (GT) [37], Polysaccharide Lyases (PL) [38], Carbohydrate Esterases (CE) [39], and Oxidoreductase (Auxiliary Activitie, AA). In addition, it also contains Carbohydrate-Binding Module (CBM) proteins [40].…”

Section: Carbohydrate-active Enzymesmentioning

confidence: 99%

Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites

et al. 2020

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Background: Secondary metabolites as natural products from endophytic fungi are important sources of pharmaceuticals. However, there is currently little understanding of endophytic fungi at the omics levels about their potential in secondary metabolites. Calcarisporium arbuscula, an endophytic fungus from the fruit bodies of Russulaceae, produces a variety of secondary metabolites with anti-cancer, anti-nematode and antibiotic activities. A comprehensive survey of the genome and transcriptome of this endophytic fungus will help to understand its capacity to biosynthesize secondary metabolites and will lay the foundation for the development of this precious resource. Results: In this study, we reported the high-quality genome sequence of C. arbuscula NRRL 3705 based on Single Molecule Real-Time sequencing technology. The genome of this fungus is over 45 Mb in size, larger than other typical filamentous fungi, and comprises 10,001 predicted genes, encoding at least 762 secretory-proteins, 386 carbohydrate-active enzymes and 177 P450 enzymes. 398 virulence factors and 228 genes related to pathogen-host interactions were also predicted in this fungus. Moreover, 65 secondary metabolite biosynthetic gene clusters were revealed, including the gene cluster for the mycotoxin aurovertins. In addition, several gene clusters were predicted to produce mycotoxins, including aflatoxin, alternariol, destruxin, citrinin and isoflavipucine. Notably, two independent gene clusters were shown that are potentially involved in the biosynthesis of alternariol. Furthermore, RNA-Seq assays showed that only expression of the aurovertin gene cluster is much stronger than expression of the housekeeping genes under laboratory conditions, consistent with the observation that aurovertins are the predominant metabolites. Gene expression of the remaining 64 gene clusters for compound backbone biosynthesis was all lower than expression of the housekeeping genes, which partially explained poor production of other secondary metabolites in this fungus. Conclusions: Our omics data, along with bioinformatics analysis, indicated that C. arbuscula NRRL 3705 contains a large number of biosynthetic gene clusters and has a huge potential to produce a profound number of secondary metabolites. This work also provides the basis for development of endophytic fungi as a new resource of natural products with promising biological activities.

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“…CAZy is known as Carbohydrate-Active enZYmes Database [37], a specialized database of carbohydrate enzymes, including a family of related enzymes that catalyze the degradation, modification, and biosynthesis of carbohydrates. It contains five main categories: Glycoside Hydrolase (GH) [38], Glycosyl Transferase (GT) [39], Polysaccharide Lyases (PL) [40], Carbohydrate Esterases (CE) [41], and Oxidoreductase (Auxiliary Activitie, AA). In addition, it also contains Carbohydrate-Binding Module (CBM) [42].…”

Section: Carbohydrate-active Enzymesmentioning

confidence: 99%

Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites

Cheng

Cao

Chen

et al. 2020

Preprint

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Background: Endophytic fungi can produce many active secondary metabolites, which are important resources of natural medicines. However, there is currently little understanding of endophytic fungi at the omics levels. Calcarisporium arbuscula, an endophytic fungus from the healthy fruit of Russulaceae, can produce a variety of secondary metabolites with anti-cancer, anti-nematode and antibiotic bioactivities. Comprehensive survey of the endophytic fungi genome and transcriptome will help to understand their capacity to biosynthesize secondary metabolites and lay the foundation for the development of these precious resources.Results: In this study，we reported the high-quality genome sequence of a strain C. arbuscula NRRL 3705 based on Single Molecule Real-Time sequencing technology. The genome of this fungus is over 45 Mb in size, relatively larger than other typical filamentous fungi, and comprises 10,001 predictable genes, encoding at least 762 secretory-proteins, 386 carbohydrate-active enzymes and 177 P450 enzymes. 398 virulence factors and 228 genes related to pathogen-host interactions were also predicted in this fungus. Moreover, 65 secondary metabolite biosynthetic gene clusters were revealed, including the gene cluster for mycotoxins aurovertins. In addition, several gene clusters were predicted to produce various mycotoxins, including aflatoxin, alternariol, destruxin, citrinin and isoflavipucine. Notably, two independent gene clusters were shown possibly involved in the biosynthesis of alternariol. Furthermore, RNA-Seq assay showed that only the expression of aurovertin gene cluster is much stronger than the housekeeping genes under laboratory conditions, consistent with that aurovertins are the predominant metabolites. The gene expression of the remaining 64 gene clusters for compound backbone biosynthesis was all lower than the housekeeping genes, which might partially explain poor production of other secondary metabolites in this fungus.Conclusions: Our omics data along with bioinformatics analysis indicated that C. arbuscula NRRL 3705 contains a large number of biosynthetic gene clusters and has a huge potential to produce profound secondary metabolites. This work also provides the basis for development of endophytic fungi as a new resource of natural products with promising biological activities.

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Carbohydrate Esterases: An Overview

Cited by 22 publications

References 135 publications

Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application

Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application

Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites

Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites

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