scholarly journals Function-Based Classification of Carbohydrate-Active Enzymes by Recognition of Short, Conserved Peptide Motifs

2013 ◽  
Vol 79 (11) ◽  
pp. 3380-3391 ◽  
Author(s):  
Peter Kamp Busk ◽  
Lene Lange
Keyword(s):  
Enzyme Activity ◽  
High Precision ◽  
Glycoside Hydrolase ◽  
Functional Prediction ◽  
Carbohydrate Active Enzymes ◽  
Pairwise Identity ◽  
Conserved Motifs ◽  
Conserved Sequences ◽  
Conserved Sequence ◽  
Peptide Pattern

ABSTRACTFunctional prediction of carbohydrate-active enzymes is difficult due to low sequence identity. However, similar enzymes often share a few short motifs, e.g., around the active site, even when the overall sequences are very different. To exploit this notion for functional prediction of carbohydrate-active enzymes, we developed a simple algorithm, peptide pattern recognition (PPR), that can divide proteins into groups of sequences that share a set of short conserved sequences. When this method was used on 118 glycoside hydrolase 5 proteins with 9% average pairwise identity and representing four characterized enzymatic functions, 97% of the proteins were sorted into groups correlating with their enzymatic activity. Furthermore, we analyzed 8,138 glycoside hydrolase 13 proteins including 204 experimentally characterized enzymes with 28 different functions. There was a 91% correlation between group and enzyme activity. These results indicate that the function of carbohydrate-active enzymes can be predicted with high precision by finding short, conserved motifs in their sequences. The glycoside hydrolase 61 family is important for fungal biomass conversion, but only a few proteins of this family have been functionally characterized. Interestingly, PPR divided 743 glycoside hydrolase 61 proteins into 16 subfamilies useful for targeted investigation of the function of these proteins and pinpointed three conserved motifs with putative importance for enzyme activity. Furthermore, the conserved sequences were useful for cloning of new, subfamily-specific glycoside hydrolase 61 proteins from 14 fungi. In conclusion, identification of conserved sequence motifs is a new approach to sequence analysis that can predict carbohydrate-active enzyme functions with high precision.

scholarly journals Genome organization of the densovirus from Bombyx mori (BmDNV-1) and enzyme activity of its capsid

2001 ◽  
Vol 82 (11) ◽  
pp. 2821-2825 ◽  
Author(s):  
Y. Li ◽  
Z. Zádori ◽  
H. Bando ◽  
R. Dubuc ◽  
G. Fédière ◽  
...  
Keyword(s):  
Amino Acids ◽  
Enzyme Activity ◽  
Bombyx Mori ◽  
Genome Sequence ◽  
Genome Organization ◽  
Phospholipase A ◽  
Sequence Motifs ◽  
Unique Region ◽  
Conserved Sequence

Bombyx mori densovirus (BmDNV-1), on the basis of the previously reported genome sequence, constitutes by itself a separate genus (Iteravirus) within the Densovirinae subfamily of parvoviruses. Inconsistencies in the genome organization, however, necessitated its reassessment. The genome sequence of new clones was determined and resulted in a completely different genome organization. The corrected sequence also contained conserved sequence motifs found in other parvoviruses. Some amino acids in the highly conserved domain in the unique region of VP1 were shared by critical amino acids in the catalytic site and Ca2+-binding loop of secreted phospholipase A2, such as from snake and bee venoms. Expression of this domain and determination of enzyme activity demonstrated that capsids have a phospholipase A2 activity thus far unknown to occur in viruses. This viral phospholipase A2, which is required shortly after entry into the cell, showed a substrate preference for phosphatidylethanolamine and phosphatidylcholine over phosphatidylinositol.

scholarly journals Ultraconserved non-coding DNA within insect phyla

2019 ◽  
Author(s):  
Thomas Brody ◽  
Amar Yavatkar ◽  
Alexander Kuzin ◽  
Ward F. Odenwald
Keyword(s):  
Genomic Sequence ◽  
Fruit Fly ◽  
Evolutionary Divergence ◽  
Regulatory Sequences ◽  
Phylogenetic Groups ◽  
Conserved Sequences ◽  
Regulatory Interactions ◽  
Conserved Sequence ◽  
Sequence Elements ◽  
Regulatory Dna

AbstractPresence of ultra-conserved sequence elements in vertebrate enhancers suggest that transcription factor regulatory interactions are shared across phylogenetically diverse species. To date evidence for similarly conserved elements among evolutionarily distant insects such as flies, mosquitos, ants and bees, has been elusive. This study has taken advantage of the availability of the assembled genomic sequence of these insects to explore the presence of ultraconserved sequence elements in these phylogenetic groups. To investigate the integrity of fly regulatory sequences across ~100 million years of evolutionary divergence from the fruitfly Drosophila melanogaster, we compared Drosophila non-coding sequences to those of Ceratitis capitata, the Mediterranean fruit fly and Musca domestica, the domestic housefly. Using various alignment techniques, Blastn, Clustal, Blat, EvoPrinter and Needle, we show that many of the conserved sequence blocks (CSBs) that constitute Drosophila cis-regulatory DNA, recognized by EvoPrinter alignment protocols, are also conserved in Ceratitis and Musca. We term the sequence elements shared among these species ultraconserved CSBs (uCSBs). The position of the uCSBs with respect to flanking genes is also conserved. The results suggest that CSBs represent the point of interaction of multiple trans-regulators whose functions and interactions are conserved across divergent genera. Blastn alignments also detect putative cis-regulatory sequences shared among evolutionarily distant mosquitos Anopheles gambiae and Culex pipiens and Aedes aegypti. We have also identified conserved sequences shared among bee species. Side by side comparison of bee and ant EvoPrints identify uCSBs shared between the two taxa, as well as more poorly conserved CSBs in either one or the other taxon but not in both. Analysis of uCSBs in dipterans, mosquitos and bees will lead to a greater understanding of their evolutionary origin and the function of their conserved sequences.

scholarly journals Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

2016 ◽  
Vol 82 (6) ◽  
pp. 1686-1692 ◽  
Author(s):  
Keith Mewis ◽  
Nicolas Lenfant ◽  
Vincent Lombard ◽  
Bernard Henrissat
Keyword(s):  
Glycoside Hydrolase ◽  
Enzyme Characterization ◽  
Glycoside Hydrolase Family ◽  
Structural Studies ◽  
Conserved Sequence ◽  
Functional Differences ◽  
Biochemical Assays ◽  
Glycoside Hydrolase Family 43 ◽  
Subfamily Classification ◽  
Hydrolase Family

ABSTRACTThe rapid rise in DNA sequencing has led to an expansion in the number of glycoside hydrolase (GH) families. The GH43 family currently contains α-l-arabinofuranosidase, β-d-xylosidase, α-l-arabinanase, and β-d-galactosidase enzymes for the debranching and degradation of hemicellulose and pectin polymers. Many studies have revealed finer details about members of GH43 that necessitate the division of GH43 into subfamilies, as was done previously for the GH5 and GH13 families. The work presented here is a robust subfamily classification that assigns over 91% of all complete GH43 domains into 37 subfamilies that correlate with conserved sequence residues and results of biochemical assays and structural studies. Furthermore, cooccurrence analysis of these subfamilies and other functional modules revealed strong associations between some GH43 subfamilies and CBM6 and CBM13 domains. Cooccurrence analysis also revealed the presence of proteins containing up to three GH43 domains and belonging to different subfamilies, suggesting significant functional differences for each subfamily. Overall, the subfamily analysis suggests that the GH43 enzymes probably display a hitherto underestimated variety of subtle specificity features that are not apparent when the enzymes are assayed with simple synthetic substrates, such as pNP-glycosides.

scholarly journals Thermal stability and kinetic constants for 129 variants of a family 1 glycoside hydrolase reveal that enzyme activity and stability can be separately designed

PLoS ONE ◽  
2017 ◽  
Vol 12 (5) ◽  
pp. e0176255 ◽  
Author(s):  
Dylan Alexander Carlin ◽  
Siena Hapig-Ward ◽  
Bill Wayne Chan ◽  
Natalie Damrau ◽  
Mary Riley ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Enzyme Activity ◽  
Glycoside Hydrolase ◽  
Kinetic Constants

scholarly journals Database Mining for Novel Bacterial β-Etherases, Glutathione-Dependent Lignin-Degrading Enzymes

2019 ◽  
Vol 86 (2) ◽  
Author(s):  
Hauke Voß ◽  
Carina Amata Heck ◽  
Marcus Schallmey ◽  
Anett Schallmey
Keyword(s):  
Biochemical Characterization ◽  
Phylogenetic Analyses ◽  
Sequence Motifs ◽  
Database Mining ◽  
Sequence Alignments ◽  
Renewable Source ◽  
Aromatic Polymer ◽  
Conserved Sequence ◽  
Peptide Pattern ◽  
Lignin Depolymerization

ABSTRACT Lignin is the most abundant aromatic polymer in nature and a promising renewable source for the provision of aromatic platform chemicals and biofuels. β-Etherases are enzymes with a promising potential for application in lignin depolymerization due to their selectivity in the cleavage of β-O-4 aryl ether bonds. However, only a very limited number of these enzymes have been described and characterized so far. Using peptide pattern recognition (PPR) as well as phylogenetic analyses, 96 putatively novel β-etherases have been identified, some even originating from bacteria outside the order Sphingomonadales. A set of 13 diverse enzymes was selected for biochemical characterization, and β-etherase activity was confirmed for all of them. Some enzymes displayed up to 3-fold higher activity than previously known β-etherases. Moreover, conserved sequence motifs specific for either LigE- or LigF-type enzymes were deduced from multiple-sequence alignments and the PPR-derived peptides. In combination with structural information available for the β-etherases LigE and LigF, insight into the potential structural and/or functional role of conserved residues within these sequence motifs is provided. Phylogenetic analyses further suggest the presence of additional bacterial enzymes with potential β-etherase activity outside the classical LigE- and LigF-type enzymes as well as the recently described heterodimeric β-etherases. IMPORTANCE The use of biomass as a renewable source and replacement for crude oil for the provision of chemicals and fuels is of major importance for current and future societies. Lignin, the most abundant aromatic polymer in nature, holds promise as a renewable starting material for the generation of required aromatic structures. However, a controlled and selective lignin depolymerization to yield desired aromatic structures is a very challenging task. In this regard, bacterial β-etherases are especially interesting, as they are able to cleave the most abundant bond type in lignin with high selectivity. With this study, we significantly expanded the toolbox of available β-etherases for application in lignin depolymerization and discovered more active as well as diverse enzymes than previously known. Moreover, the identification of further β-etherases by sequence database mining in the future will be facilitated considerably through our deduced etherase-specific sequence motifs.

Analysis of carbohydrate-active enzymes in Thermogemmatispora sp. strain T81 reveals carbohydrate degradation ability

2018 ◽  
Vol 64 (12) ◽  
pp. 992-1003 ◽  
Author(s):  
Atilio Tomazini ◽  
Sadhana Lal ◽  
Riffat Munir ◽  
Matthew Stott ◽  
Bernard Henrissat ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Type Strain ◽  
Whole Genome Sequence ◽  
Carbohydrate Active Enzymes ◽  
Bioinformatics Analyses ◽  
Carbohydrate Polymers ◽  
Carbohydrate Degradation ◽  
Wide Range ◽  
Genes Encoding ◽  
Degradation Ability

The phylum Chloroflexi is phylogenetically diverse and is a deeply branching lineage of bacteria that express a broad spectrum of physiological and metabolic capabilities. Members of the order Ktedonobacteriales, including the families Ktedonobacteriaceae, Thermosporotrichaceae, and Thermogemmatisporaceae, all have flexible aerobic metabolisms capable of utilizing a wide range of carbohydrates. A number of species within these families are considered cellulolytic and are capable of using cellulose as a sole carbon and energy source. In contrast, Ktedonobacter racemifer, the type strain of the order, does not appear to possess this cellulolytic phenotype. In this study, we confirmed the ability of Thermogemmatispora sp. strain T81 to hydrolyze cellulose, determined the whole-genome sequence of Thermogemmatispora sp. T81, and using comparative bioinformatics analyses, identified genes encoding putative carbohydrate-active enzymes (CAZymes) in the Thermogemmatispora sp. T81, Thermogemmatispora onikobensis, and Ktedonobacter racemifer genomes. Analyses of the Thermogemmatispora sp. T81 genome identified 64 CAZyme gene sequences belonging to 57 glycoside hydrolase families. The genome of Thermogemmatispora sp. T81 encodes 19 genes for putative extracellular CAZymes, similar to the number of putative extracellular CAZymes identified in T. onikobensis (17) and K. racemifer (17), despite K. racemifer not possessing a cellulolytic phenotype. These results suggest that these members of the order Ktedonobacteriales may use a broader range of carbohydrate polymers than currently described.

scholarly journals Sucrose Phosphorylase and Related Enzymes in Glycoside Hydrolase Family 13: Discovery, Application and Engineering

2020 ◽  
Vol 21 (7) ◽  
pp. 2526 ◽  
Author(s):  
Jorick Franceus ◽  
Tom Desmet
Keyword(s):  
Glycoside Hydrolase ◽  
Enzyme Engineering ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Active Enzymes ◽  
Sucrose Phosphorylase ◽  
Engineering Studies ◽  
The Past ◽  
Hydrolase Family ◽  
Glycoside Hydrolase Family Gh13 ◽  
Made In

Sucrose phosphorylases are carbohydrate-active enzymes with outstanding potential for the biocatalytic conversion of common table sugar into products with attractive properties. They belong to the glycoside hydrolase family GH13, where they are found in subfamily 18. In bacteria, these enzymes catalyse the phosphorolysis of sucrose to yield α-glucose 1-phosphate and fructose. However, sucrose phosphorylases can also be applied as versatile transglucosylases for the synthesis of valuable glycosides and sugars because their broad promiscuity allows them to transfer the glucosyl group of sucrose to a diverse collection of compounds other than phosphate. Numerous process and enzyme engineering studies have expanded the range of possible applications of sucrose phosphorylases ever further. Moreover, it has recently been discovered that family GH13 also contains a few novel phosphorylases that are specialised in the phosphorolysis of sucrose 6F-phosphate, glucosylglycerol or glucosylglycerate. In this review, we provide an overview of the progress that has been made in our understanding and exploitation of sucrose phosphorylases and related enzymes over the past ten years.

scholarly journals β-Glucan phosphorylases in carbohydrate synthesis

2021 ◽  
Author(s):  
Zorica Ubiparip ◽  
Marc De Doncker ◽  
Koen Beerens ◽  
Jorick Franceus ◽  
Tom Desmet
Keyword(s):  
Glycoside Hydrolase ◽  
Degree Of Polymerization ◽  
Special Focus ◽  
Carbohydrate Active Enzymes ◽  
Carbohydrate Synthesis ◽  
Key Points ◽  
Reversible Degradation ◽  
Nucleotide Sugars ◽  
Sugar Phosphates ◽  
Made In

Abstract β-Glucan phosphorylases are carbohydrate-active enzymes that catalyze the reversible degradation of β-linked glucose polymers, with outstanding potential for the biocatalytic bottom-up synthesis of β-glucans as major bioactive compounds. Their preference for sugar phosphates (rather than nucleotide sugars) as donor substrates further underlines their significance for the carbohydrate industry. Presently, they are classified in the glycoside hydrolase families 94, 149, and 161 (www.cazy.org). Since the discovery of β-1,3-oligoglucan phosphorylase in 1963, several other specificities have been reported that differ in linkage type and/or degree of polymerization. Here, we present an overview of the progress that has been made in our understanding of β-glucan and associated β-glucobiose phosphorylases, with a special focus on their application in the synthesis of carbohydrates and related molecules. Key points • Discovery, characteristics, and applications of β-glucan phosphorylases. • β-Glucan phosphorylases in the production of functional carbohydrates.

GLYCOSIDE HYDROLASE ACTIVITY IN BIRCH AND MAPLE XYLEM SAP AND XYLEM TISSUE

1963 ◽  
Vol 41 (12) ◽  
pp. 1605-1612 ◽  
Author(s):  
S. M. Martin ◽  
G. A. Adams
Keyword(s):  
Enzyme Activity ◽  
Glycoside Hydrolase ◽  
Amylase Activity ◽  
Xylem Sap ◽  
Hydrolase Activity ◽  
Xylem Tissue ◽  
Per Se ◽  
Maple Sap

In both maple and birch saps there is significant but low glycoside hydrolase activity. Maple sap preparations were higher in invertase and lower in amylase activity than the corresponding birch preparations; invertase and amylase activity was approximately the same in the two xylem tissues. Sucrose predominates in maple sap and glucose and fructose in birch sap but this difference cannot be ascribed to enzyme activity in either the sap per se or in the xylem tissue of the tree trunks.

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