Essays in biochemistry最新文献_第10页

N-glycan breakdown by bacterial CAZymes. 细菌酵素分解n -聚糖。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220256

Lucy I Crouch

引用次数: 2

Carbohydrate esterases involved in deacetylation of food components by the human gut microbiota. 碳水化合物酯酶参与人体肠道菌群对食物成分的去乙酰化。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220161

Sabina Leanti La Rosa, Lars J Lindstad, Bjørge Westereng

{"title":"Carbohydrate esterases involved in deacetylation of food components by the human gut microbiota.","authors":"Sabina Leanti La Rosa, Lars J Lindstad, Bjørge Westereng","doi":"10.1042/EBC20220161","DOIUrl":"https://doi.org/10.1042/EBC20220161","url":null,"abstract":"Non-carbohydrate modifications such as acetylations are widespread in food stuffs as well as they play important roles in diverse biological processes. These modifications meet the gut environment and are removed from their carbohydrate substrates by the resident microbiota. Among the most abundant modifications are O-acetylations, contributing to polysaccharides physico-chemical properties such as viscosity and gelling ability, as well as reducing accessibility for glycosyl hydrolases, and thus hindering polysaccharide degradation. Of particular note, O-acetylations increase the overall complexity of a polymer, thus requiring a more advanced degrading machinery for microbes to utilize it. This minireview describes acetylesterases from the gut microbiota that deacetylate various food polysaccharides, either as natural components of food, ingredients, stabilizers of microbial origin, or as part of microbes for food and beverage preparations. These enzymes include members belonging to at least 8 families in the CAZy database, as well as a large number of biochemically characterized esterases that have not been classified yet. Despite different structural folds, most of these acetylesterases have a common acid-base mechanism and belong to the SGNH hydrolase superfamily. We highlight examples of acetylesterases that are highly specific to one substrate and to the position of the acetyl group on the glycosyl residue of the carbohydrate, while other members that have more broad substrate specificity. Current research aimed at unveiling the functions and regioselectivity of acetylesterases will help providing fundamental mechanistic understanding on how dietary components are utilized in the human gut and will aid developing applications of these enzymes to manufacture novel industrial products.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"443-454"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1d/18/ebc-67-ebc20220161.PMC10154613.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9408311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Glycoside hydrolases active on microbial exopolysaccharide α-glucans: structures and function. 微生物外多糖α-葡聚糖活性的糖苷水解酶:结构和功能。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220219

Takatsugu Miyazaki

{"title":"Glycoside hydrolases active on microbial exopolysaccharide α-glucans: structures and function.","authors":"Takatsugu Miyazaki","doi":"10.1042/EBC20220219","DOIUrl":"https://doi.org/10.1042/EBC20220219","url":null,"abstract":"Glucose is the most abundant monosaccharide in nature and is an important energy source for living organisms. Glucose exists primarily as oligomers or polymers and organisms break it down and consume it. Starch is an important plant-derived α-glucan in the human diet. The enzymes that degrade this α-glucan have been well studied as they are ubiquitous throughout nature. Some bacteria and fungi produce α-glucans with different glucosidic linkages compared with that of starch, and their structures are quite complex and not fully understood. Compared with enzymes that degrade the α-(1→4) and α-(1→6) linkages in starch, biochemical and structural studies of the enzymes that catabolize α-glucans from these microorganisms are limited. This review focuses on glycoside hydrolases that act on microbial exopolysaccharide α-glucans containing α-(1→6), α-(1→3), and α-(1→2) linkages. Recently acquired information regarding microbial genomes has contributed to the discovery of enzymes with new substrate specificities compared with that of previously studied enzymes. The discovery of new microbial α-glucan-hydrolyzing enzymes suggests previously unknown carbohydrate utilization pathways and reveals strategies for microorganisms to obtain energy from external sources. In addition, structural analysis of α-glucan degrading enzymes has revealed their substrate recognition mechanisms and expanded their potential use as tools for understanding complex carbohydrate structures. In this review, the author summarizes the recent progress in the structural biology of microbial α-glucan degrading enzymes, touching on previous studies of microbial α-glucan degrading enzymes.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"505-520"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9333334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Enzymatic systems for carbohydrate utilization and biosynthesis in Xanthomonas and their role in pathogenesis and tissue specificity. 黄单胞菌碳水化合物利用和生物合成的酶系统及其在发病机制和组织特异性中的作用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220128

Priscila O Giuseppe, Isabela M Bonfim, Mario T Murakami

{"title":"Enzymatic systems for carbohydrate utilization and biosynthesis in Xanthomonas and their role in pathogenesis and tissue specificity.","authors":"Priscila O Giuseppe, Isabela M Bonfim, Mario T Murakami","doi":"10.1042/EBC20220128","DOIUrl":"https://doi.org/10.1042/EBC20220128","url":null,"abstract":"Xanthomonas plant pathogens can infect hundreds of agricultural plants. These bacteria exploit sophisticated molecular strategies based on multiple secretion systems and their associated virulence factors to overcome the plant defenses, including the physical barrier imposed by the plant cell walls and the innate immune system. Xanthomonads are equipped with a broad and diverse repertoire of Carbohydrate-Active enZymes (CAZymes), which besides enabling the utilization of complex plant carbohydrates as carbon and energy source, can also play pivotal roles in virulence and bacterial lifestyle in the host. CAZymes in xanthomonads are often organized in multienzymatic systems similar to the Polysaccharide Utilization Loci (PUL) from Bacteroidetes known as CUT systems (from Carbohydrate Utilization systems associated with TonB-dependent transporters). Xanthomonas bacteria are also recognized to synthesize distinct exopolysaccharides including xanthan gum and untapped exopolysaccharides associated with biofilm formation. Here, we summarize the current knowledge on the multifaceted roles of CAZymes in xanthomonads, connecting their function with pathogenicity and tissue specificity.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"455-470"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9333353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Effect of multimodularity and spatial organization of glycoside hydrolases on catalysis. 糖苷水解酶的多模块性和空间组织对催化的影响。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220167

Víctor Barba-Cedillo, Cédric Y Montanier

{"title":"Effect of multimodularity and spatial organization of glycoside hydrolases on catalysis.","authors":"Víctor Barba-Cedillo, Cédric Y Montanier","doi":"10.1042/EBC20220167","DOIUrl":"https://doi.org/10.1042/EBC20220167","url":null,"abstract":"The wide diversity among the carbohydrate-active enzymes (CAZymes) reflects the equally broad versatility in terms of composition and chemicals bonds found in the plant cell wall polymers on which they are active. This diversity is also expressed through the various strategies developed to circumvent the recalcitrance of these substrates to biological degradation. Glycoside hydrolases (GHs) are the most abundant of the CAZymes and are expressed as isolated catalytic modules or in association with carbohydrate-binding module (CBM), acting in synergism within complex arrays of enzymes. This multimodularity can be even more complex. The cellulosome presents a scaffold protein immobilized to the outer membrane of some microorganisms on which enzymes are grafted to prevent their dispersion and increase catalytic synergism. In polysaccharide utilization loci (PUL), GHs are also distributed across the membranes of some bacteria to co-ordinate the deconstruction of polysaccharides and the internalization of metabolizable carbohydrates. Although the study and characterization of these enzymatic activities need to take into account the entirety of this complex organization-in particular because of the dynamics involved in it-technical problems limit the present study to isolated enzymes. However, these enzymatic complexes also have a spatiotemporal organization, whose still neglected aspect must be considered. In the present review, the different levels of multimodularity that can occur in GHs will be reviewed, from its simplest forms to the most complex. In addition, attempts to characterize or study the effect on catalytic activity of the spatial organization within GHs will be addressed.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"629-638"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9338594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Mannuronate C-5 epimerases and their use in alginate modification. 甘露酸C-5酶及其在海藻酸盐修饰中的应用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220151

Agnes Beenfeldt Petersen, Anne Tøndervik, Margrethe Gaardløs, Helga Ertesvåg, Håvard Sletta, Finn Lillelund Aachmann

{"title":"Mannuronate C-5 epimerases and their use in alginate modification.","authors":"Agnes Beenfeldt Petersen, Anne Tøndervik, Margrethe Gaardløs, Helga Ertesvåg, Håvard Sletta, Finn Lillelund Aachmann","doi":"10.1042/EBC20220151","DOIUrl":"https://doi.org/10.1042/EBC20220151","url":null,"abstract":"Alginate is a polysaccharide consisting of β-D-mannuronate (M) and α-L-guluronate (G) produced by brown algae and some bacterial species. Alginate has a wide range of industrial and pharmaceutical applications, owing mainly to its gelling and viscosifying properties. Alginates with high G content are considered more valuable since the G residues can form hydrogels with divalent cations. Alginates are modified by lyases, acetylases, and epimerases. Alginate lyases are produced by alginate-producing organisms and by organisms that use alginate as a carbon source. Acetylation protects alginate from lyases and epimerases. Following biosynthesis, alginate C-5 epimerases convert M to G residues at the polymer level. Alginate epimerases have been found in brown algae and alginate-producing bacteria, predominantly Azotobacter and Pseudomonas species. The best characterised epimerases are the extracellular family of AlgE1-7 from Azotobacter vinelandii(Av). AlgE1-7 all consist of combinations of one or two catalytic A-modules and one to seven regulatory R-modules, but even though they are sequentially and structurally similar, they create different epimerisation patterns. This makes the AlgE enzymes promising for tailoring of alginates to have the desired properties. The present review describes the current state of knowledge regarding alginate-active enzymes with focus on epimerases, characterisation of the epimerase reaction, and how alginate epimerases can be used in alginate production.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"615-627"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9326309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

The interplay between lytic polysaccharide monooxygenases and glycoside hydrolases. 多糖单加氧酶与糖苷水解酶的相互作用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220156

Morten Sørlie, Malene Billeskov Keller, Peter Westh

{"title":"The interplay between lytic polysaccharide monooxygenases and glycoside hydrolases.","authors":"Morten Sørlie, Malene Billeskov Keller, Peter Westh","doi":"10.1042/EBC20220156","DOIUrl":"https://doi.org/10.1042/EBC20220156","url":null,"abstract":"In nature, enzymatic degradation of recalcitrant polysaccharides such as chitin and cellulose takes place by a synergistic interaction between glycoside hydrolases (GHs) and lytic polysaccharide monooxygenases (LPMOs). The two different families of carbohydrate-active enzymes use two different mechanisms when breaking glycosidic bonds between sugar moieties. GHs employ a hydrolytic activity and LPMOs are oxidative. Consequently, the topologies of the active sites differ dramatically. GHs have tunnels or clefts lined with a sheet of aromatic amino acid residues accommodating single polymer chains being threaded into the active site. LPMOs are adapted to bind to the flat crystalline surfaces of chitin and cellulose. It is believed that the LPMO oxidative mechanism provides new chain ends that the GHs can attach to and degrade, often in a processive manner. Indeed, there are many reports of synergies as well as rate enhancements when LPMOs are applied in concert with GHs. Still, these enhancements vary in magnitude with respect to the nature of the GH and the LPMO. Moreover, impediment of GH catalysis is also observed. In the present review, we discuss central works where the interplay between LPMOs and GHs has been studied and comment on future challenges to be addressed to fully use the potential of this interplay to improve enzymatic polysaccharide degradation.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"551-559"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9333332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Mucin utilization by gut microbiota: recent advances on characterization of key enzymes. 肠道菌群对粘蛋白的利用:关键酶表征的最新进展。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220121

Grete Raba, Ana S Luis

{"title":"Mucin utilization by gut microbiota: recent advances on characterization of key enzymes.","authors":"Grete Raba, Ana S Luis","doi":"10.1042/EBC20220121","DOIUrl":"https://doi.org/10.1042/EBC20220121","url":null,"abstract":"The gut microbiota interacts with the host through the mucus that covers and protects the gastrointestinal epithelium. The main component of the mucus are mucins, glycoproteins decorated with hundreds of different O-glycans. Some microbiota members can utilize mucin O-glycans as carbons source. To degrade these host glycans the bacteria express multiple carbohydrate-active enzymes (CAZymes) such as glycoside hydrolases, sulfatases and esterases which are active on specific linkages. The studies of these enzymes in an in vivo context have started to reveal their importance in mucin utilization and gut colonization. It is now clear that bacteria evolved multiple specific CAZymes to overcome the diversity of linkages found in O-glycans. Additionally, changes in mucin degradation by gut microbiota have been associated with diseases like obesity, diabetes, irritable bowel disease and colorectal cancer. Thereby understanding how CAZymes from different bacteria work to degrade mucins is of critical importance to develop new treatments and diagnostics for these increasingly prevalent health problems. This mini-review covers the recent advances in biochemical characterization of mucin O-glycan-degrading CAZymes and how they are connected to human health.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"345-353"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10154618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9408135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Revisiting the role of electron donors in lytic polysaccharide monooxygenase biochemistry. 重述电子给体在多糖单加氧酶生化中的作用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220164

Glyn R Hemsworth

{"title":"Revisiting the role of electron donors in lytic polysaccharide monooxygenase biochemistry.","authors":"Glyn R Hemsworth","doi":"10.1042/EBC20220164","DOIUrl":"https://doi.org/10.1042/EBC20220164","url":null,"abstract":"The plant cell wall is rich in carbohydrates and many fungi and bacteria have evolved to take advantage of this carbon source. These carbohydrates are largely locked away in polysaccharides and so these organisms deploy a range of enzymes that can liberate individual sugars from these challenging substrates. Glycoside hydrolases (GHs) are the enzymes that are largely responsible for bringing about this sugar release; however, 12 years ago, a family of enzymes known as lytic polysaccharide monooxygenases (LPMOs) were also shown to be of key importance in this process. LPMOs are copper-dependent oxidative enzymes that can introduce chain breaks within polysaccharide chains. Initial work demonstrated that they could activate O2 to attack the substrate through a reaction that most likely required multiple electrons to be delivered to the enzyme. More recently, it has emerged that LPMO kinetics are significantly improved if H2O2 is supplied to the enzyme as a cosubstrate instead of O2. Only a single electron is required to activate an LPMO and H2O2 cosubstrate and the enzyme has been shown to catalyse multiple turnovers following the initial one-electron reduction of the copper, which is not possible if O2 is used. This has led to further studies of the roles of the electron donor in LPMO biochemistry, and this review aims to highlight recent findings in this area and consider how ongoing research could impact our understanding of the interplay between redox processes in nature.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"585-595"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10154616/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9400470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Hemicellulolytic enzymes in lignocellulose processing. 木质纤维素加工中的半纤维素水解酶。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220154

Heidi Østby, Anikó Várnai

{"title":"Hemicellulolytic enzymes in lignocellulose processing.","authors":"Heidi Østby, Anikó Várnai","doi":"10.1042/EBC20220154","DOIUrl":"https://doi.org/10.1042/EBC20220154","url":null,"abstract":"Lignocellulosic biomass is the most abundant source of carbon-based material on a global basis, serving as a raw material for cellulosic fibers, hemicellulosic polymers, platform sugars, and lignin resins or monomers. In nature, the various components of lignocellulose (primarily cellulose, hemicellulose, and lignin) are decomposed by saprophytic fungi and bacteria utilizing specialized enzymes. Enzymes are specific catalysts and can, in many cases, be produced on-site at lignocellulose biorefineries. In addition to reducing the use of often less environmentally friendly chemical processes, the application of such enzymes in lignocellulose processing to obtain a range of specialty products can maximize the use of the feedstock and valorize many of the traditionally underutilized components of lignocellulose, while increasing the economic viability of the biorefinery. While cellulose has a rich history of use in the pulp and paper industries, the hemicellulosic fraction of lignocellulose remains relatively underutilized in modern biorefineries, among other reasons due to the heterogeneous chemical structure of hemicellulose polysaccharides, the composition of which varies significantly according to the feedstock and the choice of pretreatment method and extraction solvent. This paper reviews the potential of hemicellulose in lignocellulose processing with focus on what can be achieved using enzymatic means. In particular, we discuss the various enzyme activities required for complete depolymerization of the primary hemicellulose types found in plant cell walls and for the upgrading of hemicellulosic polymers, oligosaccharides, and pentose sugars derived from hemicellulose depolymerization into a broad spectrum of value-added products.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":"67 3","pages":"533-550"},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10160854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10080793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2