Essays in biochemistry最新文献_第10页

Role of carbohydrate-active enzymes in mycorrhizal symbioses. 糖活性酶在菌根共生中的作用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220127

Yuhua Gong, Annie Lebreton, Feng Zhang, Francis Martin

引用次数: 3

Copper radical oxidases: galactose oxidase, glyoxal oxidase, and beyond! 铜自由基氧化酶:半乳糖氧化酶、乙二醛氧化酶等!

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220124

Jessica K Fong, Harry Brumer

引用次数: 3

Glucuronoyl esterases - enzymes to decouple lignin and carbohydrates and enable better utilization of renewable plant biomass. 葡萄糖醛酸酯酶-将木质素和碳水化合物解耦并使可再生植物生物量得到更好利用的酶。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220155

Johan Larsbrink, Leila Lo Leggio

{"title":"Glucuronoyl esterases - enzymes to decouple lignin and carbohydrates and enable better utilization of renewable plant biomass.","authors":"Johan Larsbrink, Leila Lo Leggio","doi":"10.1042/EBC20220155","DOIUrl":"https://doi.org/10.1042/EBC20220155","url":null,"abstract":"Glucuronoyl esterases (GEs) are microbial enzymes able to cleave covalent linkages between lignin and carbohydrates in the plant cell wall. GEs are serine hydrolases found in carbohydrate esterase family 15 (CE15), which belongs to the large α/β hydrolase superfamily. GEs have been shown to reduce plant cell wall recalcitrance by hydrolysing the ester bonds found between glucuronic acid moieties on xylan polysaccharides and lignin. In recent years, the exploration of CE15 has broadened significantly and focused more on bacterial enzymes, which are more diverse in terms of sequence and structure to their fungal counterparts. Similar to fungal GEs, the bacterial enzymes are able to improve overall biomass deconstruction but also appear to have less strict substrate preferences for the uronic acid moiety. The structures of bacterial GEs reveal that they often have large inserts close to the active site, with implications for more extensive substrate interactions than the fungal GEs which have more open active sites. In this review, we highlight the recent work on GEs which has predominantly regarded bacterial enzymes, and discuss similarities and differences between bacterial and fungal enzymes in terms of the biochemical properties, diversity in sequence and modularity, and structural variations that have been discovered thus far in CE15.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":null,"pages":null},"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/8a/82/ebc-67-ebc20220155.PMC10154605.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9463758","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

On the impact of carbohydrate-binding modules (CBMs) in lytic polysaccharide monooxygenases (LPMOs). 糖结合模块(CBMs)对多糖单加氧酶(LPMOs)的影响。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220162

Zarah Forsberg, Gaston Courtade

引用次数: 5

Butyrate-producing colonic clostridia: picky glycan utilization specialists. 产生丁酸的结肠梭菌:挑剔的聚糖利用专家。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220125

Maria Louise Leth, Michael Jakob Pichler, Maher Abou Hachem

{"title":"Butyrate-producing colonic clostridia: picky glycan utilization specialists.","authors":"Maria Louise Leth, Michael Jakob Pichler, Maher Abou Hachem","doi":"10.1042/EBC20220125","DOIUrl":"https://doi.org/10.1042/EBC20220125","url":null,"abstract":"Butyrate-producing human gut microbiota members are recognized for their strong association with a healthy immune-homeostasis and protection from inflammatory disorders and colorectal cancer. These effects are attributed to butyrate, the terminal electron sink of glycan fermentation by prevalent and abundant colonic Firmicutes from the Lachnospiraceae and Oscillospiraceae families. Remarkably, our insight into the glycan utilization mechanisms and preferences of butyrogenic Firmicutes remains very limited as compared with other gut symbionts, especially from the Bacteroides, Bifidobacterium, and Lactobacillus genera. Here, we summarize recent findings on the strategies that colonic butyrate producers have evolved to harvest energy from major dietary fibres, especially plant structural and storage glycans, such as resistant starch, xylans, and mannans. Besides dietary fibre, we also present the unexpected discovery of a conserved protein apparatus that confers the growth of butyrate producers on human milk oligosaccharides (HMOs), which are unique to mother's milk. The dual dietary fibre/HMO utilization machinery attests the adaptation of this group to both the infant and adult guts. These finding are discussed in relation to the early colonization of butyrogenic bacteria and the maturation of the microbiota during the transition from mother's milk to solid food. To date, the described butyrogenic Firmicutes are glycan utilization specialists that target only a few glycans in a highly competitive manner relying on co-regulated glycan utilization loci. We describe the common pillars of this machinery, highlighting butyrate producers as a source for discovery of biochemically and structurally novel carbohydrate active enzymes.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9688388","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: 7

Enzyme synergy for plant cell wall polysaccharide degradation. 植物细胞壁多糖降解的酶协同作用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220166

Ahmed Khamassi, Claire Dumon

引用次数: 3

A special issue of Essays in Biochemistry on current advances about CAZymes and their impact and key role in human health and environment. 《生物化学论文》的特刊，关于酶的最新进展及其对人类健康和环境的影响和关键作用。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20230004

Mirjam Czjzek, Elizabeth Ficko-Blean, Jean-Guy Berrin

{"title":"A special issue of Essays in Biochemistry on current advances about CAZymes and their impact and key role in human health and environment.","authors":"Mirjam Czjzek, Elizabeth Ficko-Blean, Jean-Guy Berrin","doi":"10.1042/EBC20230004","DOIUrl":"https://doi.org/10.1042/EBC20230004","url":null,"abstract":"Carbohydrate active enzymes (CAZymes) and their biochemical characterization have been the subject of extensive research over the past ten years due to their importance to carbohydrate metabolism in different biological contexts. For instance, the understanding that 'polysaccharide utilizing loci' (PUL) systems hosted by specific 'carbohydrate degraders' in the intestinal microbiota play key roles in health and disease, such as Crohn's disease, ulcerative colitis or colorectal cancer to name the most well-characterized, has led to an outstanding effort in trying to decipher the molecular mechanisms by which these processes are organized and regulated. The past 10 years has also seen the expansion of CAZymes with auxiliary activities, such as lytic polysaccharide monooxygenases (LPMOs) or even sulfatases, and interest has grown in general about the enzymes needed to remove the numerous decorations and modifications of complex biomass, such as carbohydrate esterases (CE). Today, the characterization of these 'modifying' enzymes allows us to tackle a much more complex biomass, which presents sulfations, methylations, acetylations or interconnections with lignin. This special issue about CAZyme biochemistry covers all these aspects, ranging from implications in disease to environmental and biotechnological impact, with a varied collection of twenty-four review articles providing current biochemical, structural and mechanistic insights into their respective topics.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2023-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9333206","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: 0

In silico modelling of the function of disease-related CAZymes. 疾病相关CAZymes功能的计算机模拟。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-18 DOI: 10.1042/EBC20220218

Alba Nin-Hill, Beatriz Piniello, Carme Rovira

{"title":"In silico modelling of the function of disease-related CAZymes.","authors":"Alba Nin-Hill, Beatriz Piniello, Carme Rovira","doi":"10.1042/EBC20220218","DOIUrl":"https://doi.org/10.1042/EBC20220218","url":null,"abstract":"In silico modelling of proteins comprises a diversity of computational tools aimed to obtain structural, electronic, and/or dynamic information about these biomolecules, capturing mechanistic details that are challenging to experimental approaches, such as elusive enzyme-substrate complexes, short-lived intermediates, and reaction transition states (TS). The present article gives the reader insight on the use of in silico modelling techniques to understand complex catalytic reaction mechanisms of carbohydrate-active enzymes (CAZymes), along with the underlying theory and concepts that are important in this field. We start by introducing the significance of carbohydrates in nature and the enzymes that process them, CAZymes, highlighting the conformational flexibility of their carbohydrate substrates. Three commonly used in silico methods (classical molecular dynamics (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and enhanced sampling techniques) are described for nonexpert readers. Finally, we provide three examples of the application of these methods to unravel the catalytic mechanisms of three disease-related CAZymes: β-galactocerebrosidase (GALC), responsible for Krabbe disease; α-mannoside β-1,6-N-acetylglucosaminyltransferase V (MGAT5), involved in cancer; and O-fucosyltransferase 1 (POFUT1), involved in several human diseases such as leukemia and the Dowling-Degos disease.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":null,"pages":null},"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/18/eb/ebc-67-ebc20220218.PMC10154626.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9408318","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

Glycosyltransferase family 47 (GT47) proteins in plants and animals. 植物和动物的糖基转移酶家族47 (GT47)蛋白。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-04-14 DOI: 10.1042/EBC20220152

Liang Zhang, Pradeep Kumar Prabhakar, Vivek S Bharadwaj, Yannick J Bomble, Maria J Peña, Breeanna R Urbanowicz

{"title":"Glycosyltransferase family 47 (GT47) proteins in plants and animals.","authors":"Liang Zhang, Pradeep Kumar Prabhakar, Vivek S Bharadwaj, Yannick J Bomble, Maria J Peña, Breeanna R Urbanowicz","doi":"10.1042/EBC20220152","DOIUrl":"https://doi.org/10.1042/EBC20220152","url":null,"abstract":"Glycosyltransferases (GTs) are carbohydrate-active enzymes that are encoded by the genomes of organisms spanning all domains of life. GTs catalyze glycosidic bond formation, transferring a sugar monomer from an activated donor to an acceptor substrate, often another saccharide. GTs from family 47 (GT47, PF03016) are involved in the synthesis of complex glycoproteins in mammals and insects and play a major role in the synthesis of almost every class of polysaccharide in plants, with the exception of cellulose, callose, and mixed linkage β-1,3/1,4-glucan. GT47 enzymes adopt a GT-B fold and catalyze the formation of glycosidic bonds through an inverting mechanism. Unlike animal genomes, which encode few GT47 enzymes, plant genomes contain 30 or more diverse GT47 coding sequences. Our current knowledge of the GT47 family across plant species brings us an interesting view, showcasing how members exhibit a great diversity in both donor and acceptor substrate specificity, even for members that are classified in the same phylogenetic clade. Thus, we discuss how plant GT47 family members represent a great case to study the relationship between substrate specificity, protein structure, and protein evolution. Most of the plant GT47 enzymes that are identified to date are involved in biosynthesis of plant cell wall polysaccharides, including xyloglucan, xylan, mannan, and pectins. This indicates unique and crucial roles of plant GT47 enzymes in cell wall formation. The aim of this review is to summarize findings about GT47 enzymes and highlight new challenges and approaches on the horizon to study this family.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9333351","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: 1

Fundamentals of HDX-MS. HDX-MS基本原理。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2023-03-29 DOI: 10.1042/EBC20220111

Vanesa Vinciauskaite, Glenn R Masson

引用次数: 6