Characterization of Plasma Membrane Proteins from Lactating Bovine Mammary Gland

Properties of proteins in the light (<d 1.03 on Ficoll and then <d 1.14 on sucrose) and heavy (d 1.03/1.05 on Ficoll and then <d 1.14 on sucrose) plasma membranes (PM) isolated from lactating bovine mammary gland were investigated. The PMs consisted of 57 ~ 62% of protein and 38 ~ 43% lipid. The lipid/protein ratio was 0.77 in the light PM and higher than 0.61 of the heavy PM. However, no appreciable differences were found between the light and heavy PMs with respect to polypeptide, amino acid, and carbohydrate compositions. The protein moiety contained approximate 5 ~ 6% carbohydrate: fucose 8 ~ 9, mannose 11 ~ 12, galactose 16, N-acetylglucosamine 32,N-acetylgalactosamine 12 ~ 15, and sialic acid 17~20 mol%. PM protein was high in the content of aspartic acid, glutamic acid, and leucine and low in proline, cystine, methionine, and histidine. On double immunodiffusion both PMs formed precipitin lines against milk fat globule membrane (MFGM) antiserum. Electrophoretic analysis on sodium dodecyl sulfate-polyacrylamide gel revealed the presence of many minor polypeptides and three major glycopeptides (PAS-I, II, and III) of molecular weights of 115,000, 94,000, and 82,000. The glycoprotein profiles of the PMs were different from those of MFGM, except that PAS-II and -III of PM corresponded to PAS-3 and -4 of MFGM, respectively.     

Amino Acid Regions of Family 45 Endoglucanases Involved in Cotton Defibrillation and in Resistance to Anionic Surfactants and Oxidizing Agents

In the detergent industry, fungal endoglucanases are used to release microfibrils from the surfaces of dyed cellulosic fabrics to enhance color brightness. Family 45 endoglucanase (glycoside hydrolase family 45, GH45) EGL3 from Humicola grisea is more resistant to anionic surfactants and oxidizing agents than family 45 endoglucanase RCE1 from Rhizopus oryzae, while in the present study, a catalytic domain of RCE1 had higher defibrillation activity on dyed cotton fabrics than did that of EGL3. To identify the amino acid regions involved in these properties, we compared the characteristics of RCE1, EGL3, and three chimeric endoglucanases, in which each of the three regions of the catalytic domain of EGL3 was replaced by the corresponding region of the catalytic domain of RCE1. Amino acids in the N-terminal region were involved in resistance to anionic surfactants and oxidizing agents. Furthermore, amino acids in the region adjacent to the N-terminal region were involved in releasing microfibrils and in binding to dyed cotton fabrics, indicating that the binding of the amino acids in this region might be important in the release of microfibrils from dyed cotton fabrics.     

糖苷水解酶7家族蛋白在纤维素降解中作用的研究进展

糖苷水解酶7家族（glycoside hydrolase family, GH7）是一类来源于真菌的水解酶,作用于纤维素结晶区或不定形区的β-1,4 键,可用于高效降解纤维素转化为可发酵的糖。GH7的成员具有高度保守序列以及相似三维结构,其催化结构域是由多个loop区围绕反向平行的β 折叠形成的β 三明治结构。目前已有17个GH7成员的结晶结构得到解析,明确了酶的结构与催化功能之间的关联,对GH7的来源及分类、蛋白序列、结构特征与催化纤维素降解功能关系的研究进展进行阐述。     

Structural Contribution of the Carbohydrate Moiety to the Alkaline Hydrolysis of Aryl Glycosylamine Linkages

Differential scanning calorimetry (DSC) thermograms of soybean protein isolate developed two peaks corresponded to 11S and 7S globulin, the denaturation temperatures of which were 93.3 and 76.5°C, respectively, with 94% water. These peaks shifted to higher temperatures with lower water contents of the sample. At 47% water, there were two peaks, at 149 and 118.7°C, and at 11% water, there was one peak at 180°C. The DSC thermogram measured during cooling and reheating gave no peak. The soybean protein isolate was heated with 24.5% water at 100°C and then mixed with more water to the water contents of 94%. This sample gave two peaks at temperatures close to those of the original soybean protein, indicating that the soybean protein was not denatured at temperatures even above 100°C when the water content was low.     

Purification of Debranching Enzyme from Mature Rice Seeds

Two indole alkaloids which induce the Epstein-Barr virus early antigen of Raji cells (B lymphocyte) were found in the cultured broth of Actinomycetes NA34-17, from which teleocidin B was also obtained. The active compounds isolated were identified from their spectral data and chemical evidence as (—)-indolactam V and (—)-14-O-acetyl indolactam V.     

A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis

Broad-specificity glycoside hydrolases (GHs) contribute to plant biomass hydrolysis by degrading a diverse range of polysaccharides, making them useful catalysts for renewable energy and biocommodity production. Discovery of new GHs with improved kinetic parameters or more tolerant substrate-binding sites could increase the efficiency of renewable bioenergy production even further. GH5 has over 50 subfamilies exhibiting selectivities for reaction with β-(1,4)–linked oligo- and polysaccharides. Among these, subfamily 4 (GH5_4) contains numerous broad-selectivity endoglucanases that hydrolyze cellulose, xyloglucan, and mixed-linkage glucans. We previously surveyed the whole subfamily and found over 100 new broad-specificity endoglucanases, although the structural origins of broad specificity remained unclear. A mechanistic understanding of GH5_4 substrate specificity would help inform the best protein design strategies and the most appropriate industrial application of broad-specificity endoglucanases. Here we report structures of 10 new GH5_4 enzymes from cellulolytic microbes and characterize their substrate selectivity using normalized reducing sugar assays and MS. We found that GH5_4 enzymes have the highest catalytic efficiency for hydrolysis of xyloglucan, glucomannan, and soluble β-glucans, with opportunistic secondary reactions on cellulose, mannan, and xylan. The positions of key aromatic residues determine the overall reaction rate and breadth of substrate tolerance, and they contribute to differences in oligosaccharide cleavage patterns. Our new composite model identifies several critical structural features that confer broad specificity and may be readily engineered into existing industrial enzymes. We demonstrate that GH5_4 endoglucanases can have broad specificity without sacrificing high activity, making them a valuable addition to the biomass deconstruction toolset.     

Phylogenetic analysis of family 6 glycoside hydrolases

Multiple sequence alignment separates members of glycoside hydrolase Family 6 into eight subfamilies: one of mainly actinobacterial endoglucanases (EGs), one of ascomycotal EGs, one of chytridiomycotal EGs and cellobiohydrolases (CBHs), one of actinobacterial and proteobacterial CBHs, one of chytridiomycotal CBHs, two of ascomycotal CBHs, and one of basidiomycotal CBHs. Each also has some proteins of unknown function. Multiple sequence alignment also extends to all of Family 6 the observation that lengths of loops that form the active-site tunnel in CBHs vary among subfamilies, and along with loop conformations, determine enzyme function.     

蜜环菌糖苷水解酶家族基因在菌索与菌丝间的差异表达分析

蜜环菌是一种兼性腐生和寄生的真菌,通过降解伴栽基质并为药用植物(天麻)或菌物(猪苓)提供营养物质,而糖苷水解酶是这一过程的主要酶类.本研究从蜜环菌Armillaria mellea 541菌株转录数据库中共获得糖苷水解酶家族基因170个,分布于39个亚家族.进一步分析发现,这些家族基因编码的糖苷水解酶家族蛋白(glyc...     

Enzymatic Synthesis of Acarviosyl-maltooligosaccharides Using Disproportionating Enzyme 1

The soluble and insoluble fractions obtained after sonication and centrifugation of Bifidobacterium adolescentis M101–4 cells were examined, and both of these fractions exhibited mitogenic activity in art assay of murine splenocytes and Peyer’s patch cells in vitro. The soluble fraction was further treated by a 6-step procedure involving proteinase K-treatment, ultrafiltration with a 50-kDa cut-off molecular-sieving membrane, anion-exchange chromatography, dialysis, ultrafiltration through a 6-kDa cut-off membrane filter, and gel-filtration to yield a soluble high molecular weight fraction (SHF) which was effective for stimulating the proliferation of murine splenocytes. Almost three quarters of this fraction by weight was found to consist of carbohydrates containing glucose and galactose as major constituents, and the average molecular weight was estimated to be between 60,000 and 2,460,000, with the main peak at 1,550,000 Da, by the retention time of gel permeation chromatography. A structural analysis by ¹H- and ¹³C-nuclear magnetic resonance and methylation indicated that SHF contained polysaccharides consisting of -4Galp1-, -4Glcp1-, and -6Glcp1- as the major residues, and Galf1- and -6Galf1- as the minor residues. Immunopotentiating SHF was found to contain galactofuranosyl residues as characteristic constituents which had not been previously detected in other soluble fractions from Gram-positive bacteria.     

纤维素酶家族及其催化结构域分子改造的新进展

纤维素酶的分子改造是其催化性能改进及催化效率提升的重要手段。近年来,组学技术与结构测定技术的迅速发展,人们已建立了包括糖苷水解酶(Glycoside hydrolase,GH)在内的碳水化合物活性酶组分数据库。通过对同一蛋白家族进行序列比对、分子进化分析与祖先基因重构,以结构模建分析为指导的纤维素酶分子改造,可以明显缩小序列或结构的搜索空间,加快酶分子改造的速度,增大理性设计成功的概率;同时针对催化中心活性架构的分析可以进一步阐明纤维素酶的催化机理与酶分子持续性降解机制。文中主要对纤维素酶家族及其催化结构域的分子改造取得的最新进展作了综述。在后基因组时代基于蛋白质家族中的海量数据分析,以其保守结构信息为指导的理性设计,将会成为纤维素酶分子改造的重要方向,从而推动生物质转化工艺的快速发展。     

Purification and Some Properties of Debranching Enzyme of Germinating Rice Endosperm

A debranching enzyme was extracted from the endosperm of germinating rice seeds and purified through three steps, namely cyclohexaamylose-coupled Sepharose 6B, Ultrogel AcA-44 and Bio-Gel P-150 column chromatography. This disc-electrophoretically homogeneous enzyme showed a specific activity of 43 units/mg of protein (30°C) with a pH optimum of 5.5. The isoelectric point was 4.9, unlike that (pI 3.5) of debranching enzyme of ungerminated rice seeds. Our enzyme hydrolyzed pullulan rapidly, and glutinous rice starch and waxy corn starch moderately. The enzyme was also able to act on phytoglycogen and glycogen unlike debranching enzymes originating in some plants.     

Purification,Characterization, and Gene Analysis of Cellulase (Cel8A) from Lysobacter sp. IB-9374

An enzyme that has both β-1,4-glucanase and chitosanase activities was found in the culture medium of the soil bacterium Lysobacter sp. IB-9374, a high lysyl endopeptidase-producing strain. The enzyme was purified to homogeneity from the culture filtrate using five purification steps and designated Cel8A. The purified Cel8A had a molecular mass of 41 kDa, as estimated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis. A pH optimum of 5.0 was found for the β-1,4-glucanase activity, and pH optima of 5.0 and 7.0 were found for the chitosanase activity. Nucleotide sequencing of the Cel8A gene yielded a deduced amino acid sequence that comprises a 33-amino acid, N-terminal signal peptide and a mature enzyme consisting of a 381-residue polypeptide with a predicted molecular mass of 41,241 Da. The amino acid sequence of the Cel8A, which contains the catalytic module of glycosyl hydrolase family 8, is homologous to β-1,3-1,4-D-glucanase from Bacillus circulans WL-12 and endoglucanase N-257 from B. circulans KSM-N257.     

Crystal Structure and Substrate Recognition of Cellobionic Acid Phosphorylase,Which Plays a Key Role in Oxidative Cellulose Degradation by Microbes

The microbial oxidative cellulose degradation system is attracting significant research attention after the recent discovery of lytic polysaccharide mono-oxygenases. A primary product of the oxidative and hydrolytic cellulose degradation system is cellobionic acid (CbA), the aldonic acid form of cellobiose. We previously demonstrated that the intracellular enzyme belonging to glycoside hydrolase family 94 from cellulolytic fungus and bacterium is cellobionic acid phosphorylase (CBAP), which catalyzes reversible phosphorolysis of CbA into glucose 1-phosphate and gluconic acid (GlcA). In this report, we describe the biochemical characterization and the three-dimensional structure of CBAP from the marine cellulolytic bacterium Saccharophagus degradans. Structures of ligand-free and complex forms with CbA, GlcA, and a synthetic disaccharide product from glucuronic acid were determined at resolutions of up to 1.6 Å. The active site is located near the dimer interface. At subsite +1, the carboxylate group of GlcA and CbA is recognized by Arg-609 and Lys-613. Additionally, one residue from the neighboring protomer (Gln-190) is involved in the carboxylate recognition of GlcA. A mutational analysis indicated that these residues are critical for the binding and catalysis of the aldonic and uronic acid acceptors GlcA and glucuronic acid. Structural and sequence comparisons with other glycoside hydrolase family 94 phosphorylases revealed that CBAPs have a unique subsite +1 with a distinct amino acid residue conservation pattern at this site. This study provides molecular insight into the energetically efficient metabolic pathway of oxidized sugars that links the oxidative cellulolytic pathway to the glycolytic and pentose phosphate pathways in cellulolytic microbes.     

Analysis of functional divergence within two structurally related glycoside hydrolase families

Two glycoside hydrolase (GH) families were analyzed to detect the presence of functional divergence using the program DIVERGE. These two families, GH7 and GH16, each contain members related by amino acid sequence similarity, retaining hydrolytic mechanisms, and catalytic residue identity. GH7 and GH16 comprise GH Clan B, with a shared β‐jelly roll topology and mechanism. GH7 contains fungal cellobiohydrolases and endoglucanases and is divided into five main subfamilies, four of the former and one of the latter. Cluster comparisons between three of the cellobiohydrolase subfamilies and the endoglucanase subfamily identified specific amino acid residues that play a role in the functional divergence between the two enzyme types. GH16 contains subfamilies of bacterial agarases, xyloglucosyl transferases, 1,3‐β‐D ‐glucanases, lichenases, and other enzymes with various substrate specificities and product profiles. Four cluster comparisons between these four main subfamilies again have identified amino acid residues involved in functional divergence between the subfamilies. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 478–495, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Extra tyrosine in the carbohydrate-binding module of Irpex lacteus Xyn10B enhances its cellulose-binding ability

The xylanase (Xyn10B) that strongly adsorbs on microcrystalline cellulose was isolated from Driselase. The Xyn10B contains a Carbohydrate-binding module family 1 (CBM1) (IrpCBM_Xyn10B) at N-terminus. The canonical essential aromatic residues required for cellulose binding were conserved in IrpCBM_Xyn10B; however, its adsorption ability was markedly higher than that typically observed for the CBM1 of an endoglucanase from Trametes hirsuta (ThCBM_EG1). An analysis of the CBM-GFP fusion proteins revealed that the binding capacity to cellulose (7.8 μmol/g) and distribution coefficient (2.0 L/μmol) of IrpCBM_Xyn10B-GFP were twofold higher than those of ThCBM_EG1-GFP (3.4 μmol/g and 1.2 L/μmol, respectively), used as a reference structure. Besides the canonical aromatic residues (W24-Y50-Y51) of typical CBM1-containing proteins, IrpCBM_Xyn10B had an additional aromatic residue (Y52). The mutation of Y52 to Ser (IrpCBM_Y52S-GFP) reduced these adsorption parameters to 4.4 μmol/g and 1.5 L/μmol, which were similar to those of ThCBM_EG1-GFP. These results indicate that Y52 plays a crucial role in strong cellulose binding.     

赤霉素诱导甘蔗节间伸长的效应与相关酶活性的关系

以甘蔗品种'新台糖22号'为试验材料,在伸长初期以200 mg/L GA3进行叶面喷施处理,对照喷清水,研究GA3处理后甘蔗节间糖苷酶、过氧化物酶、过氧化氢酶的变化,以揭示赤霉素诱导甘蔗节间伸长与相关酶活性的关系.结果表明:(1)GA3处理的株高在各个时期显著高于对照,而且在处理后7、14和28 d分别比对照提高了17.32%、14.50%和8.35%,GA3处理引起甘蔗植株表现的高度优势一直保持到后期,节间伸长效果主要是在茎的中部(5～10节).(2)GA3处理后α-葡萄糖苷酶和α-甘露糖苷酶的活性较对照显著下降;POD和β-半乳糖苷酶的活性也略有下降;α-半乳糖苷酶、β-N-乙酰氨基已糖苷酶、过氧化氢酶的活性显著提高;β-葡萄糖苷酶的活性也有一定程度提高.由此推测,外源GA3主要通过调节α-葡萄糖苷酶活性、α-甘露糖苷酶、α-半乳糖苷酶、β-N-乙酰氨基已糖苷酶活性和过氧化氢酶,其次是POD、β-半乳糖苷酶和β-葡萄糖苷酶活性,最终达到节间伸长效果.     

Machine learning reveals sequence-function relationships in family 7 glycoside hydrolases

Family 7 glycoside hydrolases (GH7) are among the principal enzymes for cellulose degradation in nature and industrially. These enzymes are often bimodular, including a catalytic domain and carbohydrate-binding module (CBM) attached via a flexible linker, and exhibit an active site that binds cello-oligomers of up to ten glucosyl moieties. GH7 cellulases consist of two major subtypes: cellobiohydrolases (CBH) and endoglucanases (EG). Despite the critical importance of GH7 enzymes, there remain gaps in our understanding of how GH7 sequence and structure relate to function. Here, we employed machine learning to gain data-driven insights into relationships between sequence, structure, and function across the GH7 family. Machine-learning models, trained only on the number of residues in the active-site loops as features, were able to discriminate GH7 CBHs and EGs with up to 99% accuracy, demonstrating that the lengths of loops A4, B2, B3, and B4 strongly correlate with functional subtype across the GH7 family. Classification rules were derived such that specific residues at 42 different sequence positions each predicted the functional subtype with accuracies surpassing 87%. A random forest model trained on residues at 19 positions in the catalytic domain predicted the presence of a CBM with 89.5% accuracy. Our machine learning results recapitulate, as top-performing features, a substantial number of the sequence positions determined by previous experimental studies to play vital roles in GH7 activity. We surmise that the yet-to-be-explored sequence positions among the top-performing features also contribute to GH7 functional variation and may be exploited to understand and manipulate function.     

Novel Dithiazine Compounds in Volatile Components from Cooked Sakuraebi (Sergia lucens Hansen)

Three novel dithiazine compounds in the aroma concentrate from cooked sakuraebi, Sergia lucens Hansen, were isolated. Their structures were confirmed as 4,6-dimethyl-2-propyl-1,3,5-dihydrodithiazine (A), 4-butyl-2,6-dimethyl-1,3,5-dihydrodithiazine (B) and pyrrolidino[1,2-e]4H-2,4-dimethyl-1,3,5-dithiazine (C) by spectroscopic analyses. The same compounds have also been found in the aroma concentrate from cooked krill. These three compounds were newly discovered as food volatiles, and among them, compound C seems to take an important role in the aroma of cooked small shrimp by its strong roasted aroma and its relatively high concentration.