Synergistic xylan decomposition by a reducing-end xylose-releasing exo-oligoxylanase with other xylanolytic enzymes derived from Paenibacillus xylaniclasticus strain TW1.

Paenibacillus xylaniclasticus strain TW1 is a promising tool for decomposing xylan-containing lignocellulosic biomass, since this strain possesses various genes encoding cellulolytic/hemicellulolytic enzymes. In this study, PxRex8A from the TW1 strain was found to be a reducing-end xylose-releasing exo-oligoxylanase of glycoside hydrolase family 8, which cleaves xylose from xylooligosacchrides of corn core xylan. In synergistic assay, the efficient decomposition of oat spelt xylan (OSX) and beech wood xylan was exemplified in the combination of endo ß-1,4-xylanase (PxXyn11A) and PxRex8A from the TW1 strain in a molar ratio of 4:1. Furthermore, it was found that the addition of ß-d-xylosidase/α-l-arabinofuranosidase (PxXyl43A) from this strain with PxXyn11A and PxRex8A achieved twice the amount of reducing sugars (1.1 mg/mL) against OSX after 24 hours compared to PxXyn11A alone (0.5 mg/mL). These results present that synergy effect of PxRex8A and PxXyl43A with PxXyn11A promotes xylan degradation into xylose.

Ngk1 kinase-mediated N-acetylglucosamine metabolism promotes UDP-GlcNAc biosynthesis in Saccharomyces cerevisiae.

N-acetylglucosamine (GlcNAc) is an important structural component of the cell wall chitin, N-glycans, glycolipids, and GPI-anchors in eukaryotes. GlcNAc kinase phosphorylates GlcNAc into GlcNAc-6-phosphate, a precursor of uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) that serves as a substrate for glycan synthesis. Although GlcNAc kinase is found widely in organisms ranging from microorganisms to mammals, it has never been found in the model yeast Saccharomyces cerevisiae. Here, we demonstrate the presence of GlcNAc metabolism for UDP-GlcNAc biosynthesis in S. cerevisiae through Ngk1, a GlcNAc kinase we discovered previously. The overexpression or deletion of Ngk1 in the presence of GlcNAc affected the amount of both UDP-GlcNAc and chitin, suggesting that GlcNAc metabolism via Ngk1 promotes UDP-GlcNAc synthesis. Our data suggest that the Ngk1-mediated GlcNAc metabolism compensates for the hexosamine pathway, a known pathway for UDP-GlcNAc synthesis.

A C1/C4-Oxidizing AA10 Lytic Polysaccharide Monooxygenase from Paenibacillus xylaniclasticus Strain TW1.

Lytic polysaccharide monooxygenases (LPMO) are key enzymes for the efficient degradation of lignocellulose biomass with cellulases. A lignocellulose-degradative strain, Paenibacillus xylaniclasticus TW1, has LPMO-encoding PxAA10A gene. Neither the C1/C4-oxidizing selectivity nor the enzyme activity of PxAA10A has ever been characterized. In this study, the C1/C4-oxidizing selectivity of PxAA10A and the boosting effect for cellulose degradation with a cellulase cocktail were investigated. The full-length PxAA10A (rPxAA10A) and the catalytic domain (rPxAA10A-CD) were heterologously expressed in Escherichia coli and purified. To identify the C1/C4-oxidizing selectivity of PxAA10A, cellohexaose was used as a substrate with the use of rPxAA10A-CD, and the products were analyzed by MALDI-TOF/MS. As a result, aldonic acid cellotetraose and cellotetraose, the products from C1-oxidization and C4-oxidization, respectively, were detected. These results indicate that PxAA10A is a C1/C4-oxidizing LPMO. It was also found that the addition of rPxAA10A into a cellulase cocktail enhanced the cellulose-degradation efficiency.

Identification and biochemical characterization of a novel N-acetylglucosamine kinase in Saccharomyces cerevisiae.

N-acetylglucosamine (GlcNAc) is a key component of glycans such as glycoprotein and the cell wall. GlcNAc kinase is an enzyme that transfers a phosphate onto GlcNAc to generate GlcNAc-6-phosphate, which can be a precursor for glycan synthesis. GlcNAc kinases have been found in a broad range of organisms, including pathogenic yeast, human and bacteria. However, this enzyme has never been discovered in Saccharomyces cerevisiae, a eukaryotic model. In this study, the first GlcNAc kinase from S. cerevisiae was identified and named Ngk1. The Km values of Ngk1 for GlcNAc and glucose were 0.11 mM and 71 mM, respectively, suggesting that Ngk1 possesses a high affinity for GlcNAc, unlike hexokinases. Ngk1 showed the GlcNAc phosphorylation activity with various nucleoside triphosphates, namely ATP, CTP, GTP, ITP, and UTP, as phosphoryl donors. Ngk1 is phylogenetically distant from known enzymes, as the amino acid sequence identity with others is only about 20% or less. The physiological role of Ngk1 in S. cerevisiae is also discussed.

Characterization of a GH Family 43 ß-Xylosidase Having a Novel Carbohydrate-binding Module from Paenibacillus xylaniclasticus Strain TW1.

Paenibacillus xylaniclasticus strain TW1, a gram-positive facultative anaerobic bacterium, was isolated as a xylanolytic microorganism from the wastes of a pineapple processing factory. A gene encoding one of its xylanolytic enzymes, a ß-xylosidase, was cloned and sequenced. Sequence analysis revealed that this ß-xylosidase, named PxXyl43A, was composed of a glycoside hydrolase (GH) family 43 subfamily 12 catalytic module and an unknown function module (UM). The full-length PxXyl43A (PxXyl43A) was heterologously expressed in Escherichia coli and purified. Recombinant PxXyl43A exhibited hydrolysis activity against both p-nitrophenyl-ß-D-xylopyranoside (pNPX) and p-nitrophenyl-α-L-arabinofuranoside at specific activities of 250 and 310 mU/mg, respectively. The optimal reaction pH and temperature for pNPX hydrolysis were 7.1 and 54 ˚C, respectively. At pH 7.0 and 54 ˚C, the K m and k cat for pNPX were 1.2 mM and 2.8 ± 0.15 s-1, respectively. It was also discovered that the recombinant unknown function module of PxXyl43A (PxXyl43A-UM) could bind to insoluble xylans like birchwood xylan and oat spelt xylan, whereas it did not bind to cellulosic substrates such as ball-milled cellulose, carboxymethyl cellulose or lichenan. The PxXyl43A-UM's binding constant value K a for oat spelt xylan was 2.0 × 10-5 M-1. These results suggest that PxXyl43A possesses a novel carbohydrate-binding module, named as CBM91, specific for xylan-containing polysaccharides.

Mitotic cyclin Clb4 is required for the intracellular adaptation to glucose starvation in Saccharomyces cerevisiae.

Cellular homeostasis in response to glucose availability is maintained through the tight coordination of various physiological processes, including cell proliferation, transcription, and metabolism. In this study, we use the budding yeast Saccharomyces cerevisiae to identify proteins implicated in carbon source-dependent modulation of physiological processes. We find that the mitotic cyclin Clb4 is required for optimal regulation of glucose-starvation-responsive pathways through the target of rapamycin complex 1. Cells lacking Clb4 are characterized by dysregulation of autophagy and impaired modulation of cell size. Notably, cell viability after prolonged glucose starvation is severely reduced by disruption of Clb4. We conclude that Clb4, in addition to its function in the cell cycle, plays a role in the intracellular adaptation to glucose starvation.

The Emi2 Protein of Saccharomyces cerevisiae is a Hexokinase Expressed under Glucose Limitation.

Hexokinases catalyze glucose phosphorylation at the first step in glycolysis in eukaryotes. In the budding yeast Saccharomyces cerevisiae , three enzymes for glucose phosphorylation have long been known: Hxk1, Hxk2, and Glk1. In this study, we focus on Emi2, a previously uncharacterized hexokinase-like protein of S. cerevisiae . Our data show that the recombinant Emi2 protein (rEmi2), expressed in Escherichia coli , possesses glucose-phosphorylating activity in the presence of ATP and Mg 2+ . It was also found that rEmi2 phosphorylates not only glucose but also fructose, mannose and glucosamine in vitro . In addition, we examined changes in the level of endogenous Emi2 protein in S. cerevisiae in the presence or absence of glucose and a non-fermentable carbon source. We found that the expression of Emi2 protein is tightly suppressed during proliferation in high glucose, while it is strongly upregulated in response to glucose limitation and the presence of a non-fermentable carbon source. Our data suggest that the expression of the endogenous Emi2 protein in S. cerevisiae is regulated under the control of Hxk2 in response to glucose availability in the environment.

Chemo-enzymatic synthesis of the glucagon containing N-linked oligosaccharide and its characterization.

The chemo-enzymatic synthesis of an artificially N-glycosylated derivative of glucagon, a peptide hormone that regulates the blood sugar level, is described. We synthesized the glycosylated glucagon by chemical synthesis of an N-acetylglucosaminyl peptide and enzymatic transfer of an oligosaccharide using the transglycosylation activity of the glycosynthase-like mutant of Mucor hiemalis endo-ß-N-acetylglucosaminidase (Endo-M) and sialo-oligosaccharide oxazoline as a donor substrate. The sialo-oligosaccharide-attached glucagon synthesized showed high resistance against protease degradation and stimulated the release of glucose from mouse hepatocytes when added to cells. The synthetic glucagon showed slightly higher activity than native glucagon and has potential as a therapeutic agent for treating diabetic patients.

Ecm33 is a novel factor involved in efficient glucose uptake for nutrition-responsive TORC1 signaling in yeast.

Glucose uptake is crucial for providing both an energy source and a signal that regulates cell proliferation. Therefore, it is important to clarify the mechanisms underlying glucose uptake and its transmission to intracellular signaling pathways. In this study, we searched for a novel regulatory factor involved in glucose-induced signaling by using Saccharomyces cerevisiae as a eukaryotic model. Requirement of the extracellular protein Ecm33 in efficient glucose uptake and full activation of the nutrient-responsive TOR kinase complex 1 (TORC1) signaling pathway is shown. Cells lacking Ecm33 elicit a series of starvation-induced pathways even in the presence of extracellular high glucose concentration. This results in delayed cell proliferation, reduced ATP, induction of autophagy, and dephosphorylation of the TORC1 substrates Atg13 and Sch9.

The signaling pathways underlying starvation-induced upregulation of α-mannosidase Ams1 in Saccharomyces cerevisiae.

BACKGROUND: Cells have evolved the mechanisms to survive nutritional shortages in the environment. In Saccharomyces cerevisiae, α-mannosidase Ams1 is known to play a role in catabolism of N-linked free oligosaccharides in the cytosol. Although, this enzyme is also known to be transported selectively from the cytosol to the vacuoles by autophagy, the physiological significance of this transport has not been clarified. METHODS: To elucidate the regulatory mechanism of the activity of Ams1, we assessed the enzymatic activity of the cell free extract of the wild-type and various gene disruptants under different nutritional conditions. In addition, the regulation of Ams1 at both transcription and post-translation was examined. RESULTS: The activity of Ams1 was significantly increased upon the depletion of glucose in the medium. Interestingly, the activity of the enzyme was also stimulated by nitrogen starvation. Our data showed that the activity of Ams1 is regulated by the stress responsive transcriptional factors Msn2/4 through the protein kinase A and the target of rapamycin complex 1 pathways. In addition, Ams1 is post-translationally activated by Pep4-dependent processing in the vacuoles. CONCLUSION: Yeast cells monitor extracellular nutrients to regulate mannoside catabolism via the cellular signaling pathway. GENERAL SIGNIFICANCE: This study revealed that intracellular Ams1 activity is exquisitely upregulated in response to nutrient starvation by induced expression as well as by Pep4-dependent enhanced activity in the vacuoles. The signaling molecules responsible for regulation of Ams1 were also clarified.

Novel properties of γ-glutamyltransferase from Pseudomonas syringae with ß-aspartyltransferase activity.

OBJECTIVES: Gene cloning, purification, and characterization of γ-glutamyltransferase from Pseudomonas syringae (PsGGT) were performed in Escherichia coli. RESULTS: PsGGT was partially purified to 13-fold, with a specific activity of 0.92 U/mg. The molecule is presumed to be a heterodimeric consisting of large (37 kDa) and small (21 kDa) subunits. The optimal pH and temperature for hydrolytic activity were 8 and 37 °C, and those for transfer activity were 9 and 50 °C, respectively. PsGGT could transfer ß-aspartyl moiety from asparagine to hydroxylamine and the γ-glutamyl moiety from glutamine to hydroxylamine. CONCLUSION: PsGGT demonstrated novel functionality on both γ-glutamyltransferase and ß-aspartyltransferase.

Effective treatment for suppression of acrylamide formation in fried potato chips using L-asparaginase from Bacillus subtilis.

It has been reported that acrylamide, a potential carcinogen, is formed from the reaction of L-asparagine (L-Asn) and reducing sugars contained in foods during heating processes and free asparagine is a limiting factor for acrylamide formation. It has been reported that potato products such as potato chips, which are made through heating processes, contain high levels of acrylamide. To decrease the amount of L-Asn in potatoes using L-asparaginase, effective treatment conditions of sliced potatoes with the enzyme have been investigated. By treating sliced potatoes with Bacillus subtilis L-asparaginase II (BAsnase; 4 U/g potato), appriximately 40 % of L-Asn in the sliced potatoes was converted into L-aspartic acid (L-Asp). To make this enzyme more effective, prior to enzymatic treatment, sliced potatoes were freeze-thawed, dried at 90 °C for 20 min, and vacuum treated for 10 min under decompressed condition, resulting in the hydrolysis of approximately 90 % of L-Asn to L-Asp. The acrylamide content of BAsnase-treated fried potato chips decreased to below 20 % of that of BAsnase-untreated fried potato chips. Treatment conditions examined in this study were found to be effective to suppress the formation of acrylamide in fried potato chips.

Ume6 transcription factor is part of a signaling cascade that regulates autophagy.

Autophagy has been implicated in a number of physiological processes important for human heath and disease. Autophagy involves the formation of a double-membrane cytosolic vesicle, an autophagosome. Central to the formation of the autophagosome is the ubiquitin-like protein autophagy-related (Atg)8 (microtubule-associated protein 1 light chain 3/LC3 in mammalian cells). Following autophagy induction, Atg8 shows the greatest change in expression of any of the proteins required for autophagy. The magnitude of autophagy is, in part, controlled by the amount of Atg8; thus, controlling Atg8 protein levels is one potential mechanism for modulating autophagy activity. We have identified a negative regulator of ATG8 transcription, Ume6, which acts along with a histone deacetylase complex including Sin3 and Rpd3 to regulate Atg8 levels; deletion of any of these components leads to an increase in Atg8 and a concomitant increase in autophagic activity. A similar regulatory mechanism is present in mammalian cells, indicating that this process is highly conserved.

The Cytoplasm-to-Vacuole Targeting Pathway: A Historical Perspective.

From today's perspective, it is obvious that macroautophagy (hereafter autophagy) is an important pathway that is connected to a range of developmental and physiological processes. This viewpoint, however, is relatively recent, coinciding with the molecular identification of autophagy-related (Atg) components that function as the protein machinery that drives the dynamic membrane events of autophagy. It may be difficult, especially for scientists new to this area of research, to appreciate that the field of autophagy long existed as a "backwater" topic that attracted little interest or attention. Paralleling the development of the autophagy field was the identification and analysis of the cytoplasm-to-vacuole targeting (Cvt) pathway, the only characterized biosynthetic route that utilizes the Atg proteins. Here, we relate some of the initial history, including some never-before-revealed facts, of the analysis of the Cvt pathway and the convergence of those studies with autophagy.

Ksp1 kinase regulates autophagy via the target of rapamycin complex 1 (TORC1) pathway.

Macroautophagy (hereafter autophagy) is a bulk degradation system conserved in all eukaryotes, which engulfs cytoplasmic components within double-membrane vesicles to allow their delivery to, and subsequent degradation within, the vacuole/lysosome. Autophagy activity is tightly regulated in response to the nutritional state of the cell and also to maintain organelle homeostasis. In nutrient-rich conditions, Tor kinase complex 1 (TORC1) is activated to inhibit autophagy, whereas inactivation of this complex in response to stress leads to autophagy induction; however, it is unclear how the activity of TORC1 is controlled to allow precise adjustments in autophagy activity. In this study, we performed genetic analyses in Saccharomyces cerevisiae to identify factors that regulate TORC1 activity. We determined that the Ksp1 kinase functions in part as a negative regulator of autophagy; deletion of KSP1 facilitated dephosphorylation of Atg13, a TORC1 substrate, which correlates with enhanced autophagy. These results suggest that Ksp1 down-regulates autophagy activity via the TORC1 pathway. The suppressive function of Ksp1 is partially activated by the Ras/cAMP-dependent protein kinase A (PKA), which is another negative regulator of autophagy. Our study therefore identifies Ksp1 as a new component that functions as part of the PKA and TORC1 signaling network to control the magnitude of autophagy.

Efficient transfer of sialo-oligosaccharide onto proteins by combined use of a glycosynthase-like mutant of Mucor hiemalis endoglycosidase and synthetic sialo-complex-type sugar oxazoline.

BACKGROUND: An efficient method for synthesizing homogenous glycoproteins is essential for elucidating the structural and functional roles of glycans of glycoproteins. We have focused on the transglycosylation activity of endo-ß-N-acetylglucosaminidase from Mucor hiemalis (Endo-M) as a tool for glycoconjugate syntheses, since it can transfer en bloc the oligosaccharide of not only high-mannose type but also complex-type N-glycan onto various acceptors having an N-acetylglucosamine residue. However, there are two major bottlenecks for its practical application: the low yield of the transglycosylation product and the difficulty to obtain the activated sugar oxazoline substrate, especially the sialo-complex type one. METHODS: We carried out the transglycosylation using a glycosynthase-like N175Q mutant of Endo-M, which was found to possess enhanced transglycosylation activity with sugar oxazoline as a donor substrate, in combination with an easy preparation of the sialo-complex-type sugar oxazoline from natural sialoglycopeptide in egg yolk. RESULTS: Endo-M-N175Q showed efficient transglycosylation toward sialo-complex-type sugar oxazoline onto bioactive peptides and bovine ribonuclease B, and each sialylated compound was obtained in significantly high yield. CONCLUSIONS: Highly efficient and simple chemo-enzymatic syntheses of various sialylated compounds were enabled, by a combination of a simple synthesis of sialo-complex-type sugar oxazoline and the Endo-M-N175Q catalyzed transglycosylation. GENERAL SIGNIFICANCE: Our method would be very useful for a practical synthesis of biologically important glycopeptides and glycoproteins.

Glucosamine induces autophagy via an mTOR-independent pathway.

Autophagy is a cellular process that nonspecifically degrades cytosolic components and is involved in many cellular responses. We found that amino sugars with a free amino group such as glucosamine, galactosamine and mannosamine induced autophagy via an mTOR-independent pathway. Glucosamine-induced autophagy at concentrations of at least 500 microM to over 40 mM. In the presence of 40 mM glucosamine, autophagy induction was initiated at 6h and reached a plateau at 36 h. Glucosamine-induced autophagy could remove accumulated ubiquitin-conjugated proteins as well as 79-glutamine repeats. Therefore, orally administered glucosamine could contribute to the prevention of neurodegenerative diseases and promotion of antiaging effects.

Efficient glycosynthase mutant derived from Mucor hiemalis endo-beta-N-acetylglucosaminidase capable of transferring oligosaccharide from both sugar oxazoline and natural N-glycan.

Endo-M, an endo-beta-N-acetylglucosaminidase from Mucor hiemalis, is a family 85 glycoside hydrolase. This enzyme is unique in that it can transfer en bloc the oligosaccharide of various types of N-glycans onto different acceptors, and thereby it enzymatically generates diverse glycoconjugates. In this study, we performed mutational and kinetic studies focusing on a key catalytic asparagine 175 of Endo-M. We have shown that most of the Asn-175 mutants had significantly diminished hydrolysis activity but acted as glycosynthases capable of using synthetic sugar oxazoline for transglycosylation. Our results confirm the critical role of this asparagine residue in promoting the formation of an oxazolinium ion intermediate in the first step of the substrate-assisted catalysis. Interestingly, the N175Q mutant was found to possess dramatically enhanced glycosynthase-like activity with sugar oxazoline in comparison with N175A and a transglycosidase-like activity with "natural" N-glycan as well. These results also implicated the significance of amide side chain in the asparagine 175 of Endo-M for promoting oxazoline transglycosylation in the second step of the catalysis. The highly efficient syntheses of glycopeptides/glycoproteins by N175Q combined with synthetic sugar oxazolines or natural N-glycan substrates were exemplified. In addition, we also identified several previously unknown residues that seem to play a role in the catalysis of Endo-M.

Glycosynthases enable a highly efficient chemoenzymatic synthesis of N-glycoproteins carrying intact natural N-glycans.

Homogeneous N-glycoproteins carrying defined natural N-glycans are essential for detailed structural and functional studies. The transglycosylation activity of the endo-beta-N-acetylglucosaminidases from Arthrobacter protophormiae (Endo-A) and Mucor hiemalis (Endo-M) holds great potential for glycoprotein synthesis, but the wild-type enzymes are not practical for making glycoproteins carrying native N-glycans because of their predominant activity for product hydrolysis. In this article, we report studies of two endoglycosidase-based glycosynthases, EndoM-N175A and EndoA-N171A, and their usefulness in constructing homogeneous N-glycoproteins carrying natural N-glycans. The oligosaccharide oxazoline corresponding to the biantennary complex-type N-glycan was synthesized and tested with the two glycosynthases. The EndoM-N175A mutant was able to efficiently transfer the complex-type glycan oxazoline to a GlcNAc peptide and GlcNAc-containing ribonuclease to form the corresponding homogeneous glycopeptide/glycoprotein. The EndoA-N171A mutant did not recognize the complex-type N-glycan oxazoline but could efficiently use the high-mannose-type glycan oxazoline for transglycosylation. These mutants possess the transglycosylation activity but lack the hydrolytic activity toward the product. Kinetic studies revealed that the dramatically enhanced synthetic efficiency of the EndoA-N171A mutant was due to the significantly reduced hydrolytic activity toward both the Man(9)GlcNAc oxazoline and the product as well as to its enhanced activity for transglycosylation. Thus, the two mutants described here represent the first endoglycosidase-based glycosynthases enabling a highly efficient synthesis of homogeneous natural N-glycoproteins.