Cooperative Hydrolysis Research Articles

A signal transmission strategy driven by gap-regulated exonuclease hydrolysis for hierarchical molecular networks

Exonucleases serve as efficient tools for signal processing and play an important role in biochemical reactions. Here, we identify the mechanism of cooperative exonuclease hydrolysis, offering a method to regulate the cooperative hydrolysis driven by exonucleases through the modulation of the number of bases in gap region. A signal transmission strategy capable of producing amplified orthogonal DNA signal is proposed to resolve the polarity of signals and byproducts, which provides a solution to overcome the signal attenuation. The gap-regulated mechanism combined with DNA strand displacement (DSD) reduces the unpredictable secondary structures, allowing for the coexistence of similar structures in hierarchical molecular networks. For the application of the strategy, a molecular computing model is constructed to solve the maximum weight clique problems (MWCP). This work enhances for our knowledge of these important enzymes and promises application prospects in molecular computing, signal detection, and nanomachines.

G-quadruplex-regulated exonuclease cooperative hydrolysis signal transduction strategy for processing molecular temporal information

Based on the enzyme-resistant properties of G-quadruplexes, combined with Exo III and Exo λ, a G-quadruplex-regulated exonuclease cooperative hydrolysis signal transduction strategy is proposed and applied to processing molecular temporal information.

Production of manno-oligosaccharide from Gleditsia microphylla galactomannan using acetic acid and ferrous chloride

A novel and efficient method for manno-oligosaccharides (MOS) production has been proposed by utilizing Gleditsia microphylla galactomannan as the starting material. This co-operative hydrolysis using ferrous chloride (Fe2+) and acetic acid (HAc) effectively improved the MOS yield and meanwhile decreased the amount of monosaccharide and the 5-hydroxymethyl-furfural (HMF). The highest yields under the optimum conditions were 46.7% by HAc hydrolysis (5 M HAc at 130 °C for 120 min); 37.3% by Fe2+ hydrolysis (0.1 M Fe2+ at 150 °C for 120 min); and 51.4% by co-operative hydrolysis (2 M HAc, 0.05 M Fe2+ at 160 °C for 10 min). From the changes in the value of M/G (mannose/galactose) ratios, it was deduced that Fe2+ predominantly cleaves the main chain, and HAc assists in the breakage of the side chain, thus resulting in the high-efficient co-operative hydrolysis for the production of MOS.

Identification of a Key Enzyme for the Hydrolysis of β-(1→3)-Xylosyl Linkage in Red Alga Dulse Xylooligosaccharide from Bifidobacterium Adolescentis.

Red alga dulse possesses a unique xylan, which is composed of a linear β-(1→3)/β-(1→4)-xylosyl linkage. We previously prepared characteristic xylooligosaccharide (DX3, (β-(1→3)-xylosyl-xylobiose)) from dulse. In this study, we evaluated the prebiotic effect of DX3 on enteric bacterium. Although DX3 was utilized by Bacteroides sp. and Bifidobacterium adolescentis, Bacteroides Ksp. grew slowly as compared with β-(1→4)-xylotriose (X3) but B. adolescentis grew similar to X3. Therefore, we aimed to find the key DX3 hydrolysis enzymes in B. adolescentis. From bioinformatics analysis, two enzymes from the glycoside hydrolase family 43 (BAD0423: subfamily 12 and BAD0428: subfamily 11) were selected and expressed in Escherichia coli. BAD0423 hydrolyzed β-(1→3)-xylosyl linkage in DX3 with the specific activity of 2988 mU/mg producing xylose (X1) and xylobiose (X2), and showed low activity on X2 and X3. BAD0428 showed high activity on X2 and X3 producing X1, and the activity of BAD0428 on DX3 was 1298 mU/mg producing X1. Cooperative hydrolysis of DX3 was found in the combination of BAD0423 and BAD0428 producing X1 as the main product. From enzymatic character, hydrolysis of X3 was completed by one enzyme BAD0428, whereas hydrolysis of DX3 needed more than two enzymes.

Metabolic cooperativity between Porphyromonas gingivalis and Treponema denticola

ABSTRACT Background Porphyromonas gingivalis and Treponema denticola are proteolytic periodontopathogens that co-localize in polymicrobial subgingival plaque biofilms, display in vitro growth symbiosis and synergistic virulence in animal models of disease. These symbioses are underpinned by a range of metabolic interactions including cooperative hydrolysis of glycine-containing peptides to produce free glycine, which T. denticola uses as a major energy and carbon source. Objective To characterize the P. gingivalis gene products essential for these interactions. Methods: The P. gingivalis transcriptome exposed to cell-free T. denticola conditioned medium was determined using RNA-seq. P. gingivalis proteases potentially involved in hydrolysis of glycine-containing peptides were identified using a bioinformatics approach. Results One hundred and thirty-twogenes displayed differential expression, with the pattern of gene expression consistent with succinate cross-feeding from T. denticola to P. gingivalis and metabolic shifts in the P. gingivalis folate-mediated one carbon superpathway. Interestingly, no P. gingivalis proteases were significantly up-regulated. Three P. gingivalis proteases were identified as candidates and inactivated to determine their role in the release of free glycine. P. gingivalis PG0753 and PG1788 but not PG1605 are involved in the hydrolysis of glycine-containing peptides, making free glycine available for T. denticola utilization. Conclusion Collectively these metabolic interactions help to partition resources and engage synergistic interactions between these two species.

Mode of Action of GH30-7 Reducing-End Xylose-Releasing Exoxylanase A (Xyn30A) from the Filamentous Fungus Talaromyces cellulolyticus.

In this study, we characterized the mode of action of reducing-end xylose-releasing exoxylanase (Rex), which belongs to the glycoside hydrolase family 30-7 (GH30-7). GH30-7 Rex, isolated from the cellulolytic fungus Talaromyces cellulolyticus (Xyn30A), exists as a dimer. The purified Xyn30A released xylose from linear xylooligosaccharides (XOSs) 3 to 6 xylose units in length with similar kinetic constants. Hydrolysis of branched, borohydride-reduced, and p-nitrophenyl XOSs clarified that Xyn30A possesses a Rex activity. 1H nuclear magnetic resonance (1H NMR) analysis of xylotriose hydrolysate indicated that Xyn30A degraded XOSs via a retaining mechanism and without recognizing an anomeric structure at the reducing end. Hydrolysis of xylan by Xyn30A revealed that the enzyme continuously liberated both xylose and two types of acidic XOSs: 22-(4-O-methyl-α-d-glucuronyl)-xylotriose (MeGlcA2Xyl3) and 22-(MeGlcA)-xylobiose (MeGlcA2Xyl2). These acidic products were also detected during hydrolysis using a mixture of MeGlcA2Xyl n (n = 2 to 14) as the substrate. This indicates that Xyn30A can release MeGlcA2Xyl n (n = 2 and 3) in an exo manner. Comparison of subsites in Xyn30A and GH30-7 glucuronoxylanase using homology modeling suggested that the binding of the reducing-end residue at subsite +2 was partially prevented by a Gln residue conserved in GH30-7 Rex; additionally, the Arg residue at subsite -2b, which is conserved in glucuronoxylanase, was not found in Xyn30A. Our results lead us to propose that GH30-7 Rex plays a complementary role in hydrolysis of xylan by fungal cellulolytic systems.IMPORTANCE Endo- and exo-type xylanases depolymerize xylan and play crucial roles in the assimilation of xylan in bacteria and fungi. Exoxylanases release xylose from the reducing or nonreducing ends of xylooligosaccharides; this is generated by the activity of endoxylanases. β-Xylosidase, which hydrolyzes xylose residues on the nonreducing end of a substrate, is well studied. However, the function of reducing-end xylose-releasing exoxylanases (Rex), especially in fungal cellulolytic systems, remains unclear. This study revealed the mode of xylan hydrolysis by Rex from the cellulolytic fungus Talaromyces cellulolyticus (Xyn30A), which belongs to the glycoside hydrolase family 30-7 (GH30-7). A conserved residue related to Rex activity is found in the substrate-binding site of Xyn30A. These findings will enhance our understanding of the function of GH30-7 Rex in the cooperative hydrolysis of xylan by fungal enzymes.

Calcium binding to a remote site can replace magnesium as cofactor for mitochondrial Hsp90 (TRAP1) ATPase activity

The Hsp90 molecular chaperones are ATP-dependent enzymes that maintain protein homeostasis and regulate many essential cellular processes. Higher eukaryotes have organelle-specific Hsp90 paralogs that are adapted to each subcellular environment. The mitochondrial Hsp90, TNF receptor–associated protein 1 (TRAP1), supports the folding and activity of electron transport components and is increasingly appreciated as a critical player in mitochondrial signaling. Calcium plays a well-known and important regulatory role in mitochondria where it can accumulate to much higher concentrations than in the cytoplasm. Surprisingly, we found here that calcium can replace magnesium, the essential enzymatic cofactor, to support TRAP1 ATPase activity. Anomalous X-ray diffraction experiments revealed a calcium-binding site within the TRAP1 nucleotide-binding pocket located near the ATP α-phosphate and completely distinct from the magnesium-binding site adjacent to the β- and γ-phosphates. In the presence of magnesium, ATP hydrolysis by TRAP1, as with other Hsp90s, was noncooperative, whereas calcium binding resulted in cooperative hydrolysis by the two protomers within the Hsp90 dimer. The structural data suggested a mechanism for this cooperative behavior. Because of the cooperativity, at high ATP concentrations, ATPase activity was higher with calcium, whereas the converse was observed at low ATP concentrations. Integrating these observations, we propose a model in which the divalent cation choice can control switching between noncooperative and cooperative TRAP1 ATPase mechanisms in response to varying ATP concentrations. This switching may facilitate coordination between cellular energetics, mitochondrial signaling, and protein homeostasis via alterations in the TRAP1 ATP-driven cycle and its consequent effects on different mitochondrial clients.

Decarboxylation of Lactones over Zn/ZSM-5: Elucidation of the Structure of the Active Site and Molecular Interactions.

Herein, we report the catalytic decarboxylation of γ-valerolactone (GVL) over Zn/ZSM-5 to butene, followed by aromatization at high yield with co-feeding of water. An evaluation of the catalytic performance after prolonged periods of time showed that a water molecule is essential to maintain the decarboxylation and aromatization activities and avoid rapid catalyst deactivation. Synchrotron X-ray powder diffraction and Rietveld refinement were then used to elucidate the structures of adsorbed GVL and immobilized Zn species in combination with EXAFS and NMR spectroscopy. A new route for the cooperative hydrolysis of GVL by framework Zn-OH and Brønsted acidic sites to butene and then to aromatic compounds has thus been demonstrated. The structures and fundamental pathways for the nucleophilic attack of terminal Zn-OH sites are comparable to those of Zn-containing enzymes in biological systems.

Decarboxylation of Lactones over Zn/ZSM‐5: Elucidation of the Structure of the Active Site and Molecular Interactions

AbstractHerein, we report the catalytic decarboxylation of γ‐valerolactone (GVL) over Zn/ZSM‐5 to butene, followed by aromatization at high yield with co‐feeding of water. An evaluation of the catalytic performance after prolonged periods of time showed that a water molecule is essential to maintain the decarboxylation and aromatization activities and avoid rapid catalyst deactivation. Synchrotron X‐ray powder diffraction and Rietveld refinement were then used to elucidate the structures of adsorbed GVL and immobilized Zn species in combination with EXAFS and NMR spectroscopy. A new route for the cooperative hydrolysis of GVL by framework Zn−OH and Brønsted acidic sites to butene and then to aromatic compounds has thus been demonstrated. The structures and fundamental pathways for the nucleophilic attack of terminal Zn−OH sites are comparable to those of Zn‐containing enzymes in biological systems.

Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) from Clostridium thermocellum.

Glucuronoxylan endo-β-1,4-xylanases cleave the xylan chain specifically at sites containing 4-O-methylglucuronic acid substitutions. These enzymes have recently received considerable attention owing to their importance in the cooperative hydrolysis of heteropolysaccharides. However, little is known about the hydrolysis of glucuronoxylans in extreme environments. Here, the structure of a thermostable family 30 glucuronoxylan endo-β-1,4-xylanase (CtXyn30A) from Clostridium thermocellum is reported. CtXyn30A is part of the cellulosome, a highly elaborate multi-enzyme complex secreted by the bacterium to efficiently deconstruct plant cell-wall carbohydrates. CtXyn30A preferably hydrolyses glucuronoxylans and displays maximum activity at pH 6.0 and 70°C. The structure of CtXyn30A displays a (β/α)8 TIM-barrel core with a side-associated β-sheet domain. Structural analysis of the CtXyn30A mutant E225A, solved in the presence of xylotetraose, revealed xylotetraose-cleavage oligosaccharides partially occupying subsites -3 to +2. The sugar ring at the +1 subsite is held in place by hydrophobic stacking interactions between Tyr139 and Tyr200 and hydrogen bonds to the OH group of Tyr227. Although family 30 glycoside hydrolases are retaining enzymes, the xylopyranosyl ring at the -1 subsite of CtXyn30A-E225A appears in the α-anomeric configuration. A set of residues were found to be strictly conserved in glucuronoxylan endo-β-1,4-xylanases and constitute the molecular determinants of the restricted specificity displayed by these enzymes. CtXyn30A is the first thermostable glucuronoxylan endo-β-1,4-xylanase described to date. This work reveals that substrate recognition by both thermophilic and mesophilic glucuronoxylan endo-β-1,4-xylanases is modulated by a conserved set of residues.

ID: 165: Parasite control by cytokine-induced guanylate-binding proteins

IFN γ is an immunomodulatory cytokine that rapidly activates potent host cell effector mechanisms to confront a variety of intracellular pathogens. Some of the most abundantly IFN γ induced proteins are the 65-kDa guanylate-binding proteins (GBPs), which mediate cell-autonomous immunity. GBPs are related to the dynamin super family of GTPases and are highly conserved throughout the vertebrate lineage. The human genome harbors seven GBPs and at least one pseudogene, whereas the mouse genome contains 11 GBPs and two pseudogenes. The gene loci of murine GBPs (mGBPs) are tandemly organized in clusters on chromosomes 3 and 5. GBPs contain a conserved GTPase-domain which binds guanine nucleotides with low affinities. This induces nucleotide dependent GBP multimerization and cooperative hydrolysis of GTP via GDP to GMP. Some GBPs are isoprenylated, endowing them with the ability to associate with intracellular membranous compartments. Murine GBPs (mGBPs) exert a major impact on cell-autonomous restriction of Toxoplasma gondii . T. gondii is an apicomplexan protozoan parasite with a broad host range, is distributed worldwide and causes serious and often fatal infections in immunocompromised hosts. T. gondii infection experiments in mice deficient for mGBP1 or mGBP2 prove that mGBPs are essential immune effector molecules mediating antiparasitic resistance. In several cell types distinct mGBPs accumulate at the parasitophorous vacuole membrane (PVM) of T. gondii . The translocation of mGBPs to the PVM is accompanied by depletion of cytosolic vesicle like structures (VLS), formation of large multimers at the PVM, subsequent loss of PVM integrity, followed by a direct assault of mGBP2 upon the plasma membrane of the parasite. These findings provide important dynamic and molecular insights into the function of cell-autonomous immunity.

Cytoskeleton Dynamics: A Continuum Cooperative Hydrolysis Model* *Supported by Chinese Universities Scientific Fund under Grant No. 2014YB029 and National Natural Science Foundation of China under Grant No. 11205123

Cytoskeleton is a network of filamentous proteins, such as actin filaments and microtubules. We propose a continuum cooperative hydrolysis model which possesses exactly analytical solution to describe the dynamics of filament. The results show that the cooperativity leads to non negative-exponential distribution of T (ATP or GTP) subunits. As an application, we investigate the treadmilling phenomenon using our model. It is shown that the cooperativity remarkably affects the length of filament.

An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence.

The nucleotide cyclic di-3',5'- adenosine monophosphate (c-di-AMP) was recently identified as an essential and widespread second messenger in bacterial signaling. Among c-di-AMP-producing bacteria, altered nucleotide levels result in several physiological defects and attenuated virulence. Thus, a detailed molecular understanding of c-di-AMP metabolism is of both fundamental and practical interest. Currently, c-di-AMP degradation is recognized solely among DHH-DHHA1 domain-containing phosphodiesterases. Using chemical proteomics, we identified the Listeria monocytogenes protein PgpH as a molecular target of c-di-AMP. Biochemical and structural studies revealed that the PgpH His-Asp (HD) domain bound c-di-AMP with high affinity and specifically hydrolyzed this nucleotide to 5'-pApA. PgpH hydrolysis activity was inhibited by ppGpp, indicating a cross-talk between c-di-AMP signaling and the stringent response. Genetic analyses supported coordinated regulation of c-di-AMP levels in and out of the host. Intriguingly, a L. monocytogenes mutant that lacks c-di-AMP phosphodiesterases exhibited elevated c-di-AMP levels, hyperinduced a host type-I IFN response, and was significantly attenuated for infection. Furthermore, PgpH homologs, which belong to the 7TMR-HD family, are widespread among hundreds of c-di-AMP synthesizing microorganisms. Thus, PgpH represents a broadly conserved class of c-di-AMP phosphodiesterase with possibly other physiological functions in this crucial signaling network.

Cooperative hydrolysis of aryl esters on functionalized membrane surfaces and in micellar solutions.

Catalytic hydrolysis of peptides, proteins, phosphates or carboxylate esters in nature is catalysed by enzymes, which are efficient, fast and selective. Most of the hydrolytic chemical catalysts published so far mimic the active site of enzymes and contain metal complexes and amino acid residues. Their synthesis can be laborious, while the hydrolytic activity is still limited compared to enzymes. We present an approach that uses fluid membranes of vesicles and micelles as a support for amphiphilic additives, which cooperatively cleave aryl ester bonds. The membrane anchored bis-Zn(II)-complex 1 is hydrolytically active and hydrolyses fluorescein diacetate (FDA) with a second order rate constant (k2) of 0.9 M(-1) s(-1). The hydrolytic activity is modulated by co-embedded membrane additives, bearing common amino acid side chain functional groups. With this approach, the hydrolytic activity of the system is enhanced up to 16 fold in comparison with cyclen 1 (k2 = 14.7 M(-1) s(-1)). DOPC and DSPC lipids form at room temperature fluid or gel phase membranes, respectively. Omitting the lipid, micellar solutions were obtained with hydrolytic activity reaching k2 = 13.4 M(-1) s(-1). It is shown that cooperative hydrolysis is favoured in fluid membranes and micelles, allowing the active moieties to arrange freely. The embedding and dynamic self-assembly of membrane active components in fluid membranes and micelles provide facile access to hydrolytically active soft interfaces.

Actin Polymerization and Depolymerization Coupled to Cooperative Hydrolysis

The hydrolysis of adenosine triphosphate (ATP) during actin (de)polymerization consists of two subprocesses, ATP cleavage and phosphate (P_{i}) release, which involve three nucleotide states of each actin protomer. A new theoretical model that explicitly incorporates these different subprocesses and states is introduced and compared with recent experimental data for actin depolymerization. These data can be explained by strongly cooperative ATP cleavage followed by strongly cooperative P_{i} release but are incompatible with random and/or vectorial subprocesses as proposed previously.

Complex cooperativity of ATP hydrolysis in the F 1-ATPase molecular motor

F 1-ATPase catalyses ATP hydrolysis and converts the cellular chemical energy into mechanical rotation. The hydrolysis reaction in F 1-ATPase does not follow the widely believed Michaelis–Menten mechanism. Instead, the hydrolysis mechanism behaves in an ATP-dependent manner. We develop a model for enzyme kinetics and hydrolysis cooperativity of F 1-ATPase which involves the binding-state changes to the coupling catalytic reactions. The quantitative analysis and modeling suggest the existence of complex cooperative hydrolysis between three different catalysis sites of F 1-ATPase. This complexity may be taken into account to resolve the arguments on the binding change mechanism in F 1-ATPase.

IIGP1, an Interferon-γ-inducible 47-kDa GTPase of the Mouse, Showing Cooperative Enzymatic Activity and GTP-dependent Multimerization

IIGP1 belongs to a well defined family of 47-kDa GTPases whose members are present at low resting levels in mouse cells but are strongly induced transcriptionally by interferons and are implicated in cell-autonomous resistance to intracellular pathogens. Recombinant IIGP1 was expressed in Escherichia coli and purified to homogeneity. Here we present a detailed biochemical characterization of IIGP1 using various biochemical and biophysical methods. IIGP1 binds to GTP and GDP with dissociation constants in the micromolar range with at least 10 times higher affinity for GDP than for GTP. IIGP1 hydrolyzes GTP to GDP, and the GTPase activity is concentration-dependent with a GTP turnover rate of 2 min-1 under saturating protein concentrations. Functional interaction between IIGP1 molecules is shown by nucleotide-dependent oligomerization in vitro. Both cooperative hydrolysis of GTP and GTP-dependent oligomerization are blocked in a mutant form of IIGP1 modified at the C terminus. IIGP1 shares micromolar nucleotide affinities and oligomerization-dependent hydrolytic activity with the 67-kDa GTPase hGBP1 (induced by type I and type II interferons), with the antiviral Mx proteins (interferon type I-induced) and with the paradigm of the self-activating large GTPases, the dynamins, with which Mx proteins show homology. The higher relative affinity for GDP and the relatively low GTPase activity distinguish IIGP1, but this study clearly adds IIGP1 and thus the p47 GTPases to the small group of cooperative GTPase families that appear to characterize the development of intracellular resistance during the interferon response to infection. The present analysis provides essential parameters to understand the molecular mechanism by which IIGP1 participates in this complex resistance program.

Production and properties of phytase and acid phosphatase from a sake koji mold, Aspergillus oryzae

We identified three types of acid phosphatase (ACP-I, ACP-II, and ACP-III) produced by Aspergillus oryzae in a submerged culture using only phytic acid as the phosphorous substrate. The optimum pH for the activities of the three enzymes was in the range of 4.5 to 5.5. Analysis of the substrate specificities of these enzymes revealed that ACP-I and ACP-III were acid phosphatases, and ACP-II was a phytase. These enzymes were produced during different periods of mycelial growth: ACP-II was produced during the early phase of cultivation (around 24 h), and ACP-I was produced between 24 to 72 h. ACP-III was detected after the production of ACP-I and ACP-II had ceased. The release of phosphate from phytic acid was expected to be due to the cooperative hydrolysis of these enzymes.

Production and Properties of Phytase and Acid Phosphatase from a Sake Koji Mold, Aspergillus oryzae

We identified three types of acid phosphatase (ACP-I, ACP-II, and ACP-III) produced by Aspergillus oryzae in a submerged culture using only phytic acid as the phosphorous substrate. The optimum pH for the activities of the three enzymes was in the range of 4.5 to 5.5. Analysis of the substrate specificities of these enzymes revealed that ACP-I and ACP-III were acid phosphatases, and ACP-II was a phytase. These enzymes were produced during different periods of mycelial growth: ACP-II was produced during the early phase of cultivation (around 24 h), and ACP-I was produced between 24 to 72 h. ACP-III was detected after the production of ACP-I and ACP-II had ceased. The release of phosphate from phytic acid was expected to be due to the cooperative hydrolysis of these enzymes.

Mechanism of ATP hydrolysis by polymeric actin

The lag between polymerization of actin and ATP hydrolysis in actin filaments was analyzed in terms of the mechanism of the hydrolysis reaction. Under the experimental conditions (100 mM KCI and 1 mM MgCI 2, or without KCI, 1 mM MgCI 2 and 0.4 mM EGTA, 25°C) ATP hydrolysis lagged behind polymerization by about 100 s independently of the concentration of polymerizing filament ends and of the actin monomer concentration. Three models of ATP hydrolysis were compared to experimental data: (i) Random ATP hydrolysis, ATP is assumed to be hydrolyzed at a rate that is independent of the type of nucleotide bound to adjacent filament subunits. (ii) Cooperative hydrolysis, the rate of ATP hydrolysis is thought to depend on the type of nucleotide bound to adjacent subunits. (iii) Sequential hydrolysis, ATP is assumed to be hydrolyzed only at the interface between ATP-subunits and ADP-subunits. The model of sequential ATP hydrolysis could be excluded. The results were in agreement with random or cooperative ATP hydrolysis. The differences of the rates of ATP hydrolysis by a random or cooperative mechanism are so small that based on the experimental results no distinction between these two mechanisms could be made. All available evidence points towards a mechanism of ATP hydrolysis in which several or perhaps many interfaces between ATP- and ADP-subunits are formed within a filament.