pKa modulation of the acid/base catalyst within GH32 and GH68: a role in substrate/inhibitor specificity?

Glycoside hydrolases of families 32 (GH32) and 68 (GH68) belong to clan GH-J, containing hydrolytic enzymes (sucrose/fructans as donor substrates) and fructosyltransferases (sucrose/fructans as donor and acceptor substrates). In GH32 members, some of the sugar substrates can also function as inhibitors, this regulatory aspect further adding to the complexity in enzyme functionalities within this family. Although 3D structural information becomes increasingly available within this clan and huge progress has been made on structure-function relationships, it is not clear why some sugars bind as inhibitors without being catalyzed. Conserved aspartate and glutamate residues are well known to act as nucleophile and acid/bases within this clan. Based on the available 3D structures of enzymes and enzyme-ligand complexes as well as docking simulations, we calculated the pKa of the acid-base before and after substrate binding. The obtained results strongly suggest that most GH-J members show an acid-base catalyst that is not sufficiently protonated before ligand entrance, while the acid-base can be fully protonated when a substrate, but not an inhibitor, enters the catalytic pocket. This provides a new mechanistic insight aiming at understanding the complex substrate and inhibitor specificities observed within the GH-J clan. Moreover, besides the effect of substrate entrance on its own, we strongly suggest that a highly conserved arginine residue (in the RDP motif) rather than the previously proposed Tyr motif (not conserved) provides the proton to increase the pKa of the acid-base catalyst.     

The role of the active site Zn in the catalytic mechanism of the GH38 Golgi α-mannosidase II: Implications from noeuromycin inhibition

Golgi α-mannosidase II (GMII) is a Family 38 glycosyl hydrolase involved in the eukaryotic N-glycosylation pathway in protein synthesis. Understanding of its catalytic mechanism has been of interest for the development of specific inhibitors that could lead to novel anti-metastatic or anti-inflammatory compounds. The active site of GMII has been characterized by structural studies of the Drosophila homologue (dGMII) and unusually contains a Zn atom which forms contacts with substrate analogues, stabilized catalytic intermediates, and other inhibitors observed in the active site. In this contribution, we analyze the structure of the sugar mimetic compound noeuromycin complexed with dGMII. Distortions of the conformation of this inhibitor, together with similar observations from other complexes, have permitted us to propose specific roles for the Zn atom in the chemical mechanism of catalysis of Family 38 glycosidase. Such insights have relevance to efforts to formulate novel, specific inhibitors of GMII.     

In silico identification of catalytic residues and domain fold of the family GH119 sharing the catalytic machinery with the α-amylase family GH57

The glycoside hydrolase family 119 (GH119) contains the α-amylase from Bacillus circulans and five other hypothetical proteins. Until now, nothing has been reported on the catalytic residues and catalytic-domain fold of GH119. Based on a detailed in silico analysis involving sequence comparison in combination with BLAST searches and structural modelling, an unambiguous relationship was revealed between the families GH119 and GH57. This includes sharing the catalytic residues, i.e. Glu231 and Asp373 as catalytic nucleophile and proton donor, respectively, in the predicted catalytic (β/α)₇-barrel domain of GH119 B. circulans α-amylase. The GH57 and GH119 families may thus define a new CAZy clan.     

Growth hormone (GH) differentially regulates NF-kB activity in preadipocytes and macrophages: implications for GH’s role in adipose tissue homeostasis in obesity

Adipose tissue remodeling in obesity involves macrophage infiltration and chronic inflammation. NF-kB-mediated chronic inflammation of the adipose tissue is directly implicated in obesity-associated insulin resistance. We have investigated the effect of growth hormone (GH) on NF-kB activity in preadipocytes (3T3-F442A) and macrophages (J774A.1). Our studies indicate that whereas GH increases NF-kB activity in preadipocytes, it decreases NF-kB activity in macrophages. This differential response of NF-kB activity to GH correlates with the GH-dependent expression of a cadre of NF-kB-activated cytokines in these two cell types. Activation of NF-kB by GH in preadipocytes heightens inflammatory response by stimulating production of multiple cytokines including TNF-α, IL-6, and MCP-1, the mediators of both local and systemic insulin resistance and chemokines that recruit macrophages. Our studies also suggest differential regulation of miR132 and SIRT1 expression as a mechanism underlying the observed variance in GH-dependent NF-kB activity and altered cytokine profile in preadipocytes and macrophages. These findings further our understanding of the complex actions of GH on adipocytes and insulin sensitivity.     

Phylogenetic Analysis of α-Galactosidases of the GH27 Family

Amino acid sequence analysis of -galactosidases and other proteins of glycoside hydrolase family 27 (GH27) allowed isolation of three major subfamilies, 27a–27c. Unique isomalto-dextranase of Arthrobacter globiformis clustered separately. Eukaryotic proteins formed five clusters on a phylogenetic tree of the family. Bacterial GH27 proteins, which are relatively few, did not form stable clusters. A monophyletic origin of the GH27 family was demonstrated with the use of related proteins of the GH36 family. The structure of the active center and evolution of -galactosidases are discussed.     

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Growth hormone (GH) treatment acts on the endocrine and autocrine/paracrine GH/IGF-axis and on TNF-α expression in bony fish pituitary and immune organs

There exist indications that the growth hormone (GH)/insulin-like growth factor (IGF) axis may play a role in fish immune regulation, and that interactions occur via tumour necrosis factor (TNF)-α at least in mammals, but no systematic data exist on potential changes in GH, IGF-I, IGF-II, GH receptor (GHR) and TNF-α expression after GH treatment. Thus, we investigated in the Nile tilapia the influence of GH injections by real-time qPCR at different levels of the GH/IGF-axis (brain, pituitary, peripheral organs) with special emphasis on the immune organs head kidney and spleen. Endocrine IGF-I served as positive control for GH treatment efficiency. Basal TNF-α gene expression was detected in all organs investigated with the expression being most pronounced in brain. Two consecutive intraperitoneal injections of bream GH elevated liver IGF-I mRNA and plasma IGF-I concentration. Also liver IGF-II mRNA and TNF-α were increased while the GHR was downregulated. In brain, no change occurred in the expression levels of all genes investigated. GH gene expression was exclusively detected in the pituitary where the GH injections elevated both GH and IGF-I gene expression. In the head kidney, GH upregulated IGF-I mRNA to an even higher extent than liver IGF-I while IGF-II and GHR gene expressions were not affected. Also in the spleen, no change occurred in GHR mRNA, however, IGF-I and IGF-II mRNAs were increased. In correlation, in situ hybridisation showed a markedly higher amount of IGF-I mRNA in head kidney and spleen after GH injection. In both immune tissues, TNF-α gene expression showed a trend to decrease after GH treatment. The stimulation of IGF-I and also partially of IGF-II expression in the fish immune organs by GH indicates a local role of the IGFs in immune organ regulation while the differential changes in TNF-α support the in mammals postulated interactions with the GH/IGF-axis which demand for further investigations.     

Age-related Changes in the Insulin Receptor β in the Gerbil Hippocampus

The insulin receptor has been reported to be associated with memory formation via the hippocampus. In this study, we observed age-related changes in the insulin receptor β immunoreactivity and its protein levels in the hippocampus of gerbils of various ages in order to identify the correlation between the insulin receptor β and aging processes in the hippocampus. Insulin receptor β immunoreactivity was mainly detected in the molecular and polymorphic layers of the dentate gyrus, and in mossy fibers, Schaffer collaterals, alveus and stratum lacunosum-moleculare of the hippocampus proper (CA1-3) of gerbils at postnatal month 1 (PM 1). Insulin receptor β immunoreactivity decreased with age in all of these structures, except for the alveus. Reduction of the insulin receptor β immunoreactivity was prominent in the molecular layer of the dentate gyrus at PM 6 and in the stratum lacunosum-moleculare of the CA1 region at PM 12, while insulin receptor β immunoreactivity was decreased in other regions in the PM 18 groups. In addition, insulin receptor β protein level in the whole hippocampus was slightly increased at PM 3, and it decreased in an age-dependent manner from PM 6 to PM 24. These reductions of the insulin receptor β in the hippocampus may be associated with age-related memory deficits in gerbils.     

SH groups in the α-naphthyl acetate esterase in the thyroid of the guinea-pig

Summary The -naphthyl acetate esterase in both group I and group II thyroid cells is shown to contain SH groups since there is a decline in activity in both cell groups when certain sulfhydryl reagents [DTNB; 5,5-Dithiobis-(2-nitrobenzoic acid)-AgNO₃-Mersalyl-PCMB (parachloro mercuribenzoate)+urea] are added to the incubation media. Thus the inhibition is by far the greatest in group I cells, which also show the greatest activity after incubation in conventional media, when long fixation and storage times are used. In all cases the inhibiting effect was complete or almost completely reversed if cysteine was added to the incubation media in equivalent concentrations to the SH blocker. There were great differences among the sulfhydryl reagents used in their ability to bring about enzyme inhibition. The alkylating agents NEM (N-ethylmaleimide) and iodoacetamide had no or little effect while PCMB could only inhibit the activity of the -naphthylacetate esterase if the enzyme was denaturated with 5 m urea. The maximal inhibitory effect of PCMB was only obtained when NaCl was added to the incubation media. The most effective inhibitor was AgNO₃.     

A new GH13 subfamily represented by the α-amylase from the halophilic archaeon Haloarcula hispanica

Extremophiles - α-Amylase catalyzes the endohydrolysis of α-1,4-glucosidic linkages in starch and related α-glucans. In the CAZy database, most α-amylases have been classified...     

Zooplankton in the ponds with tropical plants in the greenhouses of the Botanical Garden of the Jagiellonian University in Kraków

The presence of P. tetraurelia was found in the pond in "The Palm-House" greenhouse.     

GH115 α-glucuronidase and GH11 xylanase from Paenibacillus sp. JDR-2: potential roles in processing glucuronoxylans

Paenibacillus sp. JDR-2 (Pjdr2) has been studied as a model for development of bacterial biocatalysts for efficient processing of xylans, methylglucuronoxylan, and methylglucuronoarabinoxylan, the predominant hemicellulosic polysaccharides found in dicots and monocots, respectively. Pjdr2 produces a cell-associated GH10 endoxylanase (Xyn10A₁) that catalyzes depolymerization of xylans to xylobiose, xylotriose, and methylglucuronoxylotriose with methylglucuronate-linked α-1,2 to the nonreducing terminal xylose. A GH10/GH67 xylan utilization regulon includes genes encoding an extracellular cell-associated Xyn10A₁ endoxylanase and an intracellular GH67 α-glucuronidase active on methylglucuronoxylotriose generated by Xyn10A₁ but without activity on methylglucuronoxylotetraose generated by a GH11 endoxylanase. The sequenced genome of Pjdr2 contains three paralogous genes potentially encoding GH115 α-glucuronidases found in certain bacteria and fungi. One of these, Pjdr2_5977, shows enhanced expression during growth on xylans along with Pjdr2_4664 encoding a GH11 endoxylanase. Here, we show that Pjdr2_5977 encodes a GH115 α-glucuronidase, Agu115A, with maximal activity on the aldouronate methylglucuronoxylotetraose selectively generated by a GH11 endoxylanase Xyn11 encoded by Pjdr2_4664. Growth of Pjdr2 on this methylglucuronoxylotetraose supports a process for Xyn11-mediated extracellular depolymerization of methylglucuronoxylan and Agu115A-mediated intracellular deglycosylation as an alternative to the GH10/GH67 system previously defined in this bacterium. A recombinantly expressed enzyme encoded by the Pjdr2 agu115A gene catalyzes removal of 4-O-methylglucuronate residues α-1,2 linked to internal xylose residues in oligoxylosides generated by GH11 and GH30 xylanases and releases methylglucuronate from polymeric methylglucuronoxylan. The GH115 α-glucuronidase from Pjdr2 extends the discovery of this activity to members of the phylum Firmicutes and contributes to a novel system for bioprocessing hemicelluloses.

     

Is neurotensin in the brain involved in thermoregulation of the monkey?

Cannulae for intracerebroventricular (ICV) infusion were implanted stereotaxically in monkeys (Macaca fasicularis) maintained post-operatively in a primate restraint chair. During each experiment, a series of physiological measures was recorded simultaneously on a polygraph which included colonic temperature, vasomotor tone, heart rate, respiratory rate, and basal metabolism as reflected by O₂ uptake. The ICV infusion in a volume of 0.5 ml of neurotensin (NT) in doses ranging from 3–150 μg produced neither a statistically significant nor consistent change in body temperature or vasomotor response. Although the highest dose of 450 μg NT infused ICV caused an immediate bradycardia and a concomitant decline in metabolic and respiratory rates, an average decline in core temperature of 0.6°C and the accompanying cutaneous vasodilation often had a latency as long as 1.0 hr. In contrast to the typical hypothermia in this species following an ICV infusion of catecholamines, implicated in the central pathways underlying thermoregulation, NT failed to elicit a coordinated set of physiological responses for heat dissipation in the monkey. Therefore, it is unlikely that this tridecapeptide plays a role in the central mechanisms mediating the control of body temperature of this primate species.     

Transmission ratio distortion at the growth hormone gene (GH1) in bovine preimplantation embryos: An in vitro culture‐induced phenomenon?

The growth hormone gene (GH1) and its polypeptide product (GH) have a crucial role in reproduction, embryogenesis and general development. A polymorphism present in the fifth exon of the bovine GH1 gene (GH1 p.Leu127Val) has been associated with GH release and milk production in cattle. The objective of the present study was to examine the genotype frequencies of the GH1 p.Leu127Val polymorphism in bovine blastocysts produced in vitro and in vivo to determine if allelic variation of the GH1 gene affects embryo development and survival. A heterozygous (p.Leu127/Val127) sire was used for in vitro fertilization of oocytes of unknown maternal genotype (n = 104) and known maternal genotype (n = 115). PCR amplification and genotyping of the GH1 gene from Day 8 blastocysts derived from these fertilized oocytes demonstrated that there was significant over-representation from the expected Mendelian ratio of GH1 p.Leu127/Leu127 homozygotes from oocytes of known maternal genotype (P = 0.006). Contrary to this, analysis of in vivo-produced bovine blastocysts of known parental GH1 genotype (n = 69) did not reveal an overrepresentation of GH1 p.Leu127/Leu127 homozygotes. These results suggest that developing in vitro-produced embryos are exposed to a selection process, probably due to a less favorable culture environment, that acts to increase the number of GH1 p.Leu127/Leu127 homozygotes, thereby giving rise to the observed transmission ratio distortion (TRD) of GH1 genotypes when compared to in vivo produced embryos.     

Changes in the rate of photosynthesis accompanying the yield increase in wheat cultivars released in the past 50 years

Photosynthetic rates in different development stages were carefully investigated in 18 cultivars of winter wheat released in the period between 1945 and 1995 in the area of Beijing, China. During this period, the recorded grain yield has increased eightfold. However, when those cultivars were planted and managed in the same environment, the difference was reduced to only 36%, indicating that agronomic practices are the most important factors for grain yield. Agronomic features have changed greatly in the past 50 years, through increasing the harvest index (R²=0.89, P<0.05), shortening plant height (R²=0.77, P<0.05) and slightly increasing flag leaf areas (R²=0.45, P<0.05), which is mostly in agreement with many other researchers. In contrast to many reports, however, this study found a genetic increase in the rate of photosynthesis per unit leaf area. From the mid-stem elongation to soft dough stages, the average photosynthetic rates at saturated photosynthetic photon flux density (P_sat) increased by 44%. In the process, the stomatal conductance (g_s) also increased by 122%. Grain yield was positively related to the mean values of P_sat (R²=0.61, P<0.01) and g_s (R²=0.67, P<0.01) in the six development stages. Our experiment may suggest that increase in grain yield was associated with the elevation of leaf photosynthetic rate and stomatal conductance over the past 50 years.