Molecular evolution of the CYTH superfamily of proteins

in FEBS Journal (2012), 279(Suppl. s1), 438

Molecular evolution of the CYTH superfamily of proteins L. Bettendorff, D. Delvaux, G. Kohn, P. Wins, B. Lakaye GIGA-Neurosciences, University of Liège, Belgium The CYTH superfamily of proteins was named ... [more ▼]

Molecular evolution of the CYTH superfamily of proteins L. Bettendorff, D. Delvaux, G. Kohn, P. Wins, B. Lakaye GIGA-Neurosciences, University of Liège, Belgium The CYTH superfamily of proteins was named after the two founding members, the CYaB adenylyl cyclase from Aeromonas hydrophila and the human 25-kDa THiamine triphosphatase (ThTPase). Members of this superfamily of proteins exist in all organisms including bacteria, archaea, plants and animals (except in birds) and can be traced back to the Last Universal Common Ancestor. They are characterized by a consensus sequence including several charged residues involved in divalent cation and triphosphate binding. Indeed, all members of the CYTH family that are characterized act on triphosphate derivatives and require at least one divalent cation for catalysis. The Nitrosomonas europaea (1) and E.coli CYTH proteins are specific inorganic triphosphatases. We propose that inorganic triphosphate (PPPi), the most simple triphosphate compound that can be imagined, is the primitive substrate of CYTH proteins. Other enzyme activities such as adenylate cyclase (in A. hydrophila), mRNA triphosphatase (in fungi and protozoans) and ThTPase (in metazoans) activities are secondary acquisitions. We show that ThTPase activity is not limited to mammals, but Sea anemone and Zebrafish CYTH proteins are already specific ThTPases and the acquisition of this enzyme activity is linked to the presence of a Trp (W53 in mammalian ThTPases) residue involved in the binding of the thiazole heterocycle of the thiamine molecule. The importance of W53 for the specificity of mammalian ThTPases is confirmed by site-directed mutagenesis. Furthermore, we propose a conserved catalytic mechanism between inorganic triphosphatases and ThTPases, based on a catalytic dyad comprising a Lys and a Tyr residue, explaining the alkaline pH optimum of CYTH proteins. (1) Delvaux et al. J. Biol. Chem 286 (2011) 34023-35 [less ▲]

Broad antibiotic resistance profile of the subclass B3 metallo-β-lactamase GOB-1, a di-zinc enzyme.

in FEBS Journal (2011), 278(8)

The metallo-β-lactamase (MBL) GOB-1 was expressed via a T7 expression system in Escherichia coli BL21(DE3). The MBL was purified to homogeneity and shown to exhibit a broad substrate profile, hydrolyzing ... [more ▼]

The metallo-β-lactamase (MBL) GOB-1 was expressed via a T7 expression system in Escherichia coli BL21(DE3). The MBL was purified to homogeneity and shown to exhibit a broad substrate profile, hydrolyzing all the tested β-lactam compounds efficiently. The GOB enzymes are unique among MBLs due to the presence of a glutamine residue at position 116, a zinc-binding residue in all known class B1 and B3 MBL structures. Here we produced and studied the Q116A, Q116N and Q116H mutants. The substrate profiles were similar for each mutant, but with significantly reduced activity compared with that of the wild-type. In contrast to the Q116H enzyme, which bound two zinc ions just like the wild-type, only one zinc ion is present in Q116A and Q116N. These results suggest that the Q116 residue plays a role in the binding of the zinc ion in the QHH site. [less ▲]

Optimization of conditions for the glycosyltransferase activity of penicillin-binding protein 1a from Thermotoga maritima.

in FEBS Journal (2010), 277(20), 4290-8

Cell wall biosynthesis is a key target for antibacterial drugs. The major constituent of the bacterial wall, peptidoglycan, is a netlike polymer responsible for the size and shape of the cell and for ... [more ▼]

Cell wall biosynthesis is a key target for antibacterial drugs. The major constituent of the bacterial wall, peptidoglycan, is a netlike polymer responsible for the size and shape of the cell and for resisting osmotic pressure. It consists of glycan chains of repeating disaccharide units cross-linked through short peptide chains. Peptidoglycan assembly is catalyzed by the periplasmic domain of bifunctional class A penicillin-binding proteins. Cross-linking of the peptide chains is catalyzed by their transpeptidase module, which can be inhibited by the most widely used antibiotics, the beta-lactams. In contrast, no drug in clinical use inhibits the polymerization of the glycan chains, catalyzed by their glycosyltransferase module, although it is an obvious target. We report here the purification of the ectodomain of the class A penicillin-binding protein 1a from Thermotoga maritima (Tm-1a*), expressed recombinantly in Escherichia coli. A detergent screen showed that detergents with shorter aliphatic chains were better solubilizers. Cyclohexyl-hexyl-beta-D-maltoside-purified Tm-1a* was found to be monomeric and to have improved thermal stability. A miniaturized, multiwell continuous fluorescence assay of the glycosyltransferase activity was used to screen for optimal reaction conditions. Tm-1a* was active as a glycosyltransferase, catalyzing the formation of glycan chains up to 16 disaccharide units long. Our results emphasize the importance of the detergent in preparing a stable monomeric ectodomain of a class A penicillin-binding protein. Our assay could be used to screen collections of compounds for inhibitors of peptidoglycan glycosyltransferases that could serve as the basis for the development of novel antibiotics. [less ▲]

Thiamin diphosphate in biological chemistry: new aspects of thiamin metabolism, especially triphosphate derivatives acting other than as cofactors

in FEBS Journal (2009), 276(11), 2917-2925

Prokaryotes, yeasts and plants synthesize thiamine (vitamin B1) via complex pathways. Animal cells capture the vitamin through specific high-affinity transporters essential for internal thiamine ... [more ▼]

Prokaryotes, yeasts and plants synthesize thiamine (vitamin B1) via complex pathways. Animal cells capture the vitamin through specific high-affinity transporters essential for internal thiamine homeostasis. Inside the cells, thiamine is phosphorylated to higher phosphate derivatives. Thiamine diphosphate (ThDP) is the best-known thiamine compound for its role as an enzymatic cofactor. However, besides ThDP, at least three other thiamine phosphates occur naturally in most cells: thiamine monophosphate (ThMP), thiamine triphosphate (ThTP) and the recently discovered adenosine thiamine triphosphate (AThTP). It was suggested that ThTP has a specific neurophysiological role, but recent data are in favor of a much more basic metabolic function. During amino acid starvation, Escherichia coli accumulate ThTP possibly acting as a signal involved in the adaptation of the bacteria to changing nutritional conditions. In animal cells, ThTP can phosphorylate some proteins, but the physiological significance of this mechanism remains unknown. AThTP, recently discovered in E. coli, accumulates during carbon starvation and might act as an alarmone. Among the proteins involved in thiamine metabolism, thiamine transporters, thiamine pyrophosphokinase and a soluble 25-kDa thiamine triphosphatase have been characterized at the molecular level, in contrast to thiamine mono- and diphosphatases whose specificities remain to be proven. A soluble enzyme catalyzing the synthesis of AThTP from ThDP and ADP or ATP has been partially characterized in E. coli, but the mechanism of ThTP synthesis remains elusive. The data reviewed here illustrate the complexity of thiamine biochemistry, which is not restricted to the cofactor role of ThDP. [less ▲]

Impact of cyclic hypoxia on HIF-1a regulation in endothelial cells: new insights for anti-tumor treatments

in FEBS Journal (2008)

Impact of cyclic hypoxia on HIF-1alpha regulation in endothelial cells - new insights for anti-tumor treatments.Martinive P, Defresne F, Quaghebeur E, Daneau G, Crokart N, Grégoire V, Gallez B, Dessy C ... [more ▼]

Impact of cyclic hypoxia on HIF-1alpha regulation in endothelial cells - new insights for anti-tumor treatments.Martinive P, Defresne F, Quaghebeur E, Daneau G, Crokart N, Grégoire V, Gallez B, Dessy C, Feron O. Unit of Pharmacology and Therapeutics, Université catholique de Louvain, Brussels, Belgium. Heterogeneities in tumor blood flow are associated with cyclic changes in pO(2) or cyclic hypoxia. A major difference from O(2) diffusion-limited or chronic hypoxia is that the tumor vasculature itself may be directly influenced by the fluctuating hypoxic environment, and the reoxygenation phases complicate the usual hypoxia-induced phenotypic pattern. Here, we determined the cyclic hypoxia-driven pathways that modulate hypoxia inducible factor (HIF)-1alpha abundance in endothelial cells to identify possible therapeutic targets. We found that exposure of endothelial cells to cycles of hypoxia/reoxygenation led to accumulation of HIF-1alpha during the hypoxic periods and the phosphorylation of protein kinase B (Akt), extracellular regulated kinase (ERK) and endothelial nitric oxide synthase (eNOS) during the reoxygenation phases. We identified stimulation of mitochondrial respiration and activation of the phosphoinositide-3 kinase (PI3K)/Akt pathway during intervening reoxygenation periods as major triggers of the stabilization of HIF-1alpha. We also found that the NOS inhibitor nitro-l-arginine methyl ester further stimulated the cyclic hypoxia-driven HIF-1alpha accumulation and the associated gain in endothelial cell survival, thereby mirroring the effects of a PI3K/Akt inhibitor. However, combination of both drugs resulted in a net reduction in HIF-1alpha and a dramatic in decrease in endothelial cell survival. In conclusion, this study identified cyclic hypoxia, as reported in many tumor types, as a unique biological challenge for endothelial cells that promotes their survival in a HIF-1alpha-dependent manner through phenotypic alterations occurring during the reoxygenation periods. These observations also indicate the potential of combining Akt-targeting drugs with anti-angiogenic drugs, in particular those interfering with the NO pathway. PMID: 19077164 [PubMed - as supplied by publisher [less ▲]

Crystal structure of a cold-adapted class C beta-lactamase.

in FEBS Journal (2008), 275(8), 1687-97

In this study, the crystal structure of a class C beta-lactamase from a psychrophilic organism, Pseudomonas fluorescens, has been refined to 2.2 A resolution. It is one of the few solved crystal ... [more ▼]

In this study, the crystal structure of a class C beta-lactamase from a psychrophilic organism, Pseudomonas fluorescens, has been refined to 2.2 A resolution. It is one of the few solved crystal structures of psychrophilic proteins. The structure was compared with those of homologous mesophilic enzymes and of another, modeled, psychrophilic protein. The elucidation of the 3D structure of this enzyme provides additional insights into the features involved in cold adaptation. Structure comparison of the psychrophilic and mesophilic beta-lactamases shows that electrostatics seems to play a major role in low-temperature adaptation, with a lower total number of ionic interactions for cold enzymes. The psychrophilic enzymes are also characterized by a decreased number of hydrogen bonds, a lower content of prolines, and a lower percentage of arginines in comparison with lysines. All these features make the structure more flexible so that the enzyme can behave as an efficient catalyst at low temperatures. [less ▲]

Creating hybrid proteins by insertion of exogenous peptides into permissive sites of a class A beta-lactamase

in FEBS Journal (2008), 275

Identification of cis-regulatory elements controlling two differentially expressed Pit-1 genes in the duplicated genome of Cyprinus carpio

in FEBS Journal (2005, July), 272(Suppl. 1), 469-470

Phosphatidylinositol 3,4,5-trisphosphate modulation in Ship2-deficient mouse embryonic fibroblasts

in FEBS Journal (2005), 272

SHIP2, the ubiquitous SH2 domain containing inositol 5-phosphatase, includes a series of protein interacting domains and has the ability to dephosphorylate phosphatidylinositol 3,4,5-trisphosphate [PtdIns ... [more ▼]

SHIP2, the ubiquitous SH2 domain containing inositol 5-phosphatase, includes a series of protein interacting domains and has the ability to dephosphorylate phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3] in vitro. The present study, which was undertaken to evaluate the impact of SHIP2 on PtdIns(3,4,5)P3 levels, was performed in a mouse embryonic fibroblast (MEF) model using SHIP2 deficient (– ⁄ –) MEF cells derived from knockout mice. PtdIns(3,4,5)P3 was upregulated in serum stimulated – ⁄ – MEF cells as compared to +⁄+ MEF cells. Although the absence of SHIP2 had no effect on basal PtdIns(3,4,5)P3 levels, we show here that this lipid was significantly upregulated in SHIP2 – ⁄ – cells but only after short-term (i.e. 5–10 min) incubation with serum. The difference in PtdIns(3,4,5)P3 levels in heterozygous fibroblast cells was intermediate between the +⁄+ and the – ⁄ – cells. In our model, insulin-like growth factor-1 stimulation did not show this upregulation. Serum stimulated phosphoinositide 3-kinase (PI 3-kinase) activity appeared to be comparable between +⁄+ and – ⁄ – cells. Moreover, protein kinase B, but not mitogen activated protein kinase activity, was also potentiated in SHIP2 deficient cells stimulated by serum. The upregulation of protein kinase B activity in serum stimulated cells was totally reversed in the presence of the PI 3-kinase inhibitor LY-294002, in both +⁄+ and – ⁄ – cells. Altogether, these data establish a link between SHIP2 and the acute control of PtdIns(3,4,5)P3 levels in intact cells [less ▲]