Dependent GTPase Activity Research Articles

Unusual weak and delayed GTPase activity of FtsZ from human pathogenic bacteria Helicobacter pylori.

Actively treadmilling FtsZ acts as the pivotal scaffold for bacterial cell divisome components providing them with a circumferential ride along the site of future division. FtsZ from slow growing Helicobacter pylori (HpFtsZ), a class I carcinogen which thrives abundantly in the acidic environment is poorly understood. We studied HpFtsZ as a function of pH, cations and time and compared it with well-studied E. coli FtsZ (EcFtsZ). HpFtsZ shows pH dependent GTPase activity which is inhibited under acidic conditions. Mg+2 ions play an indispensable role in its GTPase activity, however, higher Mg+2 levels negatively affect its activity. As compared to EcFtsZ, HpFtsZ exhibits lower and slower nucleotide hydrolyzing activity. Molecular Dynamics Simulation studies of FtsZ reveal that GTP binding induces a rewiring of the hydrogen bond network which results in reduction of the binding cleft volume leading to the spontaneous release of GTP. The GTPase activity is linked to the extent of reduction in the binding cleft volume, which is also supported by the binding free energy analysis. Evidently, HpFtsZ is a pH sensitive GTPase with low efficiency that may reflect on the overall slow growth rate of H. pylori.

Targeting ANXA7/LAMP5-mTOR axis attenuates spinal cord injury by inhibiting neuronal apoptosis via enhancing autophagy in mice

Spinal cord injury (SCI) could lead to severe disabilities in motor and sensory functions, and cause a heavy burden on patient physiology and psychology due to lack of specific repair measures so far. ANXA7 is an annexin with Ca2+ -dependent GTPase activity, which were mainly expressed in neuron in spinal cord and downregulated significantly after SCI in mice. In our study, GTPase activity activation of ANXA7 plays the protective role in neuron after OGD/R through inhibiting neuron apoptosis, which mediated by enhancing autophagy via mTOR/TFEB pathway. We also discovered that ANXA7 has significant interaction with neural-specific lysosomal-associated membrane protein LAMP5, which together with ANXA7 regulates autophagy and apoptosis. Asp411 mutation of ANXA7 obviously impaired the interaction of ANXA7 and LAMP5 compared with the wild type. Furthermore, it was found that activation of ANXA7 could help to stabilize the protein expression of LAMP5. Overexpression of LAMP5 could attenuate the destruction of lysosomal acidic environment, inhibition of autophagy and activation of apoptosis caused by ANXA7 downregulation after OGD/R. We verified that injecting ANXA7 overexpression lentivirus and activation of ANXA7 both have significant repair effects on SCI mice by using CatWalk assay and immunohistochemistry staining. In summary, our findings clarify the new role of ANXA7 and LAMP5 in SCI, provided a new specific target of neuronal repair and discovered new molecular mechanisms of ANXA7 to regulate autophagy and apoptosis. Targeting ANXA7 may be a prospective therapeutic strategy for SCI in future.

Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export

Eukaryotic ribosomes are assembled by a complex pathway that extends from the nucleolus to the cytoplasm and is powered by many energy-consuming enzymes 1-3. Nuclear export is a key, irreversible step in pre-ribosome maturation4-8, but mechanisms underlying the timely acquisition of export competence remain poorly understood. Here we show that a conserved GTPase Nug2/Nog2 (called NGP-1, Gnl2 or nucleostemin 2 in human9) plays a key role in the timing of export competence. Nug2 binds the inter-subunit face of maturing, nucleoplasmic pre-60S particles, and the location clashes with the position of Nmd3, a key pre-60S export adaptor10. Nug2 and Nmd3 are not present on the same pre-60S particles, with Nug2 binding prior to Nmd3. Depletion of Nug2 causes premature Nmd3 binding to the pre-60S particles, whereas mutations in the G-domain of Nug2 block Nmd3 recruitment, resulting in severe 60S export defects. Two pre-60S remodeling factors, the Rea1 ATPase and its co-substrate Rsa4, are present on Nug2-associated particles, and both show synthetic lethal interactions with nug2 mutants. Release of Nug2 from pre-60S particles requires both its K+-dependent GTPase activity and the remodeling ATPase activity of Rea1. We conclude that Nug2 is a regulatory GTPase that monitors pre-60S maturation, with release from its placeholder site linked to recruitment of the nuclear export machinery.

Two Homologous EF-G Proteins from Pseudomonas aeruginosa Exhibit Distinct Functions

Genes encoding two proteins corresponding to elongation factor G (EF-G) were cloned from Pseudomonas aeruginosa. The proteins encoded by these genes are both members of the EFG I subfamily. The gene encoding one of the forms of EF-G is located in the str operon and the resulting protein is referred to as EF-G1A while the gene encoding the other form of EF-G is located in another part of the genome and the resulting protein is referred to as EF-G1B. These proteins were expressed and purified to 98% homogeneity. Sequence analysis indicated the two proteins are 90/84% similar/identical. In other organisms containing multiple forms of EF-G a lower degree of similarity is seen. When assayed in a poly(U)-directed poly-phenylalanine translation system, EF-G1B was 75-fold more active than EF-G1A. EF-G1A pre-incubate with ribosomes in the presence of the ribosome recycling factor (RRF) decreased polymerization of poly-phenylalanine upon addition of EF-G1B in poly(U)-directed translation suggesting a role for EF-G1A in uncoupling of the ribosome into its constituent subunits. Both forms of P. aeruginosa EF-G were active in ribosome dependent GTPase activity. The kinetic parameters (K M) for the interaction of EF-G1A and EF-G1B with GTP were 85 and 70 μM, respectively. However, EF-G1B exhibited a 5-fold greater turnover number (observed k cat) for the hydrolysis of GTP than EF-G1A; 0.2 s-1 vs. 0.04 s-1. These values resulted in specificity constants (k cat obs/K M) for EF-G1A and EF-G1B of 0.5 x 103 s-1 M-1 and 3.0 x 103 s-1 M-1, respectively. The antibiotic fusidic acid (FA) completely inhibited poly(U)-dependent protein synthesis containing P. aeruginosa EF-G1B, but the same protein synthesis system containing EF-G1A was not affected. Likewise, the activity of EF-G1B in ribosome dependent GTPase assays was completely inhibited by FA, while the activity of EF-G1A was not affected.

The N‐terminal regions of eukaryotic acidic phosphoproteins P1 and P2 are crucial for heterodimerization and assembly into the ribosomal GTPase‐associated center

Acidic phosphoproteins P1 and P2 form a heterodimer and play a crucial role in assembly of the GTPase-associated center in eukaryotic ribosomes and in ribosomal interaction with translation factors. We investigated the structural elements within P1 and P2 essential for their dimerization and for ribosomal function. Truncation of the N-terminal 10 amino acids in either P1 or P2 and swapping of the N-terminal 10 amino acid sequences between these two proteins disrupted their dimerization, binding to P0 and P0 binding to rRNA. In contrast, truncation of the C-terminal halves of P1 and P2 as well as swapping of these parts between them gave no significant effects. The protein dimers containing the C-terminal truncation mutants or swapped variants were assembled with P0 onto Escherichia coli 50 S subunits deficient in the homologous protein L10 and L7/L12 and gave reduced ribosomal activity in terms of eukaryotic elongation factor dependent GTPase activity and polyphenylalanine synthesis. The results indicate that the N-terminal 10 amino acid sequences of both P1 and P2 are crucial for P1-P2 heterodimerization and for their functional assembly with P0 into the GTPase-associated center, whereas the C-terminal halves of P1 and P2 are not essential for the assembly.

Applications of plant antiviral proteins.

Ribosome-inactivating proteins (RIPs) from plant extracts have been known for centuries for their numerous and seemingly unrelated properties including antitumor activity, abortifacient activity and anti-arthritic activity (reviewed in 1)-2). The first study documented in Western literature of the antiviral property of a RIP was the description of an extract from pokeweed and its inhibition of viral replication when applied to heterologous plants (3). Several years hence, the enzymatic activity of RIPs was elucidated when Endo and colleagues described the removal of a particular adenine corresponding to A4324, from a highly-conserved stem-loop structure within the 28S rRNA of rat (4)-5). This depurination was found to block the binding of elongation factor (EF)-1 and inhibit EF-2 dependent GTPase activity, thereby causing an overall reduction in cellular translation (6-7). Because of the targeted activity and resulting cytotoxicity of RIPs, they are valued as selective cell-killing agents. Several have been used as the toxic moiety of immunotoxins directed against cancerous and virus-infected cells (8-11). The search for more and different RIPs has led to the realization that they are almostKeywordsAntiviral ActivityTobacco Mosaic VirusPotato VirusAntiviral AgentSalicylic Acid LevelThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Mutation in the beta-tubulin signature motif suppresses microtubule GTPase activity and dynamics, and slows mitosis.

We introduced a threonine-to-glycine point mutation at position 143 in the "tubulin signature motif" 140Gly-Gly-Gly-Thr-Gly-Ser-Gly146 of Saccharomyces cerevisiae beta-tubulin. In an electron diffraction model of the tubulin dimer, this sequence comes close to the phosphates of a guanine nucleotide bound in the beta-tubulin exchangeable E site. Both the GTP-binding affinity and the microtubule (MT)-dependent GTPase activity of tubulin isolated from haploid tub2-T143G mutant cells were reduced by at least 15-fold, compared to tubulin isolated from control wild-type cells. The growing and shortening dynamics of MTs assembled from alphabeta:Thr143Gly-mutated dimers were also strongly suppressed, compared to control MTs. The in vitro properties of the mutated MTs (slower growing and more stable) are consistent with the effects of the tub2-T143G mutation in haploid cells. The average length of MT spindles in large-budded mutant cells was only 3.7 +/- 0.2 microm, approximately half of the size of MT arrays in large-budded wild-type cells (average length = 7.1 +/- 0.4 microm), suggesting that there is a delay in mitosis in the mutant cells. There was also a higher proportion of large-budded cells with unsegregated nuclei in mutant cultures (30% versus 12% for wild-type cells), again suggesting such a delay. The results show that beta:Thr143 of the tubulin signature motif plays an important role in GTP binding and hydrolysis by the beta-tubulin E site and support the idea that tubulins belong to a family of proteins within the GTPase superfamily that are structurally distinct from the classic GTPases, such as EF-Tu and p21(ras). The data also suggest that MT dynamics are critical for MT function in yeast cells and that spindle MT assembly and disassembly could be coordinated with other cell-cycle events by regulating beta-tubulin GTPase activity.

The effect of ribosome-inactivating proteins on the ribosome from the hyperthermophilic archaeon Sulfolobus solfataricus.

Protein synthesis in the thermoacidophilic archaeon Sulfolobus solfataricus (Ss) was inhibited by polynucleotide:adenosine glycosylase activity of some type 1 ribosome-inactivating proteins (RIP). The target of RIP was S. solfataricus rRNA that was depurinated thus producing inactive ribosomes. The amount of RIP required to half-inactivated Ss-ribosomes was comparable to that needed for eubacterial ribosomes, but two orders of magnitude higher than that required for mammalian ribosomes. In addition, RIP treated Ss-ribosomes were also less efficient in stimulating the ribosome dependent GTPase activity of the S. solfataricus elongation factor 2 (SsEF-2) thus suggesting that the inhibition of protein synthesis was probably due to the lack of the interaction between depurinated Ss-ribosomes and SsEF-2. Since SsEF-2 protects Ss-ribosomes against RIP activity it can be hypothesised that also on Ss-ribosomes the sites of interaction for the translocation factor 2 and the RIP are topographically close.

The 24-kDa subunit of the bovine mitochondrial NADH:ubiquinone oxidoreductase is a G protein.

Based on the results obtained from GTP overlay assay, immunoprecipitation, two dimensional electrophoresis and radiolabeled GTP binding, we provide evidence that the bona fide subunit of Complex I, the long known 24 kDa protein is a G protein. Bacterially expressed 24 kDa protein with additional N-terminal methionine and alanine residues or naturally expressed truncated isoform fail to bind GTP suggesting that secondary modification/ processed N-terminal end is necessary for GTP binding. Competitive inhibition of binding of radiolabeled GTP to electroblotted 24 kDa protein with unlabelled nucleotides showed that the protein binds GTP and GDP with high affinity in presence of Mg2+, and has decreased to very low affinity for ITP, CTP, GMP and UTP. A comparative binding of [gamma-35S]-GTP to Complex I and 24 kDa protein (electroblotted) suggests that the GTP binding in the native Complex is solely due to 24 kDa protein. Further, four fold difference in the binding affinities between native Complex I and 24 kDa protein (electroblotted) as seen by Scatchard analysis of the binding data indicates that protein undergoes structural rearrangement in Complex I bound form, that presumably triggers divalent cation dependent GTPase activity in native complex. We were unable to detect the effect of GTP/ GDP on the ubiquinone/ferricyanide reductase activity. Since the subunit is found missing in tissues affected by mitochondrial respiratory chain diseases, we presume that the subunit has regulatory role in the Complex I function in the electron transport chain.

Escherichia coli cell-division gene ftsZ encodes a novel GTP-binding protein.

Escherichia coli divides by forming a septum across the middle of the cell. The biochemical mechanism underlying this process is unknown. Genetic evidence suggests that of all the fts (filamentation temperature sensitive) genes involved in E. coli cell division, ftsZ plays a central role at the earliest known step of septation. Here we show that FtsZ protein binds GTP in vitro using unusual sequence elements. In contrast, such binding to the product of the conditional-lethal ftsZ84 allele is impaired. Purified FtsZ displays a Mg(2+)-dependent GTPase activity which is markedly reduced in the FtsZ84 protein. FtsZ copurifies with near stoichiometric amounts of noncovalently-bound GDP, implying the presence of a GTPase cycle in vivo, similar to that known for signal-transducing GTP-binding proteins. We also show that a small fraction of FtsZ exists as a distinct membrane-associated species that binds GTP. The membrane association of FtsZ and the known ability of GTPases to act as molecular switches implicate FtsZ in a GTP-activated signal transduction pathway that may regulate the start of septation in E. coli.

The mode of action of Shiga toxin on peptide elongation of eukaryotic protein synthesis.

The effect of Shiga toxin, from Shigella dysenteriae 1, on the component reactions of peptide elongation were investigated. Enzymic binding of [3H]phenylalanine-tRNA to reticulocyte ribosomes was inhibited by 50% at 7 nM toxin. Elongation factor 1 (eEF-1)-dependent GTPase activity was also inhibited. Both reactions were not restored by addition of excess eEF-1 protein. In contrast, toxin concentrations of 200 nM were required to inhibit by 50% the elongation factor 2 (eEF-2)-dependent translocation of aminoacyl-tRNA on ribosomes. Addition of excess eEF-2 restored translocation activity. The eEF-2-dependent GTPase activity was unaffected at toxin concentrations below 100 nM, and Shiga-toxin concentrations of up to 1,000 nM did not affect either GTP.eEF-2.ribosome complex-formation or peptidyltransferase activity. Thus Shiga toxin closely resembles alpha-sarcin in action, both being primary inhibitors of eEF-1-dependent reactions. In contrast, the 60 S ribosome inactivators ricin and phytolaccin are primary inhibitors of eEF-2-dependent reactions of peptide elongation.

The ligand- and microtubule assembly-induced GTPase activity of purified calf brain tubulin

Calf brain tubulin purified by means of ammonium sulfate fractionation, ion-exchange chromatography, and MgCl 2 precipitation contains a low level of Mg 2+ -dependent GTPase activity, the protein preparation being essentially homogeneous according to conventional procedures. Tubulin was freed from this possibly contaminant enzyme activity by Sephacryl S300 gel chromatography. Soluble tubulin itself showed a ligand-induced Mg 2+-dependent GTPase activity in the presence of colchicine, but not of tropolone methyl ether, podophyllotoxin, or vinblastine. Tubulin also hydrolyzed GTP when assembling into microtubules. This reaction proceeded in a nonlinear fashion and was suppressed together with microtubule assembly by lowering the protein concentration under the critical concentration, adequately modifying assembly buffer conditions, or using Ca 2+, tropolone methyl ether, podophyllotoxin, or vinblastine. The number of molecules of GTP hydrolyzed per molecule of tubulin polymerized was estimated to vary between 0.9 and 2.1, depending on whether morpholineethanesulfonate or phosphate assembly buffers were employed.

The number of copies of ribosome-bound proteins L7 and L12 required for protein synthesis activity.

Poly(U)-dependent poly(Phe) synthesis and elongation factor G (EF-G)-dependent GTPase activity were used to study the partial reconstitution of L7/L12-deficient ribosomes with proteins L7/L12 and fluorescent conjugates. Seventy-five per cent of these activities are restored when unmodified L7/L12 dimer is added to L7/L12-deficient cores at a ratio of 1:1. Various covalent fluorescent conjugates of L7/L12 bind to these cores about as well as unmodified protein. A fluorescein-5-isothiocyanate derivative of L12 shows almost no functional activity when bound. However, mixed reconstitutes of this conjugate and unmodified L12 have 75% functional activity when half the protein is unmodified. These results can be explained by a model in which there are two independent binding sites on the ribosome for two dimers of L7/L12. The binding of dimers to ribosomes is totally random and complete; the particle is 100% active so long as it has one active dimer bound to either one of the two sites. However, more complex models cannot be ruled out. An 5-(iodoacetamidoethyl)-aminonaphthalene-1-sulfonic acid (IAEDANS) derivative of L7 is labeled semispecifically at the COOH terminus. This conjugate shows partial functional activity. When assay results are analyzed using the above model, it appears that the specific COOH-terminal modification has no effect on activity. However, all but a small fraction of the nonspecific IAEDANS modifications lead to inactivation.

Molecular mechanisms of photoreception. IV. Ca 2+-inhibited GTPase of rod outer segments of the frog retina

Ca 2+-dependent GTPase activity is found to be present in the rod outer segments of frog retina. GTPase localization in rod outer segments is shown by fractionating the rod outer segment preparation in the sucrose density gradient. The enzyme is readily washed out of cells with isotonic NaCl solution. The K m is 0.6 mM for GTP. The activity is inhibited by 78 ± 12% with the increase in Ca 2+ concentration from 10 −9 to 10 −7 M. GTP hydrolysis is inhibited by the same concentrations of Ca 2+ which block the sodium conductivity of the rod outer segment cytoplasmic membrane (Hagins, W.A. and Yoshikami, S. (1974) Exp. Eye Res. 18, 299–305).

The coupling with polypeptide synthesis of the GTPase activity dependent on elongation factor G.

The coupling with polypeptide synthesis of the ribosome-elongation factor G (EF-G)-dependent GTPase activity was studied in a highly purified system with well characterized NH4Cl-washed ribosomes which were from 55 to 67% active in poly(U)-directed polyphenylalanine synthesis. The lowest stoichiometries of total GTP hydrolysis to polyphenylalanine incorporation (2.4 to 2.8) were observed at concentrations of MgCl2 (4 to 6.5 mM) slightly lower than the Mg2+ optimum for polyphenylalanine synthesis (7 to 8 mM), in a system containing 80 mM NH4Cl or KCl. For minimal stoichiometry, the concentration of EF-G should be rate-limiting, whereas that of EF-T (EF-Tu.EF-Ts) and aminoacyl-tRNA should be in excess, since the coupling of the EF-G GTPase activity depends on ribosomes in pretranslocative state. Under this condition, the apparent Km values for GTP of GTPase activity and polyphenylalanine synthesis are identical, and they are about an order of magnitude lower than the Km of the ribosome-EF-G-dependent GTPase activity uncoupled from polypeptide synthesis. The stoichiometry was calculated without the usual correction fro GTP hydrolysis obtained in the same system lacking elongation factor T or aminoacyl-tRNA. Such a correction causes overestimation of the uncoupled EF-G GTPase activity still present in the complete system, leading to artificially low stoichiometric values.

Role of 5S RNA in assembly and function of the 50S subunit from Escherichia coli.

Total reconstitution experiments performed under various conditions revealed that 5S RNA plays an important role during the last assembly step in vitro leading to an active 50S particle. For the preceding steps this RNA species is dispensable. However, 50S RNA can be integrated efficiently during any of the assembly steps in vitro. The 47S particle, reconstituted in two steps and lacking 5S RNA, shows low but significant activity in many functional tests. High activity could be obtained by incubating this particle with 5S RNA alone, demonstrating the importance of the 5S RNA in generating an active ribosomal conformation. In particular, the activity of the peptidyltransferase (peptidyl-tRNA:aminoacyl-tRNA N-peptidyltransferase; EC 2.3.2.12) center is drastically influenced by 5S RNA. No significant factor-dependent tRNA binding to the A-site was observed with the 47S particle, in contrast to the corresponding P-site binding. The elongation factor G dependent GTPase activity was not affected by the lack of 5S RNA.

Involvement of 50S ribosomal proteins L6 and L10 in the ribosome dependent GTPase activity of elongation factor G

CsCI-prepared 50S cores in the presence of groups of individual split proteins were tested for their capacity to support EF-G dependent GTP hydrolysis. The activity of cores prepared at 40 mM Mg 2+ could be restored by adding L7 L12 and L10 together, each in an amount of two copies per 50S particle, which abolishes the difference in activity between L7 and L12. In the range of 20-2 mM Mg 2+, 50S cores lose the protein L6, which is also required for GTP hydrolysis. L10 cannot replace L6, or vice versa .

Recycling of initiation factors IF-1, IF-2 and IF-3.

Initiation of protein synthesis in Escherichia coli is a catalytic process, provided that conditions for hydrolysis of GTP are present. This means that the initiation factors IF‐1, IF‐2 and IF‐3 are released at a certain stage of initiation complex formation, whereafter they recycle and are reutilized in another round of initiation.Experiments presented in this paper provide evidence for the mechanism of recycling, in which the hydrolysis of GTP and IF‐1 both play a predominant role. We demonstrate that binding of fMet‐tRNA, which is dependent on IF‐2, is a stoichiometric process in a system devoid of IF‐1. Addition of IF‐1 converts it into a catalytic process, however, only if GTP can be hydrolysed. No such conversion takes place with 5′‐guanylylmethylenediphosphonate. The same observation is valid for the uncoupled IF‐2 dependent GTPase activity.In the process of initiation IF‐1 acts as a recycling promoting factor, which displays analogous properties to elongation factor EF‐Ts. We postulate that a ribosomal‐bound IF‐2 · GDP complex is converted into an IF‐2 · GTP complex, which is released and is capable of starting a new cycle of initiation.Furthermore, kinetic evidence is presented that IF‐3 recycles even at the level of 30‐S initiation complex formation, irrespective of whether conditions for hydrolysis of GTP are provided.

The mechanism of cycloheximide inhibition of protein synthesis in rabbit reticulocytes

Cycloheximide blocks the movement of peptidyl-tRNA from acceptor (aminoacyl) site to the donor (peptidyl) site on reticulocyte ribosomes. This translocation reaction is dependent upon the transfer enzyme, TF-II, and GTP hydrolysis. Cycloheximide has no effect on the ribosome dependent GTPase activity of TF-II or on the peptidyl transferase reaction by which peptides on tRNA in the donor ribosomal site are transferred to an amino acid on tRNA in the acceptor site.