Differential Behavior of Missense Mutations in the Intersubunit Contact Domain of the Human Pyruvate Kinase M2 Isozyme

In this study, we attempted to understand the mechanism of regulation of the activity and allosteric behavior of the pyruvate kinase M₂ enzyme and two of its missense mutations, H391Y and K422R, found in cells from Bloom syndrome patients, prone to develop cancer. Results show that despite the presence of mutations in the intersubunit contact domain, the K422R and H391Y mutant proteins maintained their homotetrameric structure, similar to the wild-type protein, but showed a loss of activity of 75 and 20%, respectively. Interestingly, H391Y showed a 6-fold increase in affinity for its substrate phosphoenolpyruvate and behaved like a non-allosteric protein with compromised cooperative binding. However, the affinity for phosphoenolpyruvate was lost significantly in K422R. Unlike K422R, H391Y showed enhanced thermal stability, stability over a range of pH values, a lesser effect of the allosteric inhibitor Phe, and resistance toward structural alteration upon binding of the activator (fructose 1,6-bisphosphate) and inhibitor (Phe). Both mutants showed a slight shift in the pH optimum from 7.4 to 7.0. Although this study signifies the importance of conserved amino acid residues in long-range communications between the subunits of multimeric proteins, the altered behavior of mutants is suggestive of their probable role in tumor-promoting growth and metabolism in Bloom syndrome patients with defective pyruvate kinase M₂.Pyruvate kinase (PK³; EC 2.7.1.40), a pacemaker of the glycolytic pathway, catalyzes irreversibly the transphosphorylation from P-enolpyruvate to ADP, generating pyruvate and ATP (1, 2). There are four different isozymes (L, R, M₁, and M₂) in mammalian tissues, which differ in their regulatory properties. These isozymes are allosteric in nature with the exception of the M₁ form, present in skeletal muscle and brain (3–7). PKM₂ is a ubiquitous prototype enzyme present in all tissues during the embryonic stage and is gradually replaced by other isozymic forms in specific tissues during development. The M₂, L, and R isozymes show homotropic cooperative activation with P-enolpyruvate and heterotropic cooperative activation with Fru-1,6-P₂ (8–10). The M₁ isozyme is regulated by neither P-enolpyruvate nor Fru-1,6-P₂ because of its intrinsic active conformation in the R-state (5, 6). Under unfavorable conditions such as hypoxia and lack of glucose supply, the anaerobic tissues and tumor cells rely heavily on PKM₂ for ATP production (7). Therefore, stringent control of PK activity is of great importance not only for cell metabolism but also for tumorigenic proliferation.The M₁ and M₂ isozymes are produced from a single gene locus by mutually exclusive alternative splicing (11–14). In the human M₁ and M₂ isozymes, the exon that is exchanged because of alternative splicing encodes 56 amino acids, in which a total of 22 amino acids differ within a length of 45 residues. The residues located in this region form the major intersubunit contact domain (8). The distinguishable kinetic properties of the M₁ and M₂ isozymes are attributed to these amino acid substitutions. It has been shown by x-ray crystallographic analyses and computer modeling that the corresponding regions of their polypeptides participate directly in the intersubunit contact, which is responsible for the intersubunit communication required for allosteric cooperativity (8, 15).PK has been largely conserved throughout evolution. The enzyme is usually a homotetramer composed of four identical subunits, and each subunit consists of four domains: the A-, B-, and C-domains and the N-terminal domain. The structure of human PKM₂ was recently determined in complex with inhibitors (16). In mammalian cells, PK activity is regulated by two different mechanisms: one at the level of expression and the other through allosteric regulation. The catalytic site usually composes a small part of the enzyme, but allosteric control is transmitted over a long range, thus increasing the number of possible residues involved in regulation. The allosteric transition in PK involves mutual rotations of the A- and C-domains within each subunit and the subunit within the tetramer (14). The residues at the subunit interfaces have the critical function of relaying the allosteric signal from and to the catalytic and regulatory sites. This region also transmits the allosteric signal between P-enolpyruvate- and Fru-1,6-P₂-binding sites. Despite the availability of structural details of several PK isozymes, it is difficult to identify the structural elements that play an important role in PK regulation and propagation of the allosteric signals. Although the role of some of the PK residues (positions 340, 389, 398, 401, 402, 408, 423, and 427) has been studied in allosteric regulation (10, 17–19) by in vitro site-directed mutagenesis, the absence of these mutations in any naturally occurring condition presents limitations in attributing a biological role to the introduced changes.The natural mutations H391Y and K422R (reported previously as K421R) were reported by us for the first time in the PKM₂ gene in a Bloom syndrome cell line and in the lymphocytes of an Indian Bloom syndrome patient, respectively (20). The two missense mutations, located in the region of the intersubunit contact domain (Fig. 1, A and B), presented with the biochemical phenotype of down-regulated enzyme activity to different extents (20) and were expected to influence the allosteric nature of the enzyme. The regulatory behavior of allosteric PK has been described by a two-state model that proposes an active (R) and an inactive (T) form of the macromolecule with differential affinity for ligands (15). Upon binding of the substrate or its analogs, the enzyme undergoes a transition from a low activity/low affinity conformation (T state) to a high activity/high affinity conformation (R state). The binding of phenylalanine produces a global structural change and exhibits reduced affinity for substrate P-enolpyruvate in the T state (21–23). Previous studies have demonstrated that each individual domain acts as a rigid body and that, upon transition from the T to the R state, the domain of the functional tetramer modifies its relative orientation by 29°. These movements bring conformational change to the active site, which, upon transition to the T state, undergoes a distortion of the P-enolpyruvate-binding site (24).Open in a separate windowFIGURE 1.A, ribbon diagram of the overall structure of PK showing the positions of the two mutations, H391Y and K422R, along with the active site and Fru-1,6-P₂-binding site. B, intersubunit contact domain of PK. The major amino acid residues and side chains at the tetramer interface region are shown.Because the mutations observed by us previously (20) are located at highly conserved positions not only in different isozymic forms but also across the species (supplemental Fig. S1) and are observed in the genetic background of a syndrome prone to cancer in early age, a study related to the structure-function correlations of these mutations is likely to provide insight into their possible biological importance, especially in the context of recent research highlighting the importance of PKM₂ in tumor promotion and growth. In this study, we investigated the role of the two natural missense mutations, after site-directed mutagenesis in the PKM₂ gene, in the regulation of allosteric properties as well as their effects on the secondary and tertiary structures in comparison with wild-type PKM₂ (PK-WT). An attempt has also been made to understand the effects of these mutations at the interface of the subunits on the signal transmission pathway within the protein.     

In silico prediction of immunogenic T cell epitopes for HLA-DQ8

Background HLA-DQ alleles are involved in the pathogenesis of hypersensitivity reactions, with HLA-DQ8 associated with several human autoimmune disorders. Limited success has been achieved using sequence-based computational techniques for predicting HLA-DQ8-restricted T cell epitopes while accuracy and efficiency of recently developed structure-based models need to be improved. Results We describe a combined structure-based prediction approach for DQ8-restricted T cell epitope prediction using a recently developed fast and accurate docking protocol, pDOCK, and molecular surface electrostatic potential (MSEP)-based clustering of pMHC binding interfaces. The prediction model was rigorously trained, tested and validated using experimentally verified DQ8 binding and non-binding peptides. High prediction accuracy (average area under the ROC curve, average AROC>0.94) is validated against experimental data. Our model also predicts all binding registers correctly and known T cell activators with 77% accuracy. We also studied the patterns of DQ8-binding peptides and reassure the existence of epitopes not conforming to binding motifs. Conclusions We have developed a model that can be successfully applied as a generic protocol for easy in silico identification of potential immunogenic T cell epitopes. The current model is therefore applicable for screening vaccine candidates irrespective of sequence motifs. We have also illustrated efficient discrimination of different categories of binders from non-binders as well as different categories of pMHC agonists from non-agonists, while accurately predicting the binding registers of DQ8-restricted peptides. This combined approach provides a set of sensitive and specific computational tools to facilitate high-throughput screening of peptides for immunotherapeutic applications such as controlling allergic and autoimmune responses.     

Relationship between cultivar difference in the sensitivity of net photosynthesis to ozone and reactive oxygen species scavenging system in Japanese winter wheat (Triticum aestivum)

To clarify the relationship between cultivar difference in the sensitivity of net photosynthesis to ozone (O(3) ) and the reactive oxygen species (ROS) scavenging system in wheat (Triticum aestivum), we investigated the effects of chronic exposure to ambient levels of O(3) on gas exchange rates, activity and concentration of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), activity of ROS scavenging enzymes and concentration of antioxidants of the flag leaf in two Japanese winter wheat cultivars (Norin 61 and Shirogane-komugi). Although the net photosynthetic rate of the flag leaf in Norin 61 was not significantly reduced by exposure to O(3) , that in Shirogane-komugi was significantly reduced by the exposure to O(3) during the anthesis and early grain-filling stages. In the two cultivars, stomatal diffusive conductance to H(2) O of the flag leaf was not significantly affected by the exposure to O(3) . The exposure to O(3) induced significant reductions in the activity and concentration of Rubisco, activities of catalase (CAT) and monodehydroascorbate reductase (MDAR) and concentrations of reduced form of ascorbate and total glutathione of the flag leaf in Shirogane-komugi. It was concluded that the sensitivity of net photosynthesis of flag leaf to O(3) is higher in Shirogane-komugi than in Norin 61, and the difference in the sensitivity to O(3) between the two cultivars is mainly due to that in the effects of O(3) on the detoxification ability of ROS, mainly determined by the activity of ROS scavenging enzymes, such as CAT and MDAR.     

Attenuation of Aβ-induced neurotoxicity by thymoquinone via inhibition of mitochondrial dysfunction and oxidative stress

Beta-amyloid (Aβ) peptides are considered to play a major role in the pathogenesis of Alzheimer's disease (AD) and compounds that can prevent pathways of Aβ-induced neurotoxicity may be potential therapeutic agents for treatment of AD. This study examined the hypothesis that thymoquinone (TQ) would reduce oxidative stress and mitochondrial dysfunction in differentiated pheochromocytoma (PC 12) cells exposed to Aβ fragment 25-35 (Aβ(25-35)). To test this hypothesis, Aβ was used to induce an in vitro model of AD in differentiated PC 12 cell line of rat. After 24?h of exposure with Aβ(25-35), a significant reduction in cell viability and mitochondrial membrane potential (MMP) was observed. In addition, a significant elevation in the TBARS content and nitric oxide (NO) and activity of acetylcholine esterase (AChE) was observed which was restored significantly by TQ pretreatment. Furthermore, TQ also ameliorated glutathione and its dependent enzymes (glutathione peroxidase, glutathione reductase) which were depleted by Aβ(25-35) in PC 12 cells. These results were supported by the immunocytochemical finding that has shown protection of cells by TQ from noxious effects of Aβ(25-35). These results indicate that TQ holds potential for neuroprotection and may be a promising approach for the treatment of neurodegenerative disorders including AD.     

Endosperm Tolerance of Paternal Aneuploidy Allows Radiation Hybrid Mapping of the Wheat D-Genome and a Measure of γ Ray-Induced Chromosome Breaks

Physical mapping and genome sequencing are underway for the ≈17 Gb wheat genome. Physical mapping methods independent of meiotic recombination, such as radiation hybrid (RH) mapping, will aid precise anchoring of BAC contigs in the large regions of suppressed recombination in Triticeae genomes. Reports of endosperm development following pollination with irradiated pollen at dosages that cause embryo abortion prompted us to investigate endosperm as a potential source of RH mapping germplasm. Here, we report a novel approach to construct RH based physical maps of all seven D-genome chromosomes of the hexaploid wheat ‘Chinese Spring’, simultaneously. An 81-member subset of endosperm samples derived from 20-Gy irradiated pollen was genotyped for deletions, and 737 markers were mapped on seven D-genome chromosomes. Analysis of well-defined regions of six chromosomes suggested a map resolution of ∼830 kb could be achieved; this estimate was validated with assays of markers from a sequenced contig. We estimate that the panel contains ∼6,000 deletion bins for D-genome chromosomes and will require ∼18,000 markers for high resolution mapping. Map-based deletion estimates revealed a majority of 1–20 Mb interstitial deletions suggesting mutagenic repair of double-strand breaks in pollen provides a useful resource for RH mapping and map based cloning studies.     

Construction of a synthetic YdbK-dependent pyruvate:H2 pathway in Escherichia coli BL21(DE3)

A synthetic pyruvate:H₂ pathway was constructed in Escherichia coli BL21(DE3) by co-expression of six proteins: E. coli YdbK, Clostridium pasteurianum [4Fe–4S]-ferredoxin, and Clostridium acetobutylicum HydF, HydE, HydG, and HydA. The effect of cofactor addition and host strain on H₂ yield and fermentation product accumulation was studied, together with in vitro reconstitution of the entire pathway. The deletion of iscR and/or the addition of thiamine pyrophosphate to the medium enhanced the total and specific activity of recombinant YdbK and increased the yield of H₂ per glucose. It was concluded that the introduced pathway outcompeted other pyruvate-consuming reactions, and that the ability to compete for pyruvate at least in part was determined by total YdbK activity. The results demonstrate the successful construction of a high-yielding H₂ pathway in a microorganism that effectively does not synthesize any H₂. The additional co-expression of Bacillus subtilis AmyE enabled starch-dependent H₂ synthesis in minimal media.     

Isolation and characterization of a Pseudomonas strain that degrades 4-acetamidophenol and 4-aminophenol

Though many microorganisms that are capable of using phenol as sole sourceof carbon have been isolated and characterized, only a few organisms degradingsubstituted phenols have been described to date. In this study, one strain ofmicroorganism that is capable of using phenol (3000 ppm), 4-aminophenol(4000 ppm) and 4-acetamidophenol (4000 ppm) as sole source of carbon andenergy was isolated and characterized. This strain was obtained by enrichmentculture from a site contaminated with compounds like 4-acetamidophenol,4-aminophenol and phenol in Pakistan at Bhai Pheru. The contaminated siteis able to support large bacterial community as indicated by the viable cellcounts (2 × 10⁴–5 × 10⁸) per gram of soil. Detailed taxonomic studies identified the organisms as Pseudomonas species designated as strain STI. The isolate also showed growth on other organic compounds like aniline, benzene, benzyl alcohol, benzyl bromide, toluene, -cresol, trichloroethylene and o-xylene. Optimum growth temperature and pH were found to be 30 °C and 7, respectively, while growth at 4, 25 and 35 °C and at pH 8 and 9 was also observed. Non growing suspended cells of strain ST1 degraded 68, 96 and 76.8% of 4-aminophenol (1000 ppm), phenol (500 ppm) and 4-acetamidophenol (1000 ppm), respectively, in 72 hrs. The isolation and characterization of Pseudomonas speciesstrain ST1, may contribute to efforts on phenolic bioremediation, particularly in anenvironment with very high levels of 4-acetamidophenol and 4-aminophenol.