Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases

Expression of foreign pathways often results in suboptimal performance due to unintended factors such as introduction of toxic metabolites, cofactor imbalances or poor expression of pathway components. In this study we report a 120% improvement in the production of the isoprenoid-derived sesquiterpene, amorphadiene, produced by an engineered strain of Escherichia coli developed to express the native seven-gene mevalonate pathway from Saccharomyces cerevisiae (Martin et al. 2003). This substantial improvement was made by varying only a single component of the pathway (HMG-CoA reductase) and subsequent host optimization to improve cofactor availability. We characterized and tested five variant HMG-CoA reductases obtained from publicly available genome databases with differing kinetic properties and cofactor requirements. The results of our in vitro and in vivo analyses of these enzymes implicate substrate inhibition of mevalonate kinase as an important factor in optimization of the engineered mevalonate pathway. Consequently, the NADH-dependent HMG-CoA reductase from Delftia acidovorans, which appeared to have the optimal kinetic parameters to balance HMG-CoA levels below the cellular toxicity threshold of E. coli and those of mevalonate below inhibitory concentrations for mevalonate kinase, was identified as the best producer for amorphadiene (54% improvement over the native pathway enzyme, resulting in 2.5 mM or 520 mg/L of amorphadiene after 48 h). We further enhanced performance of the strain bearing the D. acidovorans HMG-CoA reductase by increasing the intracellular levels of its preferred cofactor (NADH) using a NAD⁺-dependent formate dehydrogenase from Candida boidinii, along with formate supplementation. This resulted in an overall improvement of the system by 120% resulting in 3.5 mM or 700 mg/L amorphadiene after 48 h of fermentation. This comprehensive study incorporated analysis of several key parameters for metabolic design such as in vitro and in vivo kinetic performance of variant enzymes, intracellular levels of protein expression, in-pathway substrate inhibition and cofactor management to enable the observed improvements. These metrics may be applied to a broad range of heterologous pathways for improving the production of biologically derived compounds.     

TOPK and PTEN participate in CHFR mediated mitotic checkpoint

Mitotic progression is regulated by co-ordinated action of several proteins and is crucial for the maintenance of genomic stability. CHFR (Check point protein with FHA and RING domains) is an E3 ubiquitin ligase and a checkpoint protein that regulates entry into mitosis. But the molecular players involved in CHFR mediated mitotic checkpoint are not completely understood. In this study, we identified TOPK/PBK, a serine/threonine kinase and PTEN, a lipid phosphatase to play an important role in CHFR mediated mitotic transitions. We demonstrated that CHFR ubiquitinates and regulates TOPK levels, which is essential for its checkpoint function. Moreover, TOPK phosphorylates and inactivates PTEN, which in turn activates Akt that leads to proper G2/M progression. Collectively, our results reveal TOPK and PTEN as new players in CHFR mediated mitotic checkpoint.     

Cyanobacteria as a source of biofertilizers for sustainable agriculture

Continuous increase in global human population and depletion of natural resources of energy posing threat to environment needs, sustainable supply of food and energy. The most ecofriendly approach ‘green technology’ has been exploited for biofertilizer preparation. Cyanobacteria are the most successful and sustained prokaryotic organism during the course of evolution. They are considered as one of the primitive life forms found on our planet. Cyanobacteria are emerging candidates for efficiently conversion of radiant energy into chemical energy. This biological system produces oxygen as a by-product. Cyanobacterial biomass can also be used for the large scale production of food, energy, biofertilizers, secondary metabolites, cosmetics and medicines. Therefore, cyanobacteria are used in ecofriendly sustainable agricultural practice for production of biomass of very high value and decreasing the level of CO_2. This review article describes the methods of mass production of cyanobacterial biofertilizers and their applications in agriculture and industrial level.     

3D-QSAR-aided design of potent c-Met inhibitors using molecular dynamics simulation and binding free energy calculation

Abstract

Mesenchymal-epithelial transition factor (c-Met) is a member of receptor tyrosine kinase. It involves in various cellular signaling pathways which includes proliferation, motility, migration, and invasion. Over-expression of c-Met has been reported in various cancers. Hence, it is an ideal therapeutic target for cancer. The main objective of the study is to identify crucial residues involved in the inhibition of c-Met kinase and to design a series of potent imidazo [4,5-b] pyrazine derivatives as c-Met inhibitors. Docking was used to identify important active site residues involved in the inhibition of c-Met kinase which was further validated by 100 ns of molecular dynamics simulation and free energy calculation using molecular mechanics generalized born surface area. Furthermore, binding energy decomposition identified that residues Tyr1230, Met1211, Asp1222, Tyr1159, Met1160, Val1092, Ala1108, and Leu1157 contributed favorably to the binding stability of compound 32. Receptor-guided Comparative Molecular Field Analysis (CoMFA) (q² = 0.751, NOC = 6, r² = 0.933) and Comparative Molecular Similarity Indices Analysis (COMSIA) (q² = 0.744, NOC = 6, r² = 0.950) models were generated based on the docked conformation of the most active compound 32. The robustness of these models was tested using various validation techniques and found to be predictive. The results of CoMFA and CoMSIA contour maps exposed the regions favorable to enhance the activity. Based on this information, 27 novel c-Met inhibitors were designed. These designed compounds exhibited potent activity than the most active compound of the existing dataset.

Communicated by Ramaswamy H. Sarma     

Proteomic Analysis of Glycated Proteins from Streptozotocin-Induced Diabetic Rat Kidney

Glycation of proteins leading to formation of advanced glycation end products (AGEs) has been considered as one of the important causes of diabetic nephropathy. Therefore, in this study, glycated proteins were detected by anti-AGE antibodies from kidney of streptozotocin-induced diabetic rat showing nephropathic symptoms, by using two dimensional electrophoresis and western blot analysis. These glycated proteins were identified and characterized by using combination of peptide mass finger printing and tandem mass spectrometric approaches. Glycated proteins identified included proteins from metabolic pathways, oxidative stress, cell signaling, and transport. Several of the proteins modified by glycation were involved in glucose metabolism. The extent of glycation was higher in diabetes compared to control, in the glycated proteins that were common to both control and diabetic kidney. Two dimensional electrophoresis proteins profiling of glycated proteins suggest that four of the glycated proteins were significantly up regulated in diabetes.     

Chronic administration of pioglitazone attenuates intracerebroventricular streptozotocin induced-memory impairment in rats

Memory impairment induced by intracerebroventricular (ICV) injection of streptozotocin (STZ) in rats is associated with impaired brain glucose and energy metabolism, oxidative stress and impaired cholinergic neurotransmission. Treatment with antioxidants and cholinergic agonists has been reported to produce beneficial effect in this model. However, no reports are available on drugs that improve glucose utilization and metabolism. In the present study, we evaluated the effects of pioglitazone on cognitive performance, oxidative stress and glucose utilization in ICV STZ injected rats (3 mg/kg, on day 1 and 3). Pioglitazone (10 and 30 mg/kg) was administered per oral (p.o.) for 14 days, starting 5 days prior to STZ injection. Cognitive performance was assessed using step-through passive avoidance and Morris water maze task. Malondialdehyde (MDA) and glutathione levels in brain were estimated as parameters of oxidative stress. Glucose utilization by brain was assessed as the amount of glucose consumed from the media by the brain. ICV STZ injected rats showed a severe deficit in learning and memory associated with increased MDA levels (+67.5%), decreased glutathione levels (-29.2%) and impaired cerebral glucose utilization (-44.4%). In contrast pioglitazone treatment improved cognitive performance, lowered oxidative stress and improved cerebral glucose utilization in ICV STZ rats. The present study demonstrates the beneficial effects of pioglitazone in the ICV STZ induced cognitive deficits, which can be exploited for the dementia associated with diabetes and age-related neurodegenerative disorder, where oxidative stress and impaired glucose and energy metabolism are involved.     

Can embryonic skipper frogs (<Emphasis Type="Italic">Euphlyctis cyanophlyctis</Emphasis>) learn to recognise kairomones in the absence of a nervous system?

In this study, we used larval Euphlyctis cyanophlyctis to determine the predator recognition mechanism. We conducted a series of experiments to determine if larval E. cyanophlyctis have the innate ability to recognise predatory odour (kairomones) as a threat or if they learn to do so during ontogeny. In the case of learning, we wanted to determine the developmental window during which learning is accomplished. Further, we tested the antipredator response of predator-naïve as well as predator-experienced tadpoles to chemical cues of different origins in order to assess if they exhibit differential responses. Our results clearly indicate that predator-naïve tadpoles of E. cyanophlyctis do not reduce their activity against predatory cues of dragonfly nymphs, suggesting that they lack the innate ability to recognise kairomones. However, they could learn to do so when trained to perceive kairomones simultaneously along with alarm cues. Surprisingly, larval E. cyanophlyctis could learn to recognise kairomones through association during embryonic stages even before the development of a nervous system. Although larval E. cyanophlyctis lack the innate ability to recognise kairomones, they were able to recognise conspecific alarm cues on the first encounter, indicating that they have the innate ability to recognise alarm cues as a potential threat.     

Measurements of the fragmentation rate constant imply that the tensile strength of fungal hyphae can change significantly during growth

Because little is known about filamentous fungal tensile strength, it is assumed to be constant in many models. A method involving off-line fragmentation and image analysis is used now to measure relative tensile strength of Aspergillus oryzae hyphae. During the course of shake-flask and fed-batch cultures, hyphal tensile strength increases during growth then decreases. Hyphal tensile strength can change up to 3-fold over time.