A possible molecular basis for photoprotection in the minor antenna proteins of plants

The bioenergetics of light-harvesting by photosynthetic antenna proteins in higher plants is well understood. However, investigation into the regulatory non-photochemical quenching (NPQ) mechanism, which dissipates excess energy in high light, has led to several conflicting models. It is generally accepted that the major photosystem II antenna protein, LHCII, is the site of NPQ, although the minor antenna complexes (CP24/26/29) are also proposed as alternative/additional NPQ sites. LHCII crystals were shown to exhibit the short excitation lifetime and several spectral signatures of the quenched state. Subsequent structure-based models showed that this quenching could be explained by slow energy trapping by the carotenoids, in line with one of the proposed models. Using Fluorescence Lifetime Imaging Microscopy (FLIM) we show that the crystal structure of CP29 corresponds to a strongly quenched conformation. Using a structure-based theoretical model we show that this quenching may be explained by the same slow, carotenoid-mediated quenching mechanism present in LHCII crystals.     

Cytotoxicity of insulin within its self-assembly and amyloidogenic pathways

Solvational perturbations were employed to selectively tune the aggregational preferences of insulin at 60 degrees C in vitro in purely aqueous acidic solution and in the presence of the model co-solvent ethanol (EtOH) (at 40%(w/w)). Dynamic light scattering (DLS), thioflavin T (ThT)-fluorescence, Fourier transform infrared (FTIR) and atomic force microscopy (AFM) techniques were employed to characterize these pathways biophysically with respect to the pre-aggregational assembly of the protein, the aggregation kinetics, and finally the aggregate secondary structure and morphology. Using cell viability assays, the results were subsequently correlated with the cytotoxicity of the insulin species that form in the two distinct aggregation pathways. In the cosolvent-free solution, predominantly dimeric insulin self-assembles via the well-known amyloidogenic pathway, yielding exclusively fibrillar aggregates, whereas in the solution containing EtOH, the aggregation of predominantly monomeric insulin proceeds via a pathway that leads to exclusively non-fibrillar, amorphous aggregates. Initially present native insulin assemblies as well as partially unfolded monomeric species and low molecular mass oligomeric aggregates could be ruled out as direct and major cytotoxic species. Apart from the slower overall aggregation kinetics under amorphous aggregate promoting conditions, which is due to the chaotropic nature of high EtOH concentrations, however, both pathways were unexpectedly found to evoke insulin aggregates that were cytotoxic to cultured rat insulinoma cells. The observed kinetics of the decrease of cell viabilities correlated well with the results of the DLS, ThT, FTIR and AFM studies, revealing that the formation of cytotoxic species correlated well with the formation of large-sized, beta-sheet-rich assemblies (>500 nm) of both fibrillar and amorphous nature. These results suggest that large-sized, beta-sheet-rich insulin assemblies of both fibrillar and amorphous nature are toxic to pancreatic beta-cells. In the light of the ongoing discussion about putative cytotoxic effects of prefibrillar and fibrillar amyloid aggregates, our results support the hypothesis that, in the case of insulin, factors other than the specific secondary or quarternary structural features of the various different aggregates may define their cytotoxic properties. Two such factors might be the aggregate size and the aggregate propensity to expose hydrophobic surfaces to a polar environment.     

The effects of various membrane physical-chemical properties on the aggregation kinetics of insulin

In a simplified approach to the in vivo situation, where pathogenic fibrillar protein deposits are often found associated with cellular membranes, the aggregation kinetics of insulin in the presence of various model biomembranes were investigated using the Thioflavin T (ThT) fluorescence assay. The lipid dynamics near the gel-fluid transition, the chain length of saturated lipids and the presence of DOPE or DOPS in DOPC-vesicles modulate the aggregation kinetics of insulin in an indifferent, an aggregation-accelerating or an aggregation-inhibiting manner, subtly depending on the pH-value and the presence of salt. The rate of insulin aggregation in bulk solution dominates the overall aggregation process in most cases at low pH, where the lipid additives exert no effect on the aggregation kinetics. The occurrence of dynamic line defects near the gel-fluid transition temperature of DSPC facilitates a partial membrane insertion of the protein, which in turn shields exposed hydrophobic protein patches from intermolecular association and hence inhibit aggregation. An exclusively aggregation-accelerating effect was observed in the presence of 0.1M NaCl for all lipid additives investigated, which is likely due to an enhanced surface accumulation of the protein. Apart from weak dipole-dipole, dipole-monopole and hydrogen bonding interactions, the release of curvature elastic stress in mixed DOPC/DOPE-membranes and preferred interactions of insulin with carboxylic groups in DOPC/DOPS-membranes favour an increased surface accumulation. At neutral pH, a partial insertion of insulin into the lipid bilayer is favoured, which accounts for the aggregation-inhibiting effect of all lipid bilayer systems studied except those containing DOPS. Generally, the extent of inhibition increases with the lipid chain length and the extent of curvature stress in mixed unsaturated lipid membranes and also when the gel-fluid transition temperature of pure phospholipids is approached. The accelerating effect of DOPS on the aggregation of insulin under net electrostatic repulsion at pH 7.4 remains to be elucidated, yet, it might result from increased surface accumulation and/or faster/more extensive unfolding of the protein without a subsequent membrane insertion. These results demonstrate that a delicate interplay between different physical and chemical properties of lipid membranes has to be taken into account in a detailed discussion of membrane-associated protein aggregation phenomena.     

Model‐based optimization and pO2 control of fed‐batch Escherichia coli and Saccharomyces cerevisiae cultivation processes

A model‐based approach for optimization and cascade control of dissolved oxygen partial pressure (pO₂) and maximization of biomass in fed‐batch cultivations is presented. The procedure is based on the off‐line model‐based optimization of the optimal feeding rate profiles and the subsequent automatic pO₂ control using a proposed cascade control technique. During the model‐based optimization of the process, feeding rate profiles are optimized with respect to the imposed technological constraints (initial and maximal cultivation volume, cultivation time, feeding rate range, maximal oxygen transfer rate and pO₂ level). The cascade pO₂ control is implemented using activation of cascades for agitation, oxygen enrichment, and correction of the preoptimized feeding rate profiles. The proposed approach is investigated in two typical fed‐batch processes with Escherichia coli and Saccharomyces cerevisiae. The obtained results show that it was possible to achieve sufficiently high biomass levels with respect to the given technological constraints and to improve controllability of the investigated processes.     

Genome Characterisation of Enteroviruses 117 and 118: A New Group within Human Enterovirus Species C

The more than 120 genotypes of human enteroviruses (HEVs) reflect a wide range of evolutionary divergence, and there are 23 currently classified as human enterovirus C species (HEV-C). Two new HEV-C (EV-C117 and EV-C118) were identified in the Community-Acquired Pneumonia Pediatric Research Initiative (CAP-PRI) study, and the present paper describes the characterisation of the complete genome of one EV-C117 strain (LIT22) and two EV-C118 (ISR38 and ISR10) strains. The EV-C117 and EV-C118 5′UTR sequences were related to those of EV-C104, EV-C105 and EV-C109, and were slightly shorter than those of other HEV A-D species. Similarity plot analyses showed that EV-C117 and EV-C118 have a P1 region that is highly divergent from that of the other HEV-C, and phylogenetic analyses highly supported a monophyletic group consisting of EV-C117, EV-C118, EV-C104, EV-C105 and EV-C109 strains. Phylogenetic, Simplot and Bootscan analyses indicated that recombination was not the main mechanism of EV-C117 and EV-C118 evolution, thus strengthening the hypothesis of the monophyletic origin of the coding regions, as in the case of other HEV-C. Phylogenetic analysis also revealed the emergence of a new group within HEV-C that is divided into two subgroups. Nucleotide and amino acid identity in VP1 sequences have been established as useful criteria for assigning new HEV types, but analysis of the complete P1 region improves resolution.     

Damage-induced chromatome dynamics link Ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair

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Transgenic neuronal overexpression reveals that stringently regulated p23 expression is critical for coordinated movement in mice

Background

Previous studies indicate a role of P2X₇ receptors in processes that lead to neuronal death. The main objective of our study was to examine whether genetic deletion or pharmacological blockade of P2X₇ receptors influenced dopaminergic cell death in various models of Parkinson's disease (PD).

Results

mRNA encoding P2X₇ and P2X₄ receptors was up-regulated after treatment of PC12 cells with 1-methyl-4-phenyl-1,2,3,6- tetrahydropyridine (MPTP). P2X₇ antagonists protected against MPTP and rotenone induced toxicity in the LDH assay, but failed to protect after rotenone treatment in the MTT assay in PC12 cells and in primary midbrain culture. In vivo MPTP and in vitro rotenone pretreatments increased the mRNA expression of P2X₇ receptors in the striatum and substantia nigra of wild-type mice. Basal mRNA expression of P2X₄ receptors was higher in P2X₇ knockout mice and was further up-regulated by MPTP treatment. Genetic deletion or pharmacological inhibition of P2X₇ receptors did not change survival rate or depletion of striatal endogenous dopamine (DA) content after in vivo MPTP or in vitro rotenone treatment. However, depletion of norepinephrine was significant after MPTP treatment only in P2X₇ knockout mice. The basal ATP content was higher in the substantia nigra of wild-type mice, but the ADP level was lower. Rotenone treatment elicited a similar reduction in ATP content in the substantia nigra of both genotypes, whereas reduction of ATP was more pronounced after rotenone treatment in striatal slices of P2X₇ deficient mice. Although the endogenous amino acid content remained unchanged, the level of the endocannabinoid, 2-AG, was elevated by rotenone in the striatum of wild-type mice, an effect that was absent in mice deficient in P2X₇ receptors.

Conclusions

We conclude that P2X₇ receptor deficiency or inhibition does not support the survival of dopaminergic neurons in an in vivo or in vitro models of PD.     

Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins

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Current state and perspectives in modeling and control of human pluripotent stem cell expansion processes in stirred‐tank bioreactors

Implementation of model‐based practices for process development, control, automation, standardization, and validation are important factors for therapeutic and industrial applications of human pluripotent stem cells. As robust cultivation strategies for pluripotent stem cell expansion and differentiation have yet to be determined, process development could be enhanced by application of mathematical models and advanced control systems to optimize growth conditions. Therefore, it is important to understand both the potential of possible applications and the apparent limitations of existing mathematical models to improve pluripotent stem cell cultivation technologies. In the present review, the authors focus on these issues as they apply to stem cell expansion processes. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:355–364, 2017     

Structure-based ligand binding sites of protein p14.5, a member of protein family YER057c/YIL051c/YjgF

Seventeen mutants with one, two or three amino acids substitutions of human protein p14.5, homologue to well-known tumor antigen from goat liver UK114 and a member of proteins YER057c/YIL051c/YjgF family, have been used for structure-functional relation studies and ligand binding analysis using cross-linking by triacryloyl-hexahydro-s-triazine (TAT), size exclusion chromatography, free fatty acid and 8-anilino-1-naphthalenesulfonic acid (ANS) binding assays. Amino acids having the most significant impact on the ligand binding activity have been determined: R107, N93, Y21 and F89. Arginine 107 has been identified as the most accessible amino acid in the cleft. Trimeric structure of protein p14.5 has been confirmed as being essential for stoichiometric small ligand binding activity and oligomeric structure of p14. Ligand binding activity may be related with the biological functions of these proteins, which still are not understood well.