SNaPe: a versatile method to generate multiplexed protein fusions using synthetic linker peptides for in vitro applications

Understanding the structure and function of protein complexes and multi‐domain proteins is highly important in biology, although the in vitro characterization of these systems is often complicated by their size or the transient nature of protein/protein interactions. To assist in the characterization of such protein complexes, we have developed a modular approach to fusion protein generation that relies upon S ortase‐mediated and Na tive chemical ligation using synthetic Pe ptide linkers (SNaPe) to link two separately expressed proteins. In this approach, we utilize two separate linking steps – sortase‐mediated and native chemical ligation – together with a library of peptide linkers to generate libraries of fusion proteins. We have demonstrated the viability of SNaPe to generate libraries from fusion protein constructs taken from the biosynthetic enzymes responsible for late stage aglycone assembly during glycopeptide antibiotic biosynthesis. Crucially, SNaPe was able to generate fusion proteins that are inaccessible via direct expression of the fusion construct itself. This highlights the advantages of SNaPe to not only access fusion proteins that have been previously unavailable for biochemical and structural characterization but also to do so in a manner that enables the linker itself to be controlled as an experimental parameter of fusion protein generation. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

Extracellular vesicle-mediated transfer of membranous components from the highly malignant T24 urinary carcinoma cell line to the non-malignant RT4 urinary papilloma cell line

This communication reports the first experimental evidence that in the bladder cancer model, membranous components labelled with the DiO dye and the cholera toxin subunit B can be transported from highly malignant (T24) to non-malignant (RT4) cells by extracellular vesicles. Taking into account the presence of stable membranous nanostructures found by scanning electron microscopy, we suggest a possible uptake mechanism in recipient cells through fusion with highly curved membranous regions.     

Mutations in DNAJC5, encoding cysteine-string protein alpha, cause autosomal-dominant adult-onset neuronal ceroid lipofuscinosis

Autosomal-dominant adult-onset neuronal ceroid lipofuscinosis (ANCL) is characterized by accumulation of autofluorescent storage material in neural tissues and neurodegeneration and has an age of onset in the third decade of life or later. The genetic and molecular basis of the disease has remained unknown for many years. We carried out linkage mapping, gene-expression analysis, exome sequencing, and candidate-gene sequencing in affected individuals from 20 families and/or individuals with simplex cases; we identified in five individuals one of two disease-causing mutations, c.346_348delCTC and c.344T>G, in DNAJC5 encoding cysteine-string protein alpha (CSPα). These mutations-causing a deletion, p.Leu116del, and an amino acid exchange, p.Leu115Arg, respectively-are located within the cysteine-string domain of the protein and affect both palmitoylation-dependent sorting and the amount of CSPα in neuronal cells. The resulting depletion of functional CSPα might cause in parallel the presynaptic dysfunction and the progressive neurodegeneration observed in affected individuals and lysosomal accumulation of misfolded and proteolysis-resistant proteins in the form of characteristic ceroid deposits in neurons. Our work represents an important step in the genetic dissection of a genetically heterogeneous group of ANCLs. It also confirms a neuroprotective role for CSPα in humans and demonstrates the need for detailed investigation of CSPα in the neuronal ceroid lipofuscinoses and other neurodegenerative diseases presenting with neuronal protein aggregation.     

Proteomic analysis of the 20S proteasome (PSMA3)-interacting proteins reveals a functional link between the proteasome and mRNA metabolism

The 26S proteasome is a large multi-subunit protein complex that exerts specific degradation of proteins in the cell. The 26S proteasome consists of the 20S proteolytic particle and the 19S regulator. In order to be targeted for proteasomal degradation most of the proteins must undergo the post-translational modification of poly-ubiquitination. However, a number of proteins can also be degraded by the proteasome via a ubiquitin-independent pathway. Such degradation is exercised largely through the binding of substrate proteins to the PSMA3 (alpha 7) subunit of the 20S complex. However, a systematic analysis of proteins interacting with PSMA3 has not yet been carried out. In this report, we describe the identification of proteins associated with PSMA3 both in the cytoplasm and nucleus. A combination of two-dimensional gel electrophoresis (2D-GE) and tandem mass-spectrometry revealed a large number of PSMA3-bound proteins that are involved in various aspects of mRNA metabolism, including splicing. In vitro biochemical studies confirmed the interactions between PSMA3 and splicing factors. Moreover, we show that 20S proteasome is involved in the regulation of splicing in vitro of SMN2 (survival motor neuron 2) gene, whose product controls apoptosis of neurons.     

Mechanoformation of neutral giant phospholipid vesicles in high ionic strength solution

We present new and simple method for formation of giant unilamellar vesicles (GUVs) in high ionic strength solutions, such as phosphate buffered saline (PBS). Mechanoformation method is an alternative method to electroformation method. The advantage of the mechanoformation procedure is that there are no limitations with respect to the ionic strength of the aqueous solutions, because there is no applied electric potential thus no current flow through the formation cell and no electrolysis is induced.     

Synanthropic birds influence the distribution of Borrelia species: analysis of Ixodes ricinus ticks feeding on passerine birds

Ixodes ricinus ticks collected from 835 birds and from vegetation in the Czech Republic were analyzed. Host-seeking ticks (n = 427) were infected predominantly by Borrelia afzelii (25%). Ticks (n = 1,012) from songbirds (Passeriformes) were infected commonly by Borrelia garinii (12.1%) and Borrelia valaisiana (13.4%). Juveniles of synanthropic birds, Eurasian blackbirds (Turdus merula) and song thrushes (Turdus philomelos), were major reservoir hosts of B. garinii.     

Factors Affecting Sleep/vigilance Behaviour in Incubating Mallards

Vigilance is a behavioural tactic that allows individuals to control their surroundings and to assess predation risk. In contrast, sleep is unique behavioural state with widely hypothesized restorative and energy‐saving functions, but reducing attentiveness and increasing susceptibility to predation. Sleeping birds resolve this conflict by interrupting sleep with short periods of eye opening (termed ‘scans’) during vigilant sleep. Miscellaneous environmental factors and sleeping postures may affect the perception of risk and corresponding vigilance level. Here, we investigated the influence of nest vegetation concealment, time of day and sleeping postures on the sleep/vigilance trade‐off in incubating Mallards (Anas platyrhynchos). We found that incubating females increased their vigilance with increasing nest vegetation cover facing the vigilant eye during both the day and the night periods; however, mean nest vegetation concealment did not affect female vigilance. Females also reduced their total vigilance along with scan frequency during the night period, while displaying the opposite pattern during the daylight. The rest‐sleeping position was preferred more during the night compared with the daylight period, and females were more vigilant in this position at night. Our data show that the nest vegetation concealment regardless of visual abilities during different light conditions, time of day and sleeping posture play an underlying role in antipredator vigilance during sleep in this cryptic ground‐nesting bird.     

Langevin Poisson-Boltzmann equation: point-like ions and water dipoles near a charged surface

Water ordering near a charged membrane surface is important for many biological processes such as binding of ligands to a membrane or transport of ions across it. In this work, the mean-field Poisson-Boltzmann theory for point-like ions, describing an electrolyte solution in contact with a planar charged surface, is modified by including the orientational ordering of water. Water molecules are considered as Langevin dipoles, while the number density of water is assumed to be constant everywhere in the electrolyte solution. It is shown that the dielectric permittivity of an electrolyte close to a charged surface is decreased due to the increased orientational ordering of water dipoles. The dielectric permittivity close to the charged surface is additionally decreased due to the finite size of ions and dipoles.