A part toolbox to tune genetic expression in Bacillus subtilis

Libraries of well-characterised components regulating gene expression levels are essential to many synthetic biology applications. While widely available for the Gram-negative model bacterium Escherichia coli, such libraries are lacking for the Gram-positive model Bacillus subtilis, a key organism for basic research and biotechnological applications. Here, we engineered a genetic toolbox comprising libraries of promoters, Ribosome Binding Sites (RBS), and protein degradation tags to precisely tune gene expression in B. subtilis. We first designed a modular Expression Operating Unit (EOU) facilitating parts assembly and modifications and providing a standard genetic context for gene circuits implementation. We then selected native, constitutive promoters of B. subtilis and efficient RBS sequences from which we engineered three promoters and three RBS sequence libraries exhibiting ∼14 000-fold dynamic range in gene expression levels. We also designed a collection of SsrA proteolysis tags of variable strength. Finally, by using fluorescence fluctuation methods coupled with two-photon microscopy, we quantified the absolute concentration of GFP in a subset of strains from the library. Our complete promoters and RBS sequences library comprising over 135 constructs enables tuning of GFP concentration over five orders of magnitude, from 0.05 to 700 μM. This toolbox of regulatory components will support many research and engineering applications in B. subtilis.     

Testosterone and Linear Social Dominance Status in Captive Male Dabbling Ducks in Winter

Dominance hierarchies play an important role in avoidance and/or solving conflicts in gregarious species. In dabbling ducks (Anas species), dominance allows for feeding‐site monopolization in winter quarters where resources are generally limited. In addition, male social rank should theoretically favour access to mates. Dominance rank can be associated with morphological traits, and is often correlated with aggressiveness, a behavioural trait generally related to high testosterone levels. In this study, we investigated the existence of a winter group structure based on dominance relationships and tested for a linear hierarchy, in three species of captive male dabbling ducks (mallard Anas platyrhynchos, pintail A. acuta and wigeon A. penelope). We then analysed the relationship between dominance ranks, morphological parameters and testosterone levels measured in early (Oct.) and mid‐winter (Dec./Jan.). We found that the three male groups of the three species exhibited a linear hierarchy. Testosterone levels differed during winter and between species. Morphologic measurements, body mass and body condition were not correlated with individual dominance ranks, whereas dominant males had higher testosterone levels than subordinates. The slopes of the relationships were similar between species and winter period, but the y‐intercepts differed between species and between early and mid‐winter phases. The linear hierarchy found in the three species indicates that dominance relationships strongly structure dabbling duck groups in winter. Lack of correlation between rank and morphological characters, but correlation of rank with testosterone levels suggests that social rank is more dependent on behavioural traits such as aggressive behaviour. The differences between species and winter periods are discussed in relation to migration and wintering phenology.     

Structure of the calcium channel beta subunit: the place of the beta-interaction domain

Voltage-gated calcium channels are key players in a number of fundamental physiological functions including contraction, secretion, transmitter release or gene activation. They allow a flux of calcium into the cell that constitutes a switch-on signal for most of these functions. The structures responsible for the shaping of these fluxes by the membrane voltage belong to the channel itself, but a number of associated proteins are known to more precisely tune this calcium entry and adapt it to the cellular demand. The calcium channel regulatory beta subunit is undoubtedly the most important one, being influent on the expression, the kinetics, the voltage-dependence of channel opening and closing and on the pharmacology of the channel. Heterologous expression, combined to mutagenesis and electrophysiological and biochemical experiments have revealed the roles of short sequences of the beta subunit, including the BID (beta-interaction domain), in the physical and functional interactions with the channel pore. The resolved crystal structure of the beta subunit now sheds new light on these sequences and their interactions with the rest of the protein. The presence of a type 3 src-homology (SH3) domain and a guanylate kinase (GK) domain confirms that the subunit belongs to the MAGUK protein family. Consistently, the polyproline binding site and the kinase function of the SH3 and the GK domains, respectively, are non functional, and the BID appears to be buried in the structure, preserving the SH3-GK interaction but not directly available for interactions with the channel pore subunit. Anchoring of the beta subunit to the channel occurs via a hydrophobic grove in the GK domain, leaving a large surface of the subunit open to other protein-protein interactions. To what extent the intramolecular SH3-GK interaction is necessary for the stabilisation of this grove in a functional unit remains to be understood. The beta subunit may thus play a key role in scaffolding multiple proteins around the channel and organizing diverse calcium-dependent signalling pathways directly linked to voltage-gated calcium entry. These findings will undoubtedly vitalize the search for new beta-specific partners and functions.     

Zinc improves gene transfer mediated by DNA/cationic polymer complexes

Background

The weak efficiency of plasmid transfer into the cytosol remains one of the major limiting factors to achieve an efficient transfection with DNA/cationic polymer complexes. We found that divalent metal Zn²⁺ can improve the polyfection efficiency, especially with DNA/histidylated polylysine (His‐pLK) complexes.

Methods and results

The supplementation of the transfection medium with 250 µM ZnCl₂ increased the polyfection of human hepatocarcinoma (HepG2) cells with a plasmid encoding EGFP complexed with pLK, polyethyleneimine and His‐pLK. Zn²⁺ is more efficient on DNA/His‐pLK complexes: the number of EGFP‐positive cells increased from 1% to more than 40%. This phenomenon is selective to Zn²⁺ because no effect was obtained with other divalent cations. The effect of zinc varies from cell to cell. The binding of Zn²⁺ to histidyl residues might increase zinc endosomal concentration favoring membrane fusion. Flow cytometry and confocal microscopy studies clearly indicate that with His‐pLK, the plasmid is better delivered in the cytosol as well as in the cell nucleus in zinc‐treated cells. An investigation conducted with the histidine‐rich peptide H5WYG showed that zinc inhibits membrane permeabilization but promotes membrane fusion as evidenced by resonance energy transfer.

Conclusions

Data reported here imply that the addition of zinc ions in the transfection medium can trigger an increase of the fusion of endosomes containing polyplexes which is more effective in the presence of histidine‐rich molecules. Consequently, the amount of plasmid in the cytosol available to reach the nucleus is increased leading to an improvement of polyfection. Copyright © 2002 John Wiley & Sons, Ltd.

     

Control of the dynamics and homeostasis of the Drosophila Hedgehog receptor Patched by two C2-WW-HECT-E3 Ubiquitin ligases

The conserved Hedgehog (HH) signals control animal development, adult stem cell maintenance and oncogenesis. In Drosophila, the HH co-receptor Patched (PTC) controls both HH gradient formation and signalling. PTC is post-translationally downregulated by HH, which promotes its endocytosis and destabilization, but the mechanisms of PTC trafficking and its importance in the control of PTC remain to be understood. PTC interacts with E3 Ubiquitin (UB)-ligases of the C2-WW-HECT family; two of them—SMURF and NEDD4—are known to regulate its levels. We demonstrate that mutation of the PTC PY motif, which mediates binding of C2-WW-HECT family members, inhibits its internalization but not its autonomous and non-autonomous signalling activities. In addition, we show that the two related UB-C2-WW-HECT ligases NEDD4 and SU(DX) regulate PTC trafficking and finely tune its accumulation through partially redundant but distinct functions. While both NEDD4 and SU(DX) promote PTC endocytosis, only SU(DX) is able to induce its lysosomal targeting and degradation. In conclusion, PTC trafficking and homeostasis are tightly regulated by a family of UB-ligases.     

A Data-Driven Design Evaluation Tool for Handheld Device Soft Keyboards

Thumb interaction is a primary technique used to operate small handheld devices such as smartphones. Despite the different techniques involved in operating a handheld device compared to a personal computer, the keyboard layouts for both devices are similar. A handheld device keyboard that considers the physical capabilities of the thumb may improve user experience. We developed and applied a design evaluation tool for different geometries of the QWERTY keyboard using a performance evaluation model. The model utilizes previously collected data on thumb motor performance and posture for different tap locations and thumb movement directions. We calculated a performance index (PI_TOT, 0 is worst and 2 is best) for 663 designs consisting in different combinations of three variables: the keyboard''s radius of curvature (R) (mm), orientation (O) (°), and vertical location on the screen (L). The current standard keyboard performed poorly (PI_TOT = 0.28) compared to other designs considered. Keyboard location (L) contributed to the greatest variability in performance out of the three design variables, suggesting that designers should modify this variable first. Performance was greatest for designs in the middle keyboard location. In addition, having a slightly upward curve (R = −20 mm) and orientated perpendicular to the thumb''s long axis (O = −20°) improved performance to PI_TOT = 1.97. Poorest performances were associated with placement of the keyboard''s spacebar in the bottom right corner of the screen (e.g., the worst was for R = 20 mm, O = 40°, L =  Bottom (PI_TOT = 0.09)). While this evaluation tool can be used in the design process as an ergonomic reference to promote user motor performance, other design variables such as visual access and usability still remain unexplored.