Native ß-barrel substrates pass through two shared intermediates during folding on the BAM complex.

The assembly of ß-barrel proteins into membranes is mediated by the evolutionarily conserved ß-barrel assembly machine (BAM) complex. In Escherichia coli, BAM folds numerous substrates which vary considerably in size and shape. How BAM is able to efficiently fold such a diverse array of ß-barrel substrates is not clear. Here, we develop a disulfide crosslinking method to trap native substrates in vivo as they fold on BAM. By placing a cysteine within the luminal wall of the BamA barrel as well as in the substrate ß-strands, we can compare the residence time of each substrate strand within the BamA lumen. We validated this method using two defective, slow-folding substrates. We used this method to characterize stable intermediates which occur during folding of two structurally different native substrates. Strikingly, these intermediates occur during identical stages of folding for both substrates: soon after folding has begun and just before folding is completed. We suggest that these intermediates arise due to barriers to folding that are common between ß-barrel substrates, and that the BAM catalyst is able to fold so many different substrates because it addresses these common challenges.

Gene duplication as a major force driving the genome expansion in some giant viruses.

IMPORTANCE: Giant viruses are noteworthy not only due to their enormous particles but also because of their gigantic genomes. In this context, a fundamental question has persisted: how did these genomes evolve? Here we present the discovery of cedratvirus pambiensis, featuring the largest genome ever described for a cedratvirus. Our data suggest that the larger size of the genome can be attributed to an unprecedented number of duplicated genes. Further investigation of this phenomenon in other viruses has illuminated gene duplication as a key evolutionary mechanism driving genome expansion in diverse giant viruses. Although gene duplication has been described as a recurrent event in cellular organisms, our data highlights its potential as a pivotal event in the evolution of gigantic viral genomes.

Dipole modelling for a robust description of subdiffractional polariton waves.

The nanophotonics of van der Waals (vdW) materials relies critically on the electromagnetic properties of polaritons defined on sub-diffraction length scales. Here, we use a full electromagnetic Hertzian dipole antenna (HDA) model to describe the hyperbolic phonon polaritons (HP2s) in vdW crystals of hexagonal boron nitride (hBN) on a gold surface. The HP2 waves are investigated by broadband synchrotron infrared nanospectroscopy (SINS) which covers the type I and type II hyperbolic bands simultaneously. Basically, polariton waves, observed by SINS, are assigned to the resultant electric field from the summation over the irradiated electric fields of dipoles distributed along the crystal edge and at the tip location and a non-propagating field. The values of polariton momenta and damping extracted from the HDA model present excellent agreement with theoretical predictions. Our analysis shows that the confinement factor of type I HP2s exceeds that of the type II ones by up to a factor of 3. We extract anti-parallel group velocities (vg) for type I (vg,typeI = -0.005c, c is the light velocity in a vacuum) in relation to type II (vg,typeII = 0.05c) polaritonic pulses, with lifetimes of ∼0.6 ps and ∼0.3 ps, respectively. Furthermore, by incorporating consolidated optical-near field theory into the HDA model, we simulate real-space images of polaritonic standing waves for hBN crystals of different shapes. This approach reproduces the experiments with a minimal computational cost. Thus, it is demonstrated that the HDA modelling self-consistently explains the measured complex-valued polariton near-field, while being a general approach applicable to other polariton types, like plasmon- and exciton-polaritons, active in the wide range of vdW materials.