Interdomain contacts control folding of transcription factor RfaH

Escherichia coli RfaH activates gene expression by tethering the elongating RNA polymerase to the ribosome. This bridging action requires a complete refolding of the RfaH C-terminal domain (CTD) from an α-helical hairpin, which binds to the N-terminal domain (NTD) in the free protein, to a β-barrel, which interacts with the ribosomal protein S10 following RfaH recruitment to its target operons. The CTD forms a β-barrel when expressed alone or proteolytically separated from the NTD, indicating that the α-helical state is trapped by the NTD, perhaps co-translationally. Alternatively, the interdomain contacts may be sufficient to drive the formation of the α-helical form. Here, we use functional and NMR analyses to show that the denatured RfaH refolds into the native state and that RfaH in which the order of the domains is reversed is fully functional in vitro and in vivo. Our results indicate that all information necessary to determine its fold is encoded within RfaH itself, whereas accessory factors or sequential folding of NTD and CTD during translation are dispensable. These findings suggest that universally conserved RfaH homologs may change folds to accommodate diverse interaction partners and that context-dependent protein refolding may be widespread in nature.     

Biphonation May Function to Enhance Individual Recognition in the Dhole, Cuon alpinus

Biphonation (two independent fundamental frequencies in a call spectrum) represents one of the most widespread nonlinear phenomena in mammalian vocalizations. Recently, the structure of biphonations was described in detail; however, their functions are poorly understood. For the dhole (Cuon alpinus), biphonic calls represent a prominent feature of vocal activity. In this species, the biphonic call is composed of two frequency components – the high‐frequency squeak and the low‐frequency yap, which also occur alone as separate calls. In this study, we test the hypothesis that the complication of call structure, resulting from the joining of these calls into the biphonic yap–squeak may enhance the potential for individual recognition in the dhole. We randomly selected for analysis 30 high‐frequency squeaks, 30 low‐frequency yaps and 30 biphonic yap–squeaks per animal from five subadult captive dholes (450 calls in total). Discriminant analysis, based on 10 squeak parameter values, showed 80.7% correct assignment to a predicted individual. For 10 yap parameters, the correct assignment was only 44.7%. However, the analysis based on 10 parameters of the biphonic yap–squeak, selected as best contributing to discrimination, showed 96.7% correct assignment to a predicted individual. The results provide strong support for the hypothesis tested showing that the joining of two independent calls into a common vocalization may function to enhance individual recognition in the dhole.     

Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia

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Spore morphology of the north Asian members of Cystopteridaceae

Spores of Cystopteridaceae from northern Asia were examined using scanning electron microscopy. To evaluate the utility of spore morphology in the taxonomy of each genus, we examined spores of 14 species: seven species each of Gymnocarpium and Cystopteris. Among these are 12 species occurring in northern Asia and two species from other regions for comparative studies. The study focused particularly on perispore characters and spore size. Spores of all species examined are monolete, bean-shaped, with a range in spore size of 26–56 × 18–37 μm for Cystopteris and 25–48 × 16–34 μm for Gymnocarpium. The perispore is morphologically diverse within Cystopteris, but less so within Gymnocarpium. The perispore of the Cystopteris spores is characterised by folds and spines that are separate or form complex sculptural elements. Sacci, ridges and flanges, sometimes on the same spore, are characteristic of the perispore of Gymnocarpium. Spores have straight laesura over which the perispore forms a crest. The crest represents a high and flat fold, which is entire, foveolate or reticulate.     

Opioid receptor selectivity profile change via isosterism for 14-O-substituted naltrexone derivatives

Isosterism is commonly used in drug discovery and development to address stability, selectivity, toxicity, pharmacokinetics, and efficacy issues. A series of 14-O-substituted naltrexone derivatives were identified as potent mu opioid receptor (MOR) antagonists with improved selectivity over the kappa opioid receptor (KOR) and the delta opioid receptor (DOR), compared to naltrexone. Since esters are not metabolically very stable under typical physiological conditions, their corresponding amide analogs were thus synthesized and biologically evaluated. Unlike their isosteres, most of these novel ligands seem to be dually selective for the MOR and the KOR over the DOR. The restricted flexibility of the amide bond linkage might be responsible for their altered selectivity profile. However, the majority of the 14-N-substituted naltrexone derivatives produced marginal or no MOR stimulation in the ³⁵S-GTP[γS] assay, which resembled their ester analogs. The current study thus indicated that the 14-substituted naltrexone isosteres are not bioisosteres since they have distinctive pharmacological profile with the regard to their opioid receptor binding affinity and selectivity.     

Heterologous Gln/Asn-Rich Proteins Impede the Propagation of Yeast Prions by Altering Chaperone Availability

Prions are self-propagating conformations of proteins that can cause heritable phenotypic traits. Most yeast prions contain glutamine (Q)/asparagine (N)-rich domains that facilitate the accumulation of the protein into amyloid-like aggregates. Efficient transmission of these infectious aggregates to daughter cells requires that chaperones, including Hsp104 and Sis1, continually sever the aggregates into smaller “seeds.” We previously identified 11 proteins with Q/N-rich domains that, when overproduced, facilitate the de novo aggregation of the Sup35 protein into the [PSI ⁺] prion state. Here, we show that overexpression of many of the same 11 Q/N-rich proteins can also destabilize pre-existing [PSI ⁺] or [URE3] prions. We explore in detail the events leading to the loss (curing) of [PSI⁺] by the overexpression of one of these proteins, the Q/N-rich domain of Pin4, which causes Sup35 aggregates to increase in size and decrease in transmissibility to daughter cells. We show that the Pin4 Q/N-rich domain sequesters Hsp104 and Sis1 chaperones away from the diffuse cytoplasmic pool. Thus, a mechanism by which heterologous Q/N-rich proteins impair prion propagation appears to be the loss of cytoplasmic Hsp104 and Sis1 available to sever [PSI ⁺].     

Biophysical modeling of in vitro and in vivo processes underlying regulated photoprotective mechanism in cyanobacteria

Non-photochemical quenching (NPQ) is a mechanism responsible for high light tolerance in photosynthetic organisms. In cyanobacteria, NPQ is realized by the interplay between light-harvesting complexes, phycobilisomes (PBs), a light sensor and effector of NPQ, the photoactive orange carotenoid protein (OCP), and the fluorescence recovery protein (FRP). Here, we introduced a biophysical model, which takes into account the whole spectrum of interactions between PBs, OCP, and FRP and describes the experimental PBs fluorescence kinetics, unraveling interaction rate constants between the components involved and their relative concentrations in the cell. We took benefit from the possibility to reconstruct the photoprotection mechanism and its parts in vitro, where most of the parameters could be varied, to develop the model and then applied it to describe the NPQ kinetics in the Synechocystis sp. PCC 6803 mutant lacking photosystems. Our analyses revealed  that while an excess of the OCP over PBs is required to obtain substantial PBs fluorescence quenching in vitro, in vivo the OCP/PBs ratio is less than unity, due to higher local concentration of PBs, which was estimated as ~10^?5 M, compared to in vitro experiments. The analysis of PBs fluorescence recovery on the basis of the generalized model of enzymatic catalysis resulted in determination of the FRP concentration in vivo close to 10% of the OCP concentration. Finally, the possible role of the FRP oligomeric state alteration in the kinetics of PBs fluorescence was shown. This paper provides the most comprehensive model of the OCP-induced PBs fluorescence quenching to date and the results are important for better understanding of the regulatory molecular mechanisms underlying NPQ in cyanobacteria.