Functional Amyloids Keep Quorum-sensing Molecules in Check

The mechanism by which extracellular metabolites, including redox mediators and quorum-sensing signaling molecules, traffic through the extracellular matrix of biofilms is poorly explored. We hypothesize that functional amyloids, abundant in natural biofilms and possessing hydrophobic domains, retain these metabolites. Using surface plasmon resonance, we demonstrate that the quorum-sensing (QS) molecules, 2-heptyl-3-hydroxy-4(1H)-quinolone and N-(3-oxododecanoyl)-l-homoserine lactone, and the redox mediator pyocyanin bind with transient affinity to functional amyloids from Pseudomonas (Fap). Their high hydrophobicity predisposes them to signal-amyloid interactions, but specific interactions also play a role. Transient interactions allow for rapid association and dissociation kinetics, which make the QS molecules bioavailable and at the same time secure within the extracellular matrix as a consequence of serial bindings. Retention of the QS molecules was confirmed using Pseudomonas aeruginosa PAO1-based 2-heptyl-3-hydroxy-4(1H)-quinolone and N-(3-oxododecanoyl)-l-homoserine lactone reporter assays, showing that Fap fibrils pretreated with the QS molecules activate the reporters even after sequential washes. Pyocyanin retention was validated by electrochemical analysis of pyocyanin-pretreated Fap fibrils subjected to the same washing process. Results suggest that QS molecule-amyloid interactions are probably important in the turbulent environments commonly encountered in natural habitats.     

Rice PCR1 influences grain weight and Zn accumulation in grains

Proteins containing a placenta‐specific 8 domain (PLAC8) function as major organ size regulators in Solanum lycopersicum and Zea may, and putative metal ion transporters in Arabidopsis thaliana, Oryza sativa and Brassica juncea. However, it is unknown how PLAC8 domain‐containing proteins fulfill such diverse roles. Here, we found that plant cadmium resistance 1 (PCR1) influences both zinc (Zn) accumulation and grain weight in rice. OsPCR1 knockout and knockdown lines produced lighter grains than the wild type, while OsPCR1 overexpression lines produced heavier grains. Furthermore, the grains of OsPCR1 knockdown lines exhibited substantially higher Zn and lower cadmium (Cd) concentrations than the control, as did yeast heterologously expressing OsPCR1. Through sequence analysis, we showed that the amino acid sequence of japonica‐type PCR1 was distinct from that of indica‐type and wild rice accessions. This difference was correlated with distinct Zn‐related phenotypes. Japonica‐type PCR1 had a shorter N‐terminus than did PCR1 in the other rice types, and yeast heterologously expressing japonica‐type PCR1 was more sensitive to Zn than was yeast expressing indica‐type PCR1. Furthermore, japonica‐type grains accumulated less Zn than did indica‐type grains. Our study suggests that rice PCR1 maintains metal ion homeostasis and grain weight and might have been selected for during domestication.     

Adventitious rooting adjuvant activity of 1,3-di(benzo[d]oxazol-5-yl)urea and 1,3-di(benzo[d]oxazol-6-yl)urea: new insights and perspectives

Here we report new insights on the adventitious rooting adjuvant activity of 1,3-di(benzo[d]oxazol-5-yl)urea (5-BDPU) and 1,3-di(benzo[d]oxazol-6-yl)urea (6-BDPU), both symmetrically substituted urea derivatives that do not show either auxin- or cytokinin-like activity per se. Our data demonstrate that these synthetic molecules enhance adventitious rooting in distantly-related herbaceous and woody species, in the presence of endogenous or exogenous auxin. For the first time, we report that BDPUs enhance adventitious rooting in the presence of either indole-3-butyric acid (IBA) or 1-naphtalene acetic acid and that their optimal concentration depends on the strength of the exogenous auxin. Trying to understand the mode of action of BDPUs, we also show that their adventitious rooting adjuvant activity correlates with high mRNA levels of auxin-responsive genes related to the adventitious rooting process at the very early stages of adventitious rooting, before the activation of cell divisions in pine hypocotyls cuttings. The high mRNA levels are measured in the presence of low auxin concentrations and BDPUs. The mRNA levels quantified in these conditions are similar to those measured in the presence of high auxin concentrations but in the absence of BDPUs. In addition, the spatial distribution of endogenous auxin is localized in globular-shaped structures of cell divisions located centrifugal to the resin canals, at the positions of adventitious root formation, in the presence of urea derivatives and IBA after 6 days of the root induction process.     

A mutation associated with centronuclear myopathy enhances the size and stability of dynamin 2 complexes in cells

Background

Dynamin 2 (Dyn2) is a ~ 100 kDa GTPase that assembles around the necks of nascent endocytic and Golgi vesicles and catalyzes membrane scission. Mutations in Dyn2 that cause centronuclear myopathy (CNM) have been shown to stabilize Dyn2 polymers against GTP-dependent disassembly in vitro. Precisely timed regulation of assembly and disassembly is believed to be critical for Dyn2 function in membrane vesiculation, and the CNM mutations interfere with this regulation by shifting the equilibrium toward the assembled state.

Methods

In this study we use two fluorescence fluctuation spectroscopy (FFS) approaches to show that a CNM mutant form of Dyn2 also has a greater propensity to self-assemble in the cytosol and on the plasma membrane of living cells.

Results

Results obtained using brightness analysis indicate that unassembled wild-type Dyn2 is predominantly tetrameric in the cytosol, although different oligomeric species are observed, depending on the concentration of expressed protein. In contrast, an R369W mutant identified in CNM patients forms higher-order oligomers at concentrations above 1 μM. Investigation of Dyn2-R369W by Total Internal Reflection Fluorescence (TIRF) FFS reveals that this mutant forms larger and more stable clathrin-containing structures on the plasma membrane than wild-type Dyn2.

Conclusions and general significance

These observations may explain defects in membrane trafficking reported in CNM patient cells and in heterologous systems expressing CNM-associated Dyn2 mutants.     

The evolution of the ribosome biogenesis pathway from a yeast perspective

Ribosome biogenesis is fundamental for cellular life, but surprisingly little is known about the underlying pathway. In eukaryotes a comprehensive collection of experimentally verified ribosome biogenesis factors (RBFs) exists only for Saccharomyces cerevisiae. Far less is known for other fungi, animals or plants, and insights are even more limited for archaea. Starting from 255 yeast RBFs, we integrated ortholog searches, domain architecture comparisons and, in part, manual curation to investigate the inventories of RBF candidates in 261 eukaryotes, 26 archaea and 57 bacteria. The resulting phylogenetic profiles reveal the evolutionary ancestry of the yeast pathway. The oldest core comprising 20 RBF lineages dates back to the last universal common ancestor, while the youngest 20 factors are confined to the Saccharomycotina. On this basis, we outline similarities and differences of ribosome biogenesis across contemporary species. Archaea, so far a rather uncharted domain, possess 38 well-supported RBF candidates of which some are known to form functional sub-complexes in yeast. This provides initial evidence that ribosome biogenesis in eukaryotes and archaea follows similar principles. Within eukaryotes, RBF repertoires vary considerably. A comparison of yeast and human reveals that lineage-specific adaptation via RBF exclusion and addition characterizes the evolution of this ancient pathway.