Phosphorylation at intrinsically disordered regions of PAM2 motif-containing proteins modulates their interactions with PABPC1 and influences mRNA fate

Cytoplasmic poly(A)-binding protein (PABP) C1 recruits different interacting partners to regulate mRNA fate. The majority of PABP-interacting proteins contain a PAM2 motif to mediate their interactions with PABPC1. However, little is known about the regulation of these interactions or the corresponding functional consequences. Through in silico analysis, we found that PAM2 motifs are generally embedded within an extended intrinsic disorder region (IDR) and are located next to cluster(s) of potential serine (Ser) or threonine (Thr) phosphorylation sites within the IDR. We hypothesized that phosphorylation at these Ser/Thr sites regulates the interactions between PAM2-containing proteins and PABPC1. In the present study, we have tested this hypothesis using complementary approaches to increase or decrease phosphorylation. The results indicate that changing the extent of phosphorylation of three PAM2-containing proteins (Tob2, Pan3, and Tnrc6c) alters their ability to interact with PABPC1. Results from experiments using phospho-blocking or phosphomimetic mutants in PAM2-containing proteins further support our hypothesis. Moreover, the phosphomimetic mutations appreciably affected the functions of these proteins in mRNA turnover and gene silencing. Taken together, these results provide a new framework for understanding the roles of intrinsically disordered proteins in the dynamic and signal-dependent control of cytoplasmic mRNA functions.     

Peptide amidation: Production of peptide hormonesin vivo andin vitro

Over half of all biologically active peptides and peptide hormones are α-amidated at their C-terminus, which is essential for their full biological activities. Amidation is accomplished through the sequential reaction of the two enzymes encoded by the single bifunctional, peptidylglycine α-amidating monooxygenase (PAM or an α-amidating enzyme). PAM catalyzes the formation of a peptide amide from peptide precursors that include a C-terminal glycine, and requires copper, molecular oxygen, and ascorbate. PAM is the only enzyme that produces peptide amidesin vivo. However, various strategies utilizing PAM, carboxypeptidase-Y enzymes, and chemical synthesis have been developed for producing peptide amidesin vitro. The growing need and importance of peptide amide drugs has highlighted the necessity for an efficientin vitro amidating system for industrial application. In recent years, recombinant systems for enzymatic amidation have received growing attention for the production of peptide hormones, like calcitonin and oxytocin. This review presents the current situation regarding amidation, with a special emphasis on the industrial production of peptide hormones.     

Hydrogen peroxide contributes to the ultraviolet-B (280–315 nm) induced oxidative stress of plant leaves through multiple pathways

Solar UV-B (280–315 nm) radiation is a developmental signal in plants but may also cause oxidative stress when combined with other environmental factors. Using computer modeling and in solution experiments we show that UV-B is capable of photosensitizing hydroxyl radical production from hydrogen peroxide. We present evidence that the oxidative effect of UV-B in leaves is at least twofold: (i) it increases cellular hydrogen peroxide concentrations, to a larger extent in pyridoxine antioxidant mutant pdx1.3-1 Arabidopsis and; (ii) is capable of a partial photo-conversion of both ‘natural’ and ‘extra’ hydrogen peroxide to hydroxyl radicals. As stress conditions other than UV can increase cellular hydrogen peroxide levels, synergistic deleterious effects of various stresses may be expected already under ambient solar UV-B.     

Motif depletion in bacteriophages infecting hosts with CRISPR systems

Background

CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.

Results

To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.

Conclusions

The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-663) contains supplementary material, which is available to authorized users.     

Secretory Granule Membrane Protein Recycles through Multivesicular Bodies

The recycling of secretory granule membrane proteins that reach the plasma membrane following exocytosis is poorly understood. As a model, peptidylglycine α‐amidating monooxygenase (PAM), a granule membrane protein that catalyzes a final step in peptide processing was examined. Ultrastructural analysis of antibody internalized by PAM and surface biotinylation showed efficient return of plasma membrane PAM to secretory granules. Electron microscopy revealed the rapid movement of PAM from early endosomes to the limiting membranes of multivesicular bodies and then into intralumenal vesicles. Wheat germ agglutinin and PAM antibody internalized simultaneously were largely segregated when they reached multivesicular bodies. Mutation of basally phosphorylated residues (Thr⁹⁴⁶, Ser⁹⁴⁹) in the cytoplasmic domain of PAM to Asp (TS/DD) substantially slowed its entry into intralumenal vesicles. Mutation of the same sites to Ala (TS/AA) facilitated the entry of internalized PAM into intralumenal vesicles and its subsequent return to secretory granules. Entry of PAM into intralumenal vesicles is also associated with a juxtamembrane endoproteolytic cleavage that releases a 100‐kDa soluble PAM fragment that can be returned to secretory granules. Controlled entry into the intralumenal vesicles of multivesicular bodies plays a key role in the recycling of secretory granule membrane proteins.     

Full-Length Recombinant Plasmodium falciparum VAR2CSA Binds Specifically to CSPG and Induces Potent Parasite Adhesion-Blocking Antibodies

Plasmodium falciparum malaria remains one of the world's leading causes of human suffering and poverty. Each year, the disease takes 1-3 million lives, mainly in sub-Saharan Africa. The adhesion of infected erythrocytes (IEs) to vascular endothelium or placenta is the key event in the pathogenesis of severe P. falciparum infection. In pregnant women, the parasites express a single and unique member of the P. falciparum erythrocyte membrane protein 1 (PfEMP1) family named VAR2CSA, which is associated with the ability of the IEs to adhere specifically to chondroitin sulphate A (CSA) in the placenta. Several Duffy-binding-like domains from VAR2CSA molecules have been shown in vitro to bind to CSA, but it has also been demonstrated that Duffy-binding-like domains from PfEMP1 proteins other than VAR2CSA can bind CSA. In addition, the specificity of the binding of VAR2CSA domains to glycosaminoglycans does not match that of VAR2CSA-expressing IEs. This has led to speculation that the domains of native VAR2CSA need to come together to form a specific binding site or that VAR2CSA might bind to CSA through a bridging molecule. Here, we describe the expression and purification of the complete extracellular region of VAR2CSA secreted at high yields from insect cells. Using surface plasmon resonance, we demonstrate that VAR2CSA alone binds with nanomolar affinity to human chondroitin sulphate proteoglycan and with significantly weaker affinity to other glycosaminoglycans, showing a specificity similar to that observed for IEs. Antibodies raised against full-length VAR2CSA completely inhibit recombinant VAR2CSA binding, as well as parasite binding to chondroitin sulphate proteoglycan. This is the first study to describe the successful production and functionality of a full-length PfEMP1. The specificity of the binding and anti-adhesion potency of induced IgG, together with high-yield production, encourages the use of full-length PfEMP1 in vaccine development strategies.     

Photosynthetic activity including the thermal‐ and chilling‐light sensitivities of a temperate Japanese brown alga Sargassum macrocarpum

The effects of irradiance, temperature, thermal‐ and chilling‐light sensitivities on the photosynthesis of a temperate alga, Sargassum macrocarpum (Fucales) were determined by a pulse amplitude modulation (PAM)‐chlorophyll fluorometer and dissolved oxygen sensors. Oxygenic photosynthesis–irradiance curves at 8, 20, and 28°C revealed that the maximum net photosynthetic rates (NP _max) and saturation irradiance were highest at 28°C, and lowest at 8°C. Gross photosynthesis and dark respiration determined over a range of temperatures (8–36°C) at 300 μmol photons m^?2 s^?1 revealed that the maximum gross photosynthetic rate (GP_max) occurred at 27.8°C, which is consistent with the highest seawater temperature in the southern distributional limit of this species in Japan. Additionally, the maximum quantum yields of photosystem II (F _v/F _m) during the 72‐h temperature exposures were stable at 8–28°C, but suddenly dropped to zero at higher temperatures, indicative of PSII deactivation. Continuous exposure (12 h) to irradiance of 200 (low) and 1000 (high) μmol photons m^?2 s^?1 at 8, 20, and 28°C revealed greater declines in their effective quantum yields (Φ _PSII) under high irradiance. While Φ _PSII under low irradiance were very similar with the initial F _v/F _m under 20 and 28°C, values rapidly decreased with exposure duration at 8°C. At this temperature, F _v/F _m did not recover to initial values even after 12 h of dark acclimation. Final F _v/F _m of alga at 28°C under high irradiance treatment also did not recover, suggesting its sensitivity to photoinhibition at both low and high temperatures. These photosynthetic characteristics reflect both the adaptation of the species to the general environmental conditions, and its ability to acclimate to seasonal changes in seawater temperature within their geographical range of distribution.     

Discovery of ML326: The first sub-micromolar,selective M5 PAM

This Letter describes the further chemical optimization of the M₅ PAM MLPCN probes ML129 and ML172. A multi-dimensional iterative parallel synthesis effort quickly explored isatin replacements and a number of southern heterobiaryl variations with no improvement over ML129 and ML172. An HTS campaign identified several weak M₅ PAMs (M₅ EC₅₀ >10 μM) with a structurally related isatin core that possessed a southern phenethyl ether linkage. While SAR within the HTS series was very shallow and unable to be optimized, grafting the phenethyl ether linkage onto the ML129/ML172 cores led to the first sub-micromolar M₅ PAM, ML326 (VU0467903), (human and rat M₅ EC₅₀s of 409 nM and 500 nM, respectively) with excellent mAChR selectivity (M₁–M₄ EC₅₀s >30 μM) and a robust 20-fold leftward shift of the ACh CRC.