Structures of Streptococcus pneumoniae PiaA and Its Complex with Ferrichrome Reveal Insights into the Substrate Binding and Release of High Affinity Iron Transporters

Iron scarcity is one of the nutrition limitations that the Gram-positive infectious pathogens Streptococcus pneumoniae encounter in the human host. To guarantee sufficient iron supply, the ATP binding cassette (ABC) transporter Pia is employed to uptake iron chelated by hydroxamate siderophore, via the membrane-anchored substrate-binding protein PiaA. The high affinity towards ferrichrome enables PiaA to capture iron at a very low concentration in the host. We presented here the crystal structures of PiaA in both apo and ferrichrome-complexed forms at 2.7 and 2.1 Å resolution, respectively. Similar to other class III substrate binding proteins, PiaA is composed of an N-terminal and a C-terminal domain bridged by an α-helix. At the inter-domain cleft, a molecule of ferrichrome is stabilized by a number of highly conserved residues. Upon ferrichrome binding, two highly flexible segments at the entrance of the cleft undergo significant conformational changes, indicating their contribution to the binding and/or release of ferrichrome. Superposition to the structure of Escherichia coli ABC transporter BtuF enabled us to define two conserved residues: Glu119 and Glu262, which were proposed to form salt bridges with two arginines of the permease subunits. Further structure-based sequence alignment revealed that the ferrichrome binding pattern is highly conserved in a series of PiaA homologs encoded by both Gram-positive and negative bacteria, which were predicted to be sensitive to albomycin, a sideromycin antibiotic derived from ferrichrome.     

Centrioles generate a local pulse of Polo/PLK1 activity to initiate mitotic centrosome assembly

Mitotic centrosomes are formed when centrioles start to recruit large amounts of pericentriolar material (PCM) around themselves in preparation for mitosis. This centrosome “maturation” requires the centrioles and also Polo/PLK1 protein kinase. The PCM comprises several hundred proteins and, in Drosophila, Polo cooperates with the conserved centrosome proteins Spd‐2/CEP192 and Cnn/CDK5RAP2 to assemble a PCM scaffold around the mother centriole that then recruits other PCM client proteins. We show here that in Drosophila syncytial blastoderm embryos, centrosomal Polo levels rise and fall during the assembly process—peaking, and then starting to decline, even as levels of the PCM scaffold continue to rise and plateau. Experiments and mathematical modelling indicate that a centriolar pulse of Polo activity, potentially generated by the interaction between Polo and its centriole receptor Ana1 (CEP295 in humans), could explain these unexpected scaffold assembly dynamics. We propose that centrioles generate a local pulse of Polo activity prior to mitotic entry to initiate centrosome maturation, explaining why centrioles and Polo/PLK1 are normally essential for this process.     

Improving transmembrane protein consensus topology prediction using inter-helical interaction

Alpha helix transmembrane proteins (αTMPs) represent roughly 30% of all open reading frames (ORFs) in a typical genome and are involved in many critical biological processes. Due to the special physicochemical properties, it is hard to crystallize and obtain high resolution structures experimentally, thus, sequence-based topology prediction is highly desirable for the study of transmembrane proteins (TMPs), both in structure prediction and function prediction. Various model-based topology prediction methods have been developed, but the accuracy of those individual predictors remain poor due to the limitation of the methods or the features they used. Thus, the consensus topology prediction method becomes practical for high accuracy applications by combining the advances of the individual predictors. Here, based on the observation that inter-helical interactions are commonly found within the transmembrane helixes (TMHs) and strongly indicate the existence of them, we present a novel consensus topology prediction method for αTMPs, CNTOP, which incorporates four top leading individual topology predictors, and further improves the prediction accuracy by using the predicted inter-helical interactions. The method achieved 87% prediction accuracy based on a benchmark dataset and 78% accuracy based on a non-redundant dataset which is composed of polytopic αTMPs. Our method derives the highest topology accuracy than any other individual predictors and consensus predictors, at the same time, the TMHs are more accurately predicted in their length and locations, where both the false positives (FPs) and the false negatives (FNs) decreased dramatically. The CNTOP is available at: http://ccst.jlu.edu.cn/JCSB/cntop/CNTOP.html.     

Halogen Engineering for Operationally Stable Perovskite Solar Cells via Sequential Deposition

The performance of perovskite solar cells (PSCs) relies on the synthesis method and chemical composition of the perovskite materials. So far, PSCs that have adopted two‐step sequential deposited perovskite with the state‐of‐art composition (FAPbI₃)_1?x(MAPbBr₃)_x (x < 0.05) have achieved record power conversion efficiency (PCE), while their one‐step antisolvent dripping counterparts with typical composition Cs_0.05FA_0.81MA_0.14Pb(I_0.85Br_0.15)₃ with more bromine have exhibited much better long‐term operational stability. Thus, halogen engineering that aims to elevate bromine content in sequential deposited perovskite film would push operational stability of PSCs toward that of antisolvent dripping deposited perovskite materials. Here, a Br‐rich seeding growth method is devised and perovskite seed solution with high bromine content is introduced into a PbI₂ precursor, leading to bromine incorporation in the resulting perovskite film. Photovoltaic devices fabricated by Br‐rich seeding growth method exhibit a PCE of 21.5%, similar to 21.6% for PSCs having lower bromine content. Whereas, the operational stability of PSCs with higher bromine content is significantly enhanced, with over 80% of initial PCE retained after 500 h tracking at maximum power point under 1‐sun illumination. This work highlights the vital importance of halogen composition for the operational stability of PSCs, and introduces an effective way to incorporate bromine into mixed‐cation‐halide perovskite film via sequential deposition method.     

Challenges in applying microarrays to environmental studies

Although DNA microarray technology has been used successfully to analyze global gene expression in pure cultures, it has not been rigorously tested and evaluated within the context of complex environmental samples. Adapting microarray hybridization for use in environmental studies faces several challenges associated with specificity, sensitivity and quantitation.     

MicroRNAs are dynamically regulated and play an important role in LPS-induced lung injury

Acute lung injury is characterized by an increase of inflammatory reaction and severe lung edema. Even if there have been great advances in the identification of genes and signaling pathways involved in acute lung injury, the fundamental mechanisms of initiation and propagation of acute lung injury have not been understood completely. A growing amount of evidence indicates that microRNAs (miRNAs) are involved in various human diseases. However, the expression profile and function of miRNAs in acute lung injury have not been investigated. Here, using real-time polymerase chain reaction analysis, we show that a collection of miRNAs is dynamically regulated in lipopolysaccharide (LPS)-induced mouse acute lung injury. Among them, miR-199a and miR-16 are the most significantly down-regulated miRNAs. To study the role of miR-199a and miR-16 in acute lung injury, an over-expression of miR-199a or miR-16 assay was performed in LPS-treated A549 cells, and then the expression of inflammatory factors was analyzed. Over-expression of miR-199a could not alter the expression level of interleukin (IL)-6 and tumor necrosis factor-alpha (TNFα), while up-regulation of miR-16 could significantly down-regulate IL-6 and TNFα expression level. Using bioinformatic analysis, we show that a 3' untranslational region (UTR) of IL-6 and TNFα contains the binding sites of miR-16. Accordingly, over-expression of miR-16 could significantly suppress the luciferase activity of reporter fusion with the binding sites of TNFα in its 3'UTR region, suggesting that miR-16 played its role in LPS-induced lung inflammation by a direct manner. In this study, we show for the first time that miRNAs are dynamically regulated and play an important function in LPS-induced lung injury.     

Proteome analysis of sorbitol fermentation specific protein in Vibrio cholerae by 2-DE and MS

Vibrio cholerae can be differentiated into epidemic and non-epidemic strains by sorbitol fermentation speed, but little research has been done on its mechanisms. In this study, we investigated differential protein expression of the two strains in response to sorbitol metabolism. V. cholerae strains were cultured in media with and without sorbitol, respectively. Proteins were separated by 2-DE, and those that showed different expression in the two media were identified by MALDI-TOF MS. Fifteen proteins in epidemic strains and 11 proteins in non-epidemic strains showed a different expression in sorbitol medium. Among them, 4 proteins were common to epidemic and non-epidemic strains. Gene sequence analysis showed that some mutations occurred in these proteins between the two strains. Potential functions of these proteins included sugar uptake, amino acid uptake, electron transport, sulfate and thiosulfate transport.     

Epitranscriptomic technologies and analyses

RNA can interact with RNA-binding proteins(RBPs), mRNA, or other non-coding RNAs(ncRNAs) to form complex regulatory networks. High-throughput CLIP-seq, degradome-seq, and RNA-RNA interactome sequencing methods represent powerful approaches to identify biologically relevant ncRNA-target and protein-ncRNA interactions. However, assigning ncRNAs to their regulatory target genes or interacting RNA-binding proteins(RBPs) remains technically challenging. Chemical modifications to mRNA also play important roles in regulating gene expression. Investigation of the functional roles of these modifications relies highly on the detection methods used. RNA structure is also critical at nearly every step of the RNA life cycle. In this review, we summarize recent advances and limitations in CLIP technologies and discuss the computational challenges of and bioinformatics tools used for decoding the functions and regulatory networks of ncRNAs. We also summarize methods used to detect RNA modifications and to probe RNA structure.