Mechanistic Insights into Dimethylsulfoniopropionate Lyase DddY, a New Member of the Cupin Superfamily

The marine osmolyte dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur molecules. Bacterial DMSP lyases cleave DMSP, producing acrylate and dimethyl sulfide (DMS), a climate-active gas with roles in global sulfur cycling and atmospheric chemistry. DddY is the only known periplasmic DMSP lyase and is present in β-, γ-, δ- and ε-proteobacteria. Unlike other known DMSP lyases, DddY has not been classified into a protein superfamily, and its structure and catalytic mechanism are unknown. Here, we determined the crystal structure of DddY from the γ-proteobacterium Acinetobacter bereziniae originally isolated from human clinical specimens. This structure revealed that DddY contains a cap domain and a catalytic domain with a Zn2 + bound at its active site. We also observed that the DddY catalytic domain adopts a typical β-barrel fold and contains two conserved cupin motifs. Therefore, we concluded that DddY should belong to the cupin superfamily. Using structural and mutational analyses, we identified key residues involved in Zn2 + coordination, DMSP binding and the catalysis of DMSP cleavage, enabling elucidation of the catalytic mechanism, in which the residue Tyr271 of DddY acts as a general base to attack DMSP. Moreover, sequence analysis suggested that this proposed mechanism is common to DddY proteins from β-, γ-, δ- and ε-proteobacteria. The DddY structure and proposed catalytic mechanism provide a better understanding of how DMSP is catabolized to generate the important climate-active gas DMS

Thermally activated delayed fluorescence materials for nondoped organic light-emitting diodes with nearly 100% exciton harvest

Funding: This study was supported by the National Natural Science Foundation of China (Nos. 52130304, 51821002, 52003185, and 52003186), the National Key Research & Development Program of China (Nos. 2020YFA0714601 and 2020YFA0714604), Suzhou Key Laboratory of Functional Nano & Soft Materials, Collaborative Innovation Center of Suzhou Nano Science & Technology, and the 111 Project.High-performance nondoped organic light-emitting diodes (OLEDs) are promising technologies for future commercial applications. Herein, we synthesized two new thermally activated delayed fluorescence (TADF) emitters that enable us, for the first time, to combine three effective approaches for enhancing the efficiency of nondoped OLEDs. First, the two emitters are designed to have high steric hindrances such that their emitting cores will be suitably isolated from those of their neighbors to minimize concentration quenching. On the other hand, each of the two emitters has two stable conformations in solid films. In their neat films, molecules with the minority conformation behave effectively as dopants in the matrix composing of the majority conformation. One hundred percent exciton harvesting is thus theoretically feasible in this unique architecture of "self-doped" neat films. Furthermore, both emitters have relatively high aspect ratios in terms of their molecular shapes. This leads to films with preferred molecular orientations enabling high populations of horizontal dipoles beneficial for optical out-coupling. With these three factors, OLEDs with nondoped emitting layers of the respective emitters both achieve nearly 100% exciton utilization and deliver over 30% external quantum efficiencies and ultralow efficiency roll-off at high brightness, which have not been observed in reported nondoped OLEDs.Publisher PDFPeer reviewe

Characterization of a cryptic plasmid pSM429 and its application for heterologous expression in psychrophilic Pseudoalteromonas

<p>Abstract</p> <p>Background</p> <p><it>Pseudoalteromonas </it>is an important genus widespread in marine environment, and a lot of psychrophilic <it>Pseudoalteromonas </it>strains thrive in deep sea and polar sea. By now, there are only a few genetic systems for <it>Pseudoalteromonas </it>reported and no commercial <it>Pseudoalteromonas </it>genetic system is available, which impedes the study of <it>Pseudoalteromonas</it>, especially for psychrophilic strains. The aim of this study is to develop a heterologous expression system for psychrophilic <it>Pseudoalteromonas</it>.</p> <p>Results</p> <p>A cryptic plasmid pSM429 isolated from psychrophilic <it>Pseudoalteromonas </it>sp. BSi20429 from the Arctic sea ice, was sequenced and characterized. The plasmid pSM429 is 3874 bp in length, with a G+C content of 28%. Four putative open reading frames (ORFs) were identified on pSM429. Based on homology, the ORF4 was predicted to encode a replication initiation (Rep) protein. A shuttle vector (<it>Escherichia coli, Pseudoalteromonas</it>), pWD, was constructed by ligating pSM429 and pUC19 and inserting a chloramphenicol acetyl transferase (CAT) cassette conferring chloramphenicol resistance. To determine the minimal replicon of pSM429 and to check the functionality of identified ORFs, various pWD derivatives were constructed. All derivatives except the two smallest ones were shown to allow replication in <it>Pseudoalteromonas </it>sp. SM20429, a plasmid-cured strain of <it>Pseudoalteromonas </it>sp. BSi20429, suggesting that the <it>orf4 </it>and its flanking intergenic regions are essential for plasmid replication. Although not essential, the sequence including some repeats between <it>orf1 </it>and <it>orf2 </it>plays important roles in segregational stability of the plasmid. With the aid of pWD-derived plasmid pWD2, the erythromycin resistance gene and the <it>cd </it>gene encoding the catalytic domain of a cold-adapted cellulase were successfully expressed in <it>Pseudoalteromonas </it>sp. SM20429.</p> <p>Conclusions</p> <p>Plasmid pSM429 was isolated and characterized, and the regions essential for plasmid replication and stability were determined, helping the development of pSM429-based shuttle vectors. The shuttle vectors pWD and its derivatives could be used as cloning vectors for <it>Pseudoalteromonas</it>, offering new perspectives in the genetic manipulation of <it>Pseudoalteromonas </it>strains. With the aid of pWD-derived vector and its host, the erythromycin resistance gene and the <it>cd </it>gene of a cold-adapted protein were successfully expressed, indicating that the potential use of this system for recombinant protein production, especially for cold-adapted proteins.</p

Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N -oxide

Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are widespread in the ocean and are important nitrogen source for bacteria. TMA monooxygenase (Tmm), a bacterial flavin-containing monooxygenase (FMO), is found widespread in marine bacteria and is responsible for converting TMA to TMAO. However, the molecular mechanism of TMA oxygenation by Tmm has not been explained. Here, we determined the crystal structures of two reaction intermediates of a marine bacterial Tmm (RnTmm) and elucidated the catalytic mechanism of TMA oxidation by RnTmm. The catalytic process of Tmm consists of a reductive half-reaction and an oxidative half-reaction. In the reductive half-reaction, FAD is reduced and a C4a-hydroperoxyflavin intermediate forms. In the oxidative half-reaction, this intermediate attracts TMA through electronic interactions. After TMA binding, NADP+ bends and interacts with D317, shutting off the entrance to create a protected micro-environment for catalysis and exposing C4a-hydroperoxyflavin to TMA for oxidation. Sequence analysis suggests that the proposed catalytic mechanism is common for bacterial Tmms. These findings reveal the catalytic process of TMA oxidation by marine bacterial Tmm and first show that NADP+ undergoes a conformational change in the oxidative half-reaction of FMOs

Experimental Gaussian Boson Sampling

Gaussian Boson sampling (GBS) provides a highly efficient approach to make use of squeezed states from parametric down-conversion to solve a classically hard-to-solve sampling problem. The GBS protocol not only significantly enhances the photon generation probability, compared to standard boson sampling with single photon Fock states, but also links to potential applications such as dense subgraph problems and molecular vibronic spectra. Here, we report the first experimental demonstration of GBS using squeezed-state sources with simultaneously high photon indistinguishability and collection efficiency. We implement and validate 3-, 4- and 5-photon GBS with high sampling rates of 832 kHz, 163 kHz and 23 kHz, respectively, which is more than 4.4, 12.0, and 29.5 times faster than the previous experiments. Further, we observe a quantum speed-up on a NP-hard optimization problem when comparing with simulated thermal sampler and uniform sampler.Comment: 12 pages, 4 figures, published online on 2nd April 201

A Preliminary Investigation of PVT1 on the Effect and Mechanisms of Hepatocellular Carcinoma: Evidence from Clinical Data, a Meta-Analysis of 840 Cases, and In Vivo Validation

Background/Aims: Hepatocellular carcinoma (HCC) remains a difficult problem that significantly affects the survival of the afflicted patients. Accumulating evidence has demonstrated the functions of long non-coding RNA (lncRNA) in HCC. In the present study, we aimed to explore the potential roles of PVT1 in the tumorigenesis and progression of HCC. Methods: In this study, quantitative reverse transcription-polymerase chain reaction (RT-qPCR) was applied to detect the differences between PVT1 expression in HCC tissues and cell lines. Then, the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were searched to confirm the relationship between PVT1 expression and HCC. Moreover, a meta-analysis comprising TCGA, GEO, and RT-qPCR was applied to estimate the expression of PVT1 in HCC. Then, cell proliferation was evaluated in vitro. A chicken chorioallantoic membrane (CAM) model of HCC was constructed to measure the effect on tumorigenicity in vivo. To further explore the sponge microRNA (miRNA) of PVT1 in HCC, we used TCGA, GEO, a gene microarray, and target prediction algorithms. TCGA and GEO and the gene microarray were used to select the differentially expressed miRNAs, and the different target prediction algorithms were applied to predict the target miRNAs of PVT1. Results: We found that PVT1 was markedly overexpressed in HCC tissue than in normal liver tissues based on both RT-qPCR and data from TCGA, and the overexpression of PVT1 was closely related to the gender and race of the patient as well as to higher HCC tumor grades. Also, a meta-analysis of 840 cases from multiple sources (TCGA, GEO and the results of our in-house RT-qPCR) showed that PVT1 gained moderate value in discriminating HCC patients from normal controls, confirming the results of RT-qPCR. Additionally, the upregulation of PVT1 could promote HCC cell proliferation in vitro and vivo. Based on the competing endogenous RNA (ceRNA) theory, the PVT1/miR-424-5p/INCENP axis was finally selected for further research. The in silico prediction revealed that there were complementary sequences between PVT1 and miR-424-5p as well as between miR-424-5p and INCENP. Furthermore, a negative correlation trend was found between miR-424-5p and PVT1 based on RT-qPCR, whereas a positive correlation trend was found between PVT1 and INCENP based on data from TCGA. Also, INCENP small interfering RNA (siRNA) could significantly inhibit cell proliferation and viability. Conclusions: We hypothesized that PVT1 could affect the biological function of HCC cells via targeting miR-424-5p and regulating INCENP. Focusing on the new insight of the PVT1/miR-424-5p/INCENP axis, this study provides a novel perspective for HCC therapeutic strategies

Structure of cryptophyte photosystem II-light-harvesting antennae supercomplex.

Cryptophytes are ancestral photosynthetic organisms evolved from red algae through secondary endosymbiosis. They have developed alloxanthin-chlorophyll a/c2-binding proteins (ACPs) as light-harvesting complexes (LHCs). The distinctive properties of cryptophytes contribute to efficient oxygenic photosynthesis and underscore the evolutionary relationships of red-lineage plastids. Here we present the cryo-electron microscopy structure of the Photosystem II (PSII)-ACPII supercomplex from the cryptophyte Chroomonas placoidea. The structure includes a PSII dimer and twelve ACPII monomers forming four linear trimers. These trimers structurally resemble red algae LHCs and cryptophyte ACPI trimers that associate with Photosystem I (PSI), suggesting their close evolutionary links. We also determine a Chl a-binding subunit, Psb-γ, essential for stabilizing PSII-ACPII association. Furthermore, computational calculation provides insights into the excitation energy transfer pathways. Our study lays a solid structural foundation for understanding the light-energy capture and transfer in cryptophyte PSII-ACPII, evolutionary variations in PSII-LHCII, and the origin of red-lineage LHCIIs

Biological Effect and Mechanism of the miR-23b-3p/ANXA2 Axis in Pancreatic Ductal Adenocarcinoma

Background/Aims: Accumulating evidence strongly suggests that microRNAs (miRNAs) modulate the expression of known tumor suppressor genes and oncogenes. In the present study, we found that the proliferation and invasion ability of pancreatic ductal adenocarcinoma (PDAC) cells were significantly suppressed by the overexpression of miR-23b-3p. In addition, there are miR-23b-3p binding sites in annexin A2 (ANXA2). Here, we investigated whether miR-23b-3p had an impact on the progression and metastasis of PDAC by targeting ANXA2. Methods: Cell proliferation, migration, and invasion, and cell cycle assays were performed to explore the effect of miR-23b-3p on various malignant phenotypes of pancreatic cancer cells. The size of tumors was observed following miR-23b-3p overexpression in an in vivo chick chorioallantoic membrane assay. Dual-luciferase reporter, quantitative real-time PCR, western blot, and immunohistochemical analyses were used to validate the relationship between miR-23b-3p and ANXA2 in vitro. Results: We observed that miR-23b-3p could bind specifically to the 3′ untranslated region of ANXA2 and inhibit its expression. MiR-23b-3p overexpression downregulated the expression of ANXA2 mRNA in PDAC cells and limited the size of tumors or even prevented tumor formation. In addition, there was a negative correlation between miR-23b-3p expression and ANXA2 protein expression in clinical specimens. Conclusion: MiR-23b-3p inhibits the development and progression of PDAC by regulating ANXA2 directly