Bacteriophage Twort protein Gp168 is a ß-clamp inhibitor by occupying the DNA sliding channel.

Bacterial chromosome replication is mainly catalyzed by DNA polymerase III, whose beta subunits enable rapid processive DNA replication. Enabled by the clamp-loading complex, the two beta subunits form a ring-like clamp around DNA and keep the polymerase sliding along. Given the essential role of ß-clamp, its inhibitors have been explored for antibacterial purposes. Similarly, ß-clamp is an ideal target for bacteriophages to shut off host DNA synthesis during host takeover. The Gp168 protein of phage Twort is such an example, which binds to the ß-clamp of Staphylococcus aureus and prevents it from loading onto DNA causing replication arrest. Here, we report a cryo-EM structure of the clamp-Gp168 complex at 3.2-Å resolution. In the structure of the complex, the Gp168 dimer occupies the DNA sliding channel of ß-clamp and blocks its loading onto DNA, which represents a new inhibitory mechanism against ß-clamp function. Interestingly, the key residues responsible for this interaction on the ß-clamp are well conserved among bacteria. We therefore demonstrate that Gp168 is potentially a cross-species ß-clamp inhibitor, as it forms complex with the Bacillus subtilis ß-clamp. Our findings reveal an alternative mechanism for bacteriophages to inhibit ß-clamp and provide a new strategy to combat bacterial drug resistance.

Systemic Expression, Purification, and Initial Structural Characterization of Bacteriophage T4 Proteins Without Known Structure Homologs.

Bacteriophage T4 of Escherichia coli is one of the most studied phages. Research into it has led to numerous contributions to phage biology and biochemistry. Coding about 300 gene products, this double-stranded DNA virus is the best-understood model in phage study and modern genomics and proteomics. Ranging from viral RNA polymerase, commonly found in phages, to thymidylate synthase, whose mRNA requires eukaryotic-like self-splicing, its gene products provide a pool of fine examples for phage research. However, there are still up to 130 gene products that remain poorly characterized despite being one of the most-studied model phages. With the recent advancement of cryo-electron microscopy, we have a glimpse of the virion and the structural proteins that present in the final assembly. Unfortunately, proteins participating in other stages of phage development are absent. Here, we report our systemic analysis on 22 of these structurally uncharacterized proteins, of which none has a known homologous structure due to the low sequence homology to published structures and does not belong to the category of viral structural protein. Using NMR spectroscopy and cryo-EM, we provided a set of preliminary structural information for some of these proteins including NMR backbone assignment for Cef. Our findings pave the way for structural determination for the phage proteins, whose sequences are mainly conserved among phages. While this work provides the foundation for structural determinations of proteins like Gp57B, Cef, Y04L, and Mrh, other in vitro studies would also benefit from the high yield expression of these proteins.

Multicore-Processor Based Software-Defined Communication/Network Platform for Underwater Internet of Things.

Software-defined acoustic modems (SDAMs) for underwater communication and networking have been an important research topic due to their flexibility and programmability. In this paper, we propose a reconfigurable platform for SDAMs based on the TI AM5728 processor, which integrates dual-core ARM Cortex-A15 CPUs and two TI C66x DSP cores. The signal processing and A/D, D/A for physical-layer communication are implemented in the DSP cores. The networking protocols and the application programs are implemented in the ARM cores. The proposed platform has the following characteristics: (1) Due to the high-performance dual-ARM cores, the whole NS3 network simulator can be run in the ARM cores. Network protocols developed in a software simulation platform (e.g., NS3 platform) can be seamlessly migrated to a hardware platform without modification. (2) A new physical-layer module associated with real acoustic channel is developed, such that a data packet generated from the application layer will be transmitted through a real acoustic channel. The results of networking experiments with five nodes are presented to demonstrate the effectiveness of the proposed platform.

M-SAC-VLADNet: A Multi-Path Deep Feature Coding Model for Visual Classification.

Vector of locally aggregated descriptor (VLAD) coding has become an efficient feature coding model for retrieval and classification. In some recent works, the VLAD coding method is extended to a deep feature coding model which is called NetVLAD. NetVLAD improves significantly over the original VLAD method. Although the NetVLAD model has shown its potential for retrieval and classification, the discriminative ability is not fully researched. In this paper, we propose a new end-to-end feature coding network which is more discriminative than the NetVLAD model. First, we propose a sparsely-adaptive and covariance VLAD model. Next, we derive the back propagation models of all the proposed layers and extend the proposed feature coding model to an end-to-end neural network. Finally, we construct a multi-path feature coding network which aggregates multiple newly-designed feature coding networks for visual classification. Some experimental results show that our feature coding network is very effective for visual classification.