AcrIIA28 is a metalloprotein that specifically inhibits targeted-DNA loading to SpyCas9 by binding to the REC3 domain.

CRISPR-Cas systems serve as adaptive immune systems in bacteria and archaea, protecting against phages and other mobile genetic elements. However, phages and archaeal viruses have developed countermeasures, employing anti-CRISPR (Acr) proteins to counteract CRISPR-Cas systems. Despite the revolutionary impact of CRISPR-Cas systems on genome editing, concerns persist regarding potential off-target effects. Therefore, understanding the structural and molecular intricacies of diverse Acrs is crucial for elucidating the fundamental mechanisms governing CRISPR-Cas regulation. In this study, we present the structure of AcrIIA28 from Streptococcus phage Javan 128 and analyze its structural and functional features to comprehend the mechanisms involved in its inhibition of Cas9. Our current study reveals that AcrIIA28 is a metalloprotein that contains Zn2+ and abolishes the cleavage activity of Cas9 only from Streptococcus pyrogen (SpyCas9) by directly interacting with the REC3 domain of SpyCas9. Furthermore, we demonstrate that the AcrIIA28 interaction prevents the target DNA from being loaded onto Cas9. These findings indicate the molecular mechanisms underlying AcrIIA28-mediated Cas9 inhibition and provide valuable insights into the ongoing evolutionary battle between bacteria and phages.

Novel structure of secreted small molecular weight antigen Mtb12 from Mycobacterium tuberculosis.

Mtb12, a small protein secreted by Mycobacterium tuberculosis, is known to elicit immune responses in individuals infected with the pathogen. It serves as an antigen recognized by the host's immune system. Due to its immunogenic properties and pivotal role in tuberculosis (TB) pathogenesis, Mtb12 is considered a promising candidate for TB diagnosis and vaccine development. However, the structural and functional properties of Mtb12 are largely unexplored, representing a significant gap in our understanding of M. tuberculosis biology. In this study, we present the first structure of Mtb12, which features a unique tertiary configuration consisting of four beta strands and four alpha helices. Structural analysis reveals that Mtb12 has a surface adorned with a negatively charged pocket adjacent to a central cavity. The features of these structural elements and their potential effects on the function of Mtb12 warrant further exploration. These findings offer valuable insights for vaccine design and the development of diagnostic tools.

Novel structure of the anti-CRISPR protein AcrIE3 and its implication on the CRISPR-Cas inhibition.

As a response to viral infections, bacteria have evolved the CRISPR-Cas system as an adaptive immune mechanism, enabling them to target and eliminate viral genetic material introduced during infection. However, viruses have also evolved mechanisms to counteract this bacterial defense, including anti-CRISPR proteins, which can inactivate the CRISPR-Cas adaptive immune system, thus aiding the viruses in their survival and replication within bacterial hosts. In this study, we establish the high-resolution crystal structure of the Type IE anti-CRISPR protein, AcrIE3. Our structural examination showed that AcrIE3 adopts a helical bundle fold comprising four α-helices, with a notably extended loop at the N-terminus. Additionally, surface analysis of AcrIE3 revealed the presence of three acidic regions, which potentially play a crucial role in the inhibitory function of this protein. The structural information we have elucidated for AcrIE3 will provide crucial insights into fully understanding its inhibitory mechanism. Furthermore, this information is anticipated to be important for the application of the AcrIE family in genetic editing, paving the way for advancements in gene editing technologies.

Molecular basis of anti-CRISPR operon repression by Aca10.

CRISPR-Cas systems are bacterial defense systems for fighting against invaders such as bacteriophages and mobile genetic elements. To escape destruction by these bacterial immune systems, phages have co-evolved multiple anti-CRISPR (Acr) proteins, which inhibit CRISPR-Cas function. Many acr genes form an operon with genes encoding transcriptional regulators, called anti-CRISPR-associated (Aca) proteins. Aca10 is the most recently discovered Aca family that is encoded within an operon containing acrIC7 and acrIC6 in Pseudomonas citronellolis. Here, we report the high-resolution crystal structure of an Aca10 protein to unveil the molecular basis of transcriptional repressor role of Aca10 in the acrIC7-acrIC6-aca10 operon. We identified that Aca10 forms a dimer in solution, which is critical for binding specific DNA. We also showed that Aca10 directly recognizes a 21 bp palindromic sequence in the promoter of the acr operon. Finally, we revealed that R44 of Aca10 is a critical residue involved in the DNA binding, which likely results in a high degree of DNA bending.

Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24.

CRISPR-Cas systems are adaptive immune systems in bacteria and archaea that provide resistance against phages and other mobile genetic elements. To fight against CRISPR-Cas systems, phages and archaeal viruses encode anti-CRISPR (Acr) proteins that inhibit CRISPR-Cas systems. The expression of acr genes is controlled by anti-CRISPR-associated (Aca) proteins encoded within acr-aca operons. AcrIF24 is a recently identified Acr that inhibits the type I-F CRISPR-Cas system. Interestingly, AcrIF24 was predicted to be a dual-function Acr and Aca. Here, we elucidated the crystal structure of AcrIF24 from Pseudomonas aeruginosa and identified its operator sequence within the regulated acr-aca operon promoter. The structure of AcrIF24 has a novel domain composition, with wing, head and body domains. The body domain is responsible for recognition of promoter DNA for Aca regulatory activity. We also revealed that AcrIF24 directly bound to type I-F Cascade, specifically to Cas7 via its head domain as part of its Acr mechanism. Our results provide new molecular insights into the mechanism of a dual functional Acr-Aca protein.

Molecular basis of neurodevelopmental disorders caused by pathogenic variants of PIDD.

PIDDosome formation followed by caspase-2 activation is critical for genotoxic stress-induced apoptotic cell death. Failure of proper caspase-2 activation causes a neurodevelopmental disorder and intellectual disability. R815W, R862W, and Q863stop mutations in p53-induced protein with a death domain (PIDD), a component of the PIDDosome, also lead to this disorder. However, the molecular mechanisms underlying this pathogenesis remain elusive. In this study, we analyzed the molecular mechanisms underlying the pathogenesis of the PIDD DD pathogenic variants R815W, R862W, and Q863stop. We determined that these mutations prevented the interaction between PIDD and RIP-associated Ich-1/Ced-3 homologous protein with a death domain (RAIDD), a molecule that mediates PIDDosome formation. The disruption of this interaction affects PIDDosome formation and caspase-2 activation.

Structure of YdjH from Acinetobacter baumannii revealed an active site of YdjH family sugar kinase.

Bacterial sugar kinase is a central enzyme for proper sugar degradation in bacteria, essential for survival and growth. Therefore, this enzyme family is a primary target for antibacterial drug development, with YdjH most preferring to phosphorylate higher-order monosaccharides with a carboxylate terminus. Sugar kinases express diverse specificity and functions, making specificity determination of this family a prominent issue. This study examines the YdjH crystal structure from Acinetobacter baumannii (abYdjH), which has an exceptionally high antibiotic resistance and is considered a superbug. Our structural and biochemical study revealed that abYdjH has a widely open lid domain and is a solution dimer. In addition, the putative active site of abYdjH was determined based on structural analysis, sequence comparison, and in silico docking. Finally, we proposed the active site-forming residues that determine various sugar specificities from abYdjH. This study contributes towards a deeper understanding of the phosphorylation process and bacterial sugar metabolism of YdjH family to design the next-generation antibiotics for targeting A. baumannii.

The structure of MucD from Pseudomonas syringae revealed N-terminal loop-mediated trimerization of HtrA-like serine protease.

Protein quality control mechanisms are essential for maintaining cellular integrity, and the HtrA family of serine proteases plays a crucial role in handling folding stress in prokaryotic periplasm. Escherichia coli harbors three HtrA members, namely, DegS, DegP, and DegQ, which share a common domain structure. MucD, a putative HtrA family member that resembles DegP, is involved in alginate biosynthesis regulation and the stress response. Pseudomonas syringae causes plant diseases and opportunistic infections in humans. This study presents the high-resolution structure of MucD from Pseudomonas syringae (psMucD), revealing its composition as a typical HtrA family serine protease with protease and PDZ domains. Its findings suggest that psMucD containing one PDZ domain is a trimer in solution, and psMucD trimerization is mediated by its N-terminal loop. Sequence and structural analyses revealed similarities and differences with other HtrA family members. Additionally, this study provides a model of psMucD's catalytic process, comparing it with other members of the HtrA family of serine proteases.

Structure of fish TRAF4 and its implication in TRAF4-mediated immune cell and platelet signaling.

Due to an increasing interest in immunity and signal transduction in teleost fish, important key signaling molecules associated with the immune response, including TRAF molecules, have been recently cloned and characterized. To better understand the role of TRAF4 in fish immune signaling and compare it with the human system, our study cloned the TRAF4 gene from the Antarctic yellowbelly rockcod Notothenia coriiceps (ncTRAF4) and purified the protein. Here, we report the first crystal structure of teleost fish TRAF4. Based on biochemical characterization, our findings elucidated the mechanisms through which signaling molecules gain cold adaptivity. Additionally, we identified a platelet receptor GPIbß homolog in N. coriiceps (ncGPIbß) and found that the "RRFERLFKEARRTS" region of this homolog directly binds to ncTRAF4, indicating that ncTRAF4 also recognizes the "RLXA" motif for receptor interactions and further TARF4-mediated cellular signaling. Collectively, our findings provide novel insights into the mechanisms of TRAF4-mediated immune cell and platelet signaling in fish and the structural flexibility-mediated cold adaptiveness of signaling molecules.

High-resolution crystal structure of Acinetobacter baumannii thioredoxin 1.

Thioredoxin (Trx) is a central component of the redox control system that maintains the redox homeostasis critical for organism survival. Owing to its central role in survival, Trx is a prospective target for novel antimicrobial agents. Herein, we report a 1.45 Å high-resolution structure of Trx1 of Acinetobacter baumannii (abTrx1), an antibiotic-resistant pathogenic superbug. Although abTrx1 exhibited the canonical Trx fold, which consists of a four-stranded ß-sheet surrounded by four α-helices, structural differences were detected in the loop forming the C-X-X-C redox center and the C-terminal. The unique CAPC sequence of the C-X-X-C motif in the abTrx1 redox center was characterized by mutagenesis. This study contributes to the field of drug designing against superbugs.

High-resolution crystal structure of the anti-CRISPR protein AcrIC5.

As a result of the long-term battle of bacteria and archaea against invaders such as viruses and genetic mobile elements, they have developed CRISPR-Cas systems for self-defense, which allows them to remove the viral genetic material introduced into host cells via infection. To fight against this bacterial immune system, however, viruses have also evolved to produce multiple anti-CRISPR proteins that can inhibit the bacterial CRISPR-Cas system. In this study, we introduced a tentative inhibitory activity against a type I-C CRISPR-Cas system by determining the crystal structure of AcrIC5 from Pseudomonas delhiensis. Structural analysis revealed that AcrIC5 was composed of noble folds comprising two antiparallel sheets and three helices. Although AcrIC5 did not directly interact with either the type I-C cascade from Neisseria lactamia or the type I-F cascade from Pseudomonas aeruginosa in our analysis, a highly acidic surface feature indicated that AcrIC5 may be DNA mimic Acrs that directly binds to the target DNA binding site in type I-C cascade and inhibits the recruitment of the target DNA to this cascade.

Structural basis for the substrate specificity of an S-formylglutathione hydrolase derived from Variovorax sp. PAMC 28711.

S-Formylglutathione hydrolase was originally known to catalyze the hydrolysis of S-formylglutathione to formate and glutathione. However, this enzyme has a broader esterase activity toward substrates containing thioester and ester bonds. In a previous study, we identified a new S-formylglutathione hydrolase (VaSFGH) gene in the Antarctic bacterium Variovorax sp. PAMC 28711, and recombinant VaSFGH protein was purified and characterized. Previous enzyme activity assays showed that VaSFGH has high activity, especially toward short-chain p-nitrophenyl esters (C2-C4). In this study, we determined the crystal structure of substrate-free VaSFGH at a resolution of 2.38 Å. In addition, p-nitrophenyl ester-bound VaSFGH structure models were generated by molecular docking simulations to obtain structural evidence of its substrate specificity. Comparative structural analysis of the apo-form and p-nitrophenyl ester-bound VaSFGH model structures revealed that large substrates could not bind inside the hydrophobic substrate-binding pocket because of the intrinsically static and relatively small substrate-binding pocket size of VaSFGH. This study provides useful information for further protein engineering of SFGHs for industrial use.

Crystal structure of a novel putative sugar isomerase from the psychrophilic bacterium Paenibacillus sp. R4.

Sugar isomerases (SIs) catalyze the reversible conversion of aldoses to ketoses. A novel putative SI gene has been identified from the genome sequence information on the psychrophilic bacterium Paenibacillus sp. R4. Here, we report the crystal structure of the putative SI from Paenibacillus sp. R4 (PbSI) at 2.98 Å resolution. It was found that the overall structure of PbSI adopts the triose-phosphate isomerase (TIM) barrel fold. PbSI was also identified to have two heterogeneous metal ions as its cofactors at the active site in the TIM barrel, one of which was confirmed as a Zn ion through X-ray anomalous scattering and inductively coupled plasma mass spectrometry analysis. Structural comparison with homologous SI proteins from mesophiles, hyperthermophiles, and a psychrophile revealed that key residues in the active site are well conserved and that dimeric PbSI is devoid of the extended C-terminal region, which tetrameric SIs commonly have. Our results provide novel structural information on the cold-adaptable SI, including information on the metal composition in the active site.

Synthesis and Electrochemical Performance of Electrostatic Self-Assembled Nano-Silicon@N-Doped Reduced Graphene Oxide/Carbon Nanofibers Composite as Anode Material for Lithium-Ion Batteries.

Silicon-carbon nanocomposite materials are widely adopted in the anode of lithium-ion batteries (LIB). However, the lithium ion (Li+) transportation is hampered due to the significant accumulation of silicon nanoparticles (Si) and the change in their volume, which leads to decreased battery performance. In an attempt to optimize the electrode structure, we report on a self-assembly synthesis of silicon nanoparticles@nitrogen-doped reduced graphene oxide/carbon nanofiber (Si@N-doped rGO/CNF) composites as potential high-performance anodes for LIB through electrostatic attraction. A large number of vacancies or defects on the graphite plane are generated by N atoms, thus providing transmission channels for Li+ and improving the conductivity of the electrode. CNF can maintain the stability of the electrode structure and prevent Si from falling off the electrode. The three-dimensional composite structure of Si, N-doped rGO, and CNF can effectively buffer the volume changes of Si, form a stable solid electrolyte interface (SEI), and shorten the transmission distance of Li+ and the electrons, while also providing high conductivity and mechanical stability to the electrode. The Si@N-doped rGO/CNF electrode outperforms the Si@N-doped rGO and Si/rGO/CNF electrodes in cycle performance and rate capability, with a reversible specific capacity reaching 1276.8 mAh/g after 100 cycles and a Coulomb efficiency of 99%.

Loss-of-function of EBP50 is a new cause of hereditary peripheral neuropathy: EBP50 functions in peripheral nerve system.

Finding causative genetic mutations is important in the diagnosis and treatment of hereditary peripheral neuropathies. This study was conducted to find new genes involved in the pathophysiology of hereditary peripheral neuropathy. We identified a new mutation in the EBP50 gene, which is co-segregated with neuropathic phenotypes, including motor and sensory deficit in a family with Charcot-Marie-Tooth disease. EBP50 is known to be important for the formation of microvilli in epithelial cells, and the discovery of this gene mutation allowed us to study the function of EBP50 in the nervous system. EBP50 was strongly expressed in the nodal and paranodal regions of sciatic nerve fibers, where Schwann cell microvilli contact the axolemma, and at the growth tips of primary Schwann cells. In addition, EBP50 expression was decreased in mouse models of peripheral neuropathy. Knockout mice were used to study EBP50 function in the peripheral nervous system. Interestingly motor function deficit and abnormal histology of nerve fibers were observed in EBP50+/- heterozygous mice at 12 months of age, but not 3 months. in vitro studies using Schwann cells showed that NRG1-induced AKT activation and migration were significantly reduced in cells overexpressing the I325V mutant of EBP50 or cells with knocked-down EBP50 expression. In conclusion, we show for the first time that loss of function due to EBP50 gene deficiency or mutation can cause peripheral neuropathy.

A 1.3 Å high-resolution crystal structure of an anti-CRISPR protein, AcrI E2.

As a result of bacterial infection with viruses, bacteria have developed CRISPR-Cas as an adaptive immune system, which allows them to destroy the viral genetic material introduced via infection. However, viruses have also evolved to develop multiple anti-CRISPR proteins, which are capable of inactivating the CRISPR-Cas adaptive immune system to combat bacteria. In this study, we aimed to elucidate the molecular mechanisms associated with anti-CRISPR proteins by determining a high-resolution crystal structure (1.3 Å) of Type I-E anti-CRISPR protein called AcrIE2. Our structural analysis revealed that AcrIE2 was composed of unique folds comprising five antiparallel ß-sheets (ß1∼ß5) surrounding one α-helix (α1) in the order, ß2ß1α1ß5ß4ß3. Structural comparison of AcrIE2 with a structural homolog called AcrIF9 showed that AcrIE2 contained a long and flexible ß4-ß5 connecting loop and a distinct surface feature. These results indicated that the inhibitory mechanism of AcrIE2 might be different from that of AcrIF9. This unique structure of AcrIE2 indicates its special mode of CRISPR-Cas inhibitory activity. Therefore, this study helps us understand the diversity in the inhibitory mechanisms of Acr family.

Crystal structure of the reactive intermediate/imine deaminase A homolog from the Antarctic bacterium Psychrobacter sp. PAMC 21119.

The RidA subfamily proteins catalyze the deamination reaction of enamine/imine intermediates, which are metabolites of amino acids such as threonine and serine. Numerous structural and functional studies have been conducted on RidA isolated from mesophiles and thermophiles. However, little is known about the structure of the RidA proteins isolated from psychrophiles. In the present study, we elucidated the crystal structure of RidA from the Antarctic bacterium Psychrobacter sp. PAMC 21119 (Pp-RidA) at 1.6 Å resolution to identify the structural properties contributing to cold-adaptability. Although the overall structure of Pp-RidA is similar to those of its homologues, it exhibits specific structural arrangements of a loop positioned near the active site, which is assumed to play a role in covering the active site of catalysis. In addition, the surface electrostatic potential of Pp-RidA suggested that it exhibits stronger electrostatic distribution relative to its homologues. Our results provide novel insights into the key determinants of cold-adaptability.

Heat dissipative mechanical damping properties of EPDM rubber composites including hybrid fillers of aluminium nitride and boron nitride.

As highly integrated electronic devices and automotive parts are becoming used in high-power and load-bearing systems, thermal conductivity and mechanical damping properties have become critical factors. In this study, we applied two different fillers of aluminium nitride (AlN) and boron nitride (BN), having polygonal and platelet shapes, respectively, into ethylene-propylene-diene monomer (EPDM) rubber to ensure improved thermo-mechanical properties of EPDM composites. These two different shapes are considered advantageous in providing effective pathways of phonon transfer as well as facilitating sliding movement of packed particles. When the volume ratio of AlN : BN was 1 : 1, the thermal conductivity of the hybrid-filler system (EPDM/AlN/BN) increased in comparison to that of the single-filler system (EPDM/AlN) of 3.03 to 4.76 W m-1 K-1. The coefficient of thermal expansion (CTE) and thermal distortion parameter (TDP) substantially decreased from 59.3 ppm °C-1 and 17.5 m K-1 of EPDM/AlN, to 39.7 ppm °C-1 and 8.4 m K-1 of EPDM/AlN/BN, representing reductions of 33 and 52%, respectively. Moreover, the damping coefficient of EPDM/AlN/BN was greatly increased to 0.5 of at 50 °C, compared to 0.03 of neat EPDM. These excellent performances likely stem from the effective packing of AlN/BN hybrid fillers, which could induce facile energy transfer and effective energy dissipation by the sliding movement of the adjacent hybrid fillers in the EPDM matrix.

Structural and biochemical characterization of TRAF5 from Notothenia coriiceps and its implications in fish immune cell signaling.

Conserved immune cell signaling in fish was recently highlighted by the identification of various immune cell signaling molecules. Tumor necrosis factor (TNF) receptor-associated factor (TRAF) proteins are critical adaptor molecules in immune cell signaling and contain E3 ubiquitin ligase activity. Here, we report the first crystal structure of the TRAF5 TRAF domain from the black rockcod (Notothenia coriiceps; ncTRAF5). Our structure revealed both similarities and differences with mammalian TRAF5. Structural and biochemical analyses indicated that ncTRAF5 forms a functional trimer unit in solution, with a structural flexibility that might be critical for imparting resistance to cold temperature-induced stress. We also found conserved surface residues on ncTRAF5 that might be critical binding hot spots for interaction with various receptors.

Molecular basis for unique specificity of human TRAF4 for platelets GPIbß and GPVI.

Tumor necrosis factor (TNF)-receptor associated factor 4 (TRAF4), an adaptor protein with E3-ligase activity, is involved in embryogenesis, cancer initiation and progression, and platelet receptor (GPIb-IX-V complex and GPVI)-mediated signaling for reactive oxygen species (ROS) production that initiates thrombosis at arterial shears. Disruption of platelet receptors and the TRAF4 interaction is a potential target for therapeutic intervention by antithrombotic drugs. Here, we report a crystal structure of TRAF4 (amino acid residues 290∼470) in complex with a peptide from the GPIbß receptor (amino acid residues 177∼181). The GPIbß peptide binds to a unique shallow surface composed of two hydrophobic pockets on TRAF4. Further studies revealed the TRAF4-binding motif Arg-Leu-X-Ala. The TRAF4-binding motif was present not only in platelet receptors but also in the TGF-ß receptor. The current structure will provide a template for furthering our understanding of the receptor-binding specificity of TRAF4, TRAF4-mediated signaling, and related diseases.