Structural and functional investigation of GajB protein in Gabija anti-phage defense.

Bacteriophages (phages) are viruses that infect bacteria and archaea. To fend off invading phages, the hosts have evolved a variety of anti-phage defense mechanisms. Gabija is one of the most abundant prokaryotic antiviral systems and consists of two proteins, GajA and GajB. GajA has been characterized experimentally as a sequence-specific DNA endonuclease. Although GajB was previously predicted to be a UvrD-like helicase, its function is unclear. Here, we report the results of structural and functional analyses of GajB. The crystal structure of GajB revealed a UvrD-like domain architecture, including two RecA-like core and two accessory subdomains. However, local structural elements that are important for the helicase function of UvrD are not conserved in GajB. In functional assays, GajB did not unwind or bind various types of DNA substrates. We demonstrated that GajB interacts with GajA to form a heterooctameric Gabija complex, but GajB did not exhibit helicase activity when bound to GajA. These results advance our understanding of the molecular mechanism underlying Gabija anti-phage defense and highlight the role of GajB as a component of a multi-subunit antiviral complex in bacteria.

The structure of AcrIE4-F7 reveals a common strategy for dual CRISPR inhibition by targeting PAM recognition sites.

Bacteria and archaea use the CRISPR-Cas system to fend off invasions of bacteriophages and foreign plasmids. In response, bacteriophages encode anti-CRISPR (Acr) proteins that potently inhibit host Cas proteins to suppress CRISPR-mediated immunity. AcrIE4-F7, which was isolated from Pseudomonas citronellolis, is a fused form of AcrIE4 and AcrIF7 that inhibits both type I-E and type I-F CRISPR-Cas systems. Here, we determined the structure of AcrIE4-F7 and identified its Cas target proteins. The N-terminal AcrIE4 domain adopts a novel α-helical fold that targets the PAM interaction site of the type I-E Cas8e subunit. The C-terminal AcrIF7 domain exhibits an αß fold like native AcrIF7, which disables target DNA recognition by the PAM interaction site in the type I-F Cas8f subunit. The two Acr domains are connected by a flexible linker that allows prompt docking onto their cognate Cas8 targets. Conserved negative charges in each Acr domain are required for interaction with their Cas8 targets. Our results illustrate a common mechanism by which AcrIE4-F7 inhibits divergent CRISPR-Cas types.

Structural Investigation of Self-Assembly and Target Binding of Anti-CRISPR AcrIIC2.

Anti-CRISPR (Acr) proteins are phage-borne inhibitors of the CRISPR-Cas immune system in archaea and bacteria. AcrIIC2 from prophages of Neisseria meningitidis disables the nuclease activity of type II-C Cas9, such that dimeric AcrIIC2 associates with the bridge helix (BH) region of Cas9 to compete with guide RNA loading. AcrIIC2 in solution readily assembles into oligomers of variable lengths, but the oligomeric states are not clearly understood. In this study, we investigated the dynamic assembly of AcrIIC2 oligomers, and identified key interactions underlying the self-association. We report that AcrIIC2 dimers associate into heterogeneous high-order oligomers with the equilibrium dissociation constant KD ∼8 µM. Oligomerization is driven by electrostatic interactions between charged residues, and rational mutagenesis produces a stable AcrIIC2 dimer with intact Cas9 binding. Remarkably, the BH peptide of Cas9 is unstructured in solution, and undergoes a coil-to-helix transition upon AcrIIC2 binding, revealing a unique folding-upon-binding mechanism for Acr recognition.

Structural and mechanistic insights into the CRISPR inhibition of AcrIF7.

The CRISPR-Cas system provides adaptive immunity for bacteria and archaea to combat invading phages and plasmids. Phages evolved anti-CRISPR (Acr) proteins to neutralize the host CRISPR-Cas immune system as a counter-defense mechanism. AcrIF7 in Pseudomonas aeruginosa prophages strongly inhibits the type I-F CRISPR-Cas system. Here, we determined the solution structure of AcrIF7 and identified its target, Cas8f of the Csy complex. AcrIF7 adopts a novel ß1ß2α1α2ß3 fold and interacts with the target DNA binding site of Cas8f. Notably, AcrIF7 competes with AcrIF2 for the same binding interface on Cas8f without common structural motifs. AcrIF7 binding to Cas8f is driven mainly by electrostatic interactions that require position-specific surface charges. Our findings suggest that Acrs of divergent origin may have acquired specificity to a common target through convergent evolution of their surface charge configurations.

Structural and mutational analyses of psychrophilic and mesophilic adenylate kinases highlight the role of hydrophobic interactions in protein thermal stability.

Protein thermal stability is an important field since thermally stable proteins are desirable in many academic and industrial settings. Information on protein thermal stabilization can be obtained by comparing homologous proteins from organisms living at distinct temperatures. Here, we report structural and mutational analyses of adenylate kinases (AKs) from psychrophilic Bacillus globisporus (AKp) and mesophilic Bacillus subtilis (AKm). Sequence and structural comparison showed suboptimal hydrophobic packing around Thr26 in the CORE domain of AKp, which was replaced with an Ile residue in AKm. Mutations that improved hydrophobicity of the Thr residue increased the thermal stability of the psychrophilic AKp, and the largest stabilization was observed for a Thr-to-Ile substitution. Furthermore, a reverse Ile-to-Thr mutation in the mesophilic AKm significantly decreased thermal stability. We determined the crystal structures of mutant AKs to confirm the impact of the residue substitutions on the overall stability. Taken together, our results provide a structural basis for the stability difference between psychrophilic and mesophilic AK homologues and highlight the role of hydrophobic interactions in protein thermal stability.

Supra-aortic low-dose contrast-enhanced time-resolved magnetic resonance (MR) angiography at 3 T: comparison with time-of-flight MR angiography and high-resolution contrast-enhanced MR angiography.

BACKGROUND: Low-dose, time-resolved, contrast-enhanced, magnetic resonance angiography (TR-CEMRA) has been described previously; however, a comparative study between low dose TR-CEMRA and time-of-flight MRA (TOF-MRA) in the diagnosis of supra-aortic arterial stenosis has not yet been published. PURPOSE: To demonstrate the feasibility and effectiveness of low-dose TR-CEMRA compared with TOF-MRA, using high-resolution contrast-enhanced MRA (HR-CEMRA) as the reference standard. MATERIAL AND METHODS: This prospective study consisted of 30 consecutive patients. All patients underwent TOF-MRA of the neck and circle of Willis and supra-aortic HR-CEMRA, followed by supra-aortic low-dose TR-CEMRA. Gadoterate meglumine (Gd-DOTA, Dotarem(®), Guerbet, Roissy CdG Cedex, France) was injected at a dose of 0.1 mmol/kg for HR-CEMRA, followed by a 0.03 mmol/kg bolus for low-dose TR-CEMRA. Three readers evaluated the assessibility and image quality, and then two readers classified each stenosis into the following categories: normal (0-30%), mild stenosis (31-50%), moderate (51-70%), severe (71-99%), and occlusion. RESULTS: TR-CEMRA and HR-CEMRA showed a greater number of assessable arterial segments than TOF-MRA (P < 0.01). For TR-CEMRA, 29 cases showed within or better than the diagnostic range, whereas all 30 cases were in the diagnostic range for TOF-MRA and HR-CEMRA. For evaluation of stenosis in a total of 743 arterial segments, both TR-CEMRA and TOF-MRA results agreed with those of HR-CEMRA in 729 segments (98.1%), with excellent inter-observer agreement of TR-CEMRA; stenosis was overestimated in nine segments (1.2%) and underestimated in five segments (0.7%). For diagnosis of stenosis using 30% as the cut-off value on HR-CEMRA, the sensitivity and specificity were 88.2% and 99.3%, respectively, for the TR-CEMRA procedure, versus 94.1% and 99.6%, respectively, for TOF-MRA. CONCLUSION: Low-dose TR-CEMRA is feasible and effective in the diagnosis of supra-aortic arterial stenosis, and could be more useful option than TOF-MRA.

In vivo non-ionizing photoacoustic mapping of sentinel lymph nodes and bladders with ICG-enhanced carbon nanotubes.

We demonstrate the feasibility of mapping a sentinel lymph node (SLN) and urinary bladder by using modified single-walled carbon nanotubes (SWNTs) as a nonionizing photoacoustic (PA) contrast agent. To improve the PA sensitivity, indocyanine green (ICG) was conjugated with SWNTs and the optical absorption of SWNTs-ICG was enhanced by approximately four times compared to that of plain SWNTs at a concentration of 0.3 µM. In vivo PA imaging results showed that the SLN and bladder were clearly visualized due to accumulation of SWNTs-ICG. This implies that the SWNTs-ICG could be potentially utilized to identify SLNs in breast cancer patients and tracking vesicoureteral reflux in combination with PA imaging.

Pulsed magneto-motive optical coherence tomography for remote cellular imaging.

We developed pulsed magneto-motive optical coherence tomography (PMM-OCT) to reduce environmental temperature in the measurement volume and to expand the effective magnetic field distance from a pulse source. The proposed PMM-OCT system consisted of a spectral-domain OCT system and a customarily designed electrical pulse generator. The enhanced magnetic field allowed the proposed system to be able to image magnetically labeled cells in a distance as far as 30 mm away from the pulse generator. As an easy and sensitive approach, our PMM-OCT may be beneficially applied to a molecular-level imaging systems.