Powerful Microbial Base-Editing Toolbox: From Optimization Strategies to Versatile Applications.

Base editors (BE) based on CRISPR systems are practical gene-editing tools which continue to drive frontier advances of life sciences. BEs are able to efficiently induce point mutations at target sites without double-stranded DNA cleavage. Hence, they are widely employed in the fields of microbial genome engineering. As applications of BEs continue to expand, the demands for base-editing efficiency, fidelity, and versatility are also on the rise. In recent years, a series of optimization strategies for BEs have been developed. By engineering the core components of BEs or adopting different assembly methods, the performance of BEs has been well optimized. Moreover, series of newly established BEs have significantly expanded the base-editing toolsets. In this Review, we will summarize the current efforts for BE optimization, introduce several novel BEs with versatility, and look forward to the broadened applications for industrial microorganisms.

Preferential Regulation of Transient Protein-Protein Interaction by the Macromolecular Crowders.

The environmental condition is a critical regulation factor for protein behavior in solution. Several studies have shown that macromolecular crowders can modulate protein structures, interactions, and functions. Recent publications described the regulation of specific interaction by macromolecular crowders. However, the other category of protein-protein interaction, namely, the transient interaction, is rarely investigated, especially from the perspective of protein structure to study transient interactions between proteins. Here, we used nuclear magnetic resonance and small-angle X-ray/neutron scattering methods to structurally investigate the ensemble of the protein complex in dilute buffer and crowded environments. Histidine phosphocarrier protein (HPr) and the N-terminal domain of enzyme I (EIN) are the important components of the bacterial phosphotransfer system. Our results show that the addition of Ficoll-70 promotes HPr molecules to form the encounter complex with EIN maintained by long-range electrostatic interaction. However, when macromolecular crowder BSA is used, the soft interaction between BSA and HPr perturbs the active site of HPr, driving HPr to form an encounter complex with EIN at the weakly charged interface. Our results indicate that different macromolecular crowders could influence transient EIN-HPr interaction through different mechanisms and provide new insights into protein-protein interaction regulation in native environments.

Preferential Interactions of a Crowder Protein with the Specific Binding Site of a Native Protein Complex.

Nonspecific binding of crowder proteins with functional proteins is likely prevalent in vivo, yet direct quantitative evidence, let alone residue-specific information, is scarce. Here we present nuclear magnetic resonance (NMR) characterization showing that bovine serum albumin weakly but preferentially interacts with the histidine carrier protein (HPr). Notably, the binding interface overlaps with that for HPr's specific partner protein, EIN, leading to competition. The crowder protein thus decreases the EIN-HPr binding affinity and accelerates the dissociation of the native complex. In contrast, Ficoll-70 stabilizes the native complex and slows its dissociation, as one would expect from excluded-volume and microviscosity effects. Our atomistic modeling of macromolecular crowding rationalizes the experimental data and provides quantitative insights into the energetics of protein-crowder interactions. The integrated NMR and modeling study yields benchmarks for the effects of crowded cellular environments on protein-protein specific interactions, with implications for evolution regarding how nonspecific binding can be minimized or exploited.

Plasmonic Gold Nanoparticles Stain Hydrogels for the Portable and High-Throughput Monitoring of Mercury Ions.

The hybrid of l-cysteine and agarose can reduce HAuCl4 and support the rapid growth of plasmonic gold nanoparticles (Au NPs) in the hydrogel phase. The l-cysteine-doped agarose hydrogel (C-AGH) not only offers the substrate the capacity to reduce Au(III) ions but also stabilizes and precisely modulates the in situ grown Au NPs with high repeatability, easy operation, and anti-interference performance. Herein, before the incubation of HAuCl4, the improved hydrogel is preincubated in the aqueous solution containing mercury ions, and the cysteine can specifically conjugate with mercury via the thiol groups. Subsequently, the responsive allochroic bands from dark blue to red can be identified in the solid hydrogel after the incubation of HAuCl4, which is attributed to the formation of regulated Au-Hg nanoamalgams. As a proof-of-concept, toxic Hg2+ ions are exploited as targets for constructing novel sensing assays based on the improved C-AGH protocol. Based on naked-eye recognition, Hg2+ could be rapidly and simply measured. Additionally, the high-throughput and trace analysis with a low limit of detection (3.7 nM) is performed using a microplate reader. On the basis of the filtering technique and remodeling of hydrogels, C-AGH working as the filtering membrane can even achieve the integration of enrichment and measurement with enhanced sensitivity. Significantly, the strategy of using an allochroic hydrogel with the staining of Au NPs can promote the rapid and primary assessment of water quality in environmental analysis.

Mercury ion-engineering Au plasmonics on MoS2 layers for absorption-shifted optical sensors.

Semiconducting MoS2 layers offer the electrons, reducing conjugated Au(I) to Au atoms, and sebsequently serve as desirable substrates for supporting the interfacial growths of gold nanostructures. Au-covering MoS2 heterostructures perform morphology-varied optical characteristics, and the surface engineering of MoS2 involved by Hg2+ ions results in the differential growths of nanostructures and morphological diversities. Naked-eye colorimetric responses to mercury ions, with a low limit of detection of 1.27 nM, are achieved based on the in situ grown heterostructures.

Kinetic Constraints in the Specific Interaction between Phosphorylated Ubiquitin and Proteasomal Shuttle Factors.

Ubiquitin (Ub) specifically interacts with the Ub-associating domain (UBA) in a proteasomal shuttle factor, while the latter is involved in either proteasomal targeting or self-assembly coacervation. PINK1 phosphorylates Ub at S65 and makes Ub alternate between C-terminally relaxed (pUbRL) and retracted conformations (pUbRT). Using NMR spectroscopy, we show that pUbRL but not pUbRT preferentially interacts with the UBA from two proteasomal shuttle factors Ubqln2 and Rad23A. Yet discriminatorily, Ubqln2-UBA binds to pUb more tightly than Rad23A does and selectively enriches pUbRL upon complex formation. Further, we determine the solution structure of the complex between Ubqln2-UBA and pUbRL and uncover the thermodynamic basis for the stronger interaction. NMR kinetics analysis at different timescales further suggests an indued-fit binding mechanism for pUb-UBA interaction. Notably, at a relatively low saturation level, the dissociation rate of the UBA-pUbRL complex is comparable with the exchange rate between pUbRL and pUbRT. Thus, a kinetic constraint would dictate the interaction between Ub and UBA, thus fine-tuning the functional state of the proteasomal shuttle factors.

Aggregation-induced responses (AIR) of 2D-derived layered nanostructures enable emerging colorimetric and fluorescence sensors.

Layered nanostructures (LNs), including two-dimensional nanosheets, nanoflakes, and planar nanodots, show large surface-to-volume ratios, unique optical properties, and desired interfacial activities. LNs are highly promising as alternative probes and platforms due to numerous merits, e.g. signal amplification, improved recognition ability, and anti-interference capacity, for emerging sensing applications. Significantly, when stimuli-responsive aggregation occurs, the modified LNs show engineered morphologies, attractive optical absorption and fluorescence characteristics, which are remarkably programmable. On the basis of the altered aggregation behaviours of LNs, as well as their modulated physical and chemical characteristics, a series of novel sensing assays exhibiting enhanced sensitivity, simple operation, multiple functions, and improved anti-interference capacity are reported, contributing to both point-of-care testing and high-throughput measurements. Herein, the aggregation-induced response sensing strategies of LNs are comprehensively summarized with the classification of materials and variation of aggregated routes aiming at understanding dimension-dependent features, expanding nanoscale biosensor applications, and addressing key issues in disease diagnosis and environmental analysis.

Requirement for p62 acetylation in the aggregation of ubiquitylated proteins under nutrient stress.

Autophagy receptor p62/SQSTM1 promotes the assembly and removal of ubiquitylated proteins by forming p62 bodies and mediating their encapsulation in autophagosomes. Here we show that under nutrient-deficient conditions, cellular p62 specifically undergoes acetylation, which is required for the formation and subsequent autophagic clearance of p62 bodies. We identify K420 and K435 in the UBA domain as the main acetylation sites, and TIP60 and HDAC6 as the acetyltransferase and deacetylase. Mechanically, acetylation at both K420 and K435 sites enhances p62 binding to ubiquitin by disrupting UBA dimerization, while K435 acetylation also directly increases the UBA-ubiquitin affinity. Furthermore, we show that acetylation of p62 facilitates polyubiquitin chain-induced p62 phase separation. Our results suggest an essential role of p62 acetylation in the selective degradation of ubiquitylated proteins in cells under nutrient stress, by specifically regulating the assembly of p62 bodies.

Solution structure of the RNA recognition domain of METTL3-METTL14 N6-methyladenosine methyltransferase.

N6-methyladenosine (m6A), a ubiquitous RNA modification, is installed by METTL3-METTL14 complex. The structure of the heterodimeric complex between the methyltransferase domains (MTDs) of METTL3 and METTL14 has been previously determined. However, the MTDs alone possess no enzymatic activity. Here we present the solution structure for the zinc finger domain (ZFD) of METTL3, the inclusion of which fulfills the methyltransferase activity of METTL3-METTL14. We show that the ZFD specifically binds to an RNA containing 5'-GGACU-3' consensus sequence, but does not to one without. The ZFD thus serves as the target recognition domain, a structural feature previously shown for DNA methyltransferases, and cooperates with the MTDs of METTL3-METTL14 for catalysis. However, the interaction between the ZFD and the specific RNA is extremely weak, with the binding affinity at several hundred micromolar under physiological conditions. The ZFD contains two CCCH-type zinc fingers connected by an anti-parallel ß-sheet. Mutational analysis and NMR titrations have mapped the functional interface to a contiguous surface. As a division of labor, the RNA-binding interface comprises basic residues from zinc finger 1 and hydrophobic residues from ß-sheet and zinc finger 2. Further we show that the linker between the ZFD and MTD of METTL3 is flexible but partially folded, which may permit the cooperation between the two domains during catalysis. Together, the structural characterization of METTL3 ZFD paves the way to elucidate the atomic details of the entire process of RNA m6A modification.

Transplantation of bone marrow-derived endothelial progenitor cells and hepatocyte stem cells from liver fibrosis rats ameliorates liver fibrosis.

AIM: To explore the effectiveness for treating liver fibrosis by combined transplantation of bone marrow-derived endothelial progenitor cells (BM-EPCs) and bone marrow-derived hepatocyte stem cells (BDHSCs) from the liver fibrosis environment. METHODS: The liver fibrosis rat models were induced with carbon tetrachloride injections for 6 wk. BM-EPCs from rats with liver fibrosis were obtained by different rates of adherence and culture induction. BDHSCs from rats with liver fibrosis were isolated by magnetic bead cell sorting. Tracing analysis was conducted by labeling EPCs with PKH26 in vitro to show EPC location in the liver. Finally, BM-EPCs and/or BDHSCs transplantation into rats with liver fibrosis were performed to evaluate the effectiveness of BM-EPCs and/or BDHSCs on liver fibrosis. RESULTS: Normal functional BM-EPCs from liver fibrosis rats were successfully obtained. The co-expression level of CD133 and VEGFR2 was 63.9% ± 2.15%. Transplanted BM-EPCs were located primarily in/near hepatic sinusoids. The combined transplantation of BM-EPCs and BDHSCs promoted hepatic neovascularization, liver regeneration and liver function, and decreased collagen formation and liver fibrosis degree. The VEGF levels were increased in the BM-EPCs (707.10 ± 54.32) and BM-EPCs/BDHSCs group (615.42 ± 42.96), compared with those in the model group and BDHSCs group (P < 0.05). Combination of BM-EPCs/BDHSCs transplantation induced maximal up-regulation of PCNA protein and HGF mRNA levels. The levels of alanine aminotransferase (AST), aspartate aminotransferase, total bilirubin (TBIL), prothrombin time (PT) and activated partial thromboplastin time in the BM-EPCs/BDHSCs group were significantly improved, to be equivalent to normal levels (P > 0.05) compared with those in the BDHSC (AST, TBIL and PT, P < 0.05) and BM-EPCs (TBIL and PT, P < 0.05) groups. Transplantation of BM-EPCs/BDHSCs combination significantly reduced the degree of liver fibrosis (staging score of 1.75 ± 0.25 vs BDHSCs 2.88 ± 0.23 or BM-EPCs 2.75 ± 0.16, P < 0.05). CONCLUSION: The combined transplantation exhibited maximal therapeutic effect compared to that of transplantation of BM-EPCs or BDHSCs alone. Combined transplantation of autogenous BM-EPCs and BDHSCs may represent a promising strategy for the treatment of liver fibrosis, which would eventually prevent cirrhosis and liver cancer.

Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch.

Ubiquitin (Ub) is an important signaling protein. Recent studies have shown that Ub can be enzymatically phosphorylated at S65, and that the resulting pUb exhibits two conformational states-a relaxed state and a retracted state. However, crystallization efforts have yielded only the structure for the relaxed state, which was found similar to that of unmodified Ub. Here we present the solution structures of pUb in both states obtained through refinement against state-specific NMR restraints. We show that the retracted state differs from the relaxed state by the retraction of the last ß-strand and by the extension of the second α-helix. Further, we show that at 7.2, the pKa value for the phosphoryl group in the relaxed state is higher by 1.4 units than that in the retracted state. Consequently, pUb exists in equilibrium between protonated and deprotonated forms and between retracted and relaxed states, with protonated/relaxed species enriched at slightly acidic pH and deprotonated/retracted species enriched at slightly basic pH. The heterogeneity of pUb explains the inability of phosphomimetic mutants to fully mimic pUb. The pH-sensitive conformational switch is likely preserved for polyubiquitin, as single-molecule FRET data indicate that pH change leads to quaternary rearrangement of a phosphorylated K63-linked diubiquitin. Because cellular pH varies among compartments and changes upon pathophysiological insults, our finding suggests that pH and Ub phosphorylation confer additional target specificities and enable an additional layer of modulation for Ub signals.