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.

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.