Directed Evolution and Rational Design of Mechanosensitive Channel MscCG2 for Improved Glutamate Excretion Efficiency

Enhanced l-serine synthesis in Corynebacterium glutamicum by exporter engineering and Bayesian optimization of the medium composition

l-serine is a versatile, high value-added amino acid, widely used in food, medicine and cosmetics. However, the low titer of l-serine has limited its industrial production. In this study, a cell factory without plasmid for efficient production of l-serine was constructed based on transport engineering. Firstly, the effects of l-serine exporter SerE overexpression and deletion on the cell growth and l-serine titer were investigated in Corynebacterium glutamicum (C. glutamicum) A36, overexpression of s erE using a plasmid led to a 15.1% increase in l-serine titer but also caused a 15.1% decrease in cell growth. Subsequently, to increase the export capacity of SerE, we conducted semi-rational design and bioinformatics analysis, combined with alanine mutation and site-specific saturation mutation. The mutant E277K was obtained and exhibited a 53.2% higher export capacity compared to wild-type SerE, resulting in l-serine titer increased by 39.6%. Structural analysis and molecular dynamics simulations were performed to elucidate the mechanism. The results showed that the mutation shortened the hydrogen bond distance between the exporter and l-serine, enhanced complex stability, and reduced the binding energy. Finally, Bayesian optimization was employed to further improve l-serine titer of the mutant strain C-E277K. Under the optimized conditions, 47.77 g/L l-serine was achieved in a 5-L bioreactor, representing the highest reported titer for C. glutamicum to date. This study provides a basis for the transformation of l-serine export pathway and offers a new strategy for increasing l-serine titer.

Impact of exporter proteins and their engineering on the productivity of Corynebacterium

Enhancing product efflux is crucial in improving fermentative bioproduction. Despite advancements in metabolic engineering guided by the design-build-test-learn cycle, membrane transport engineering of product efflux remains underdeveloped, limiting the efficient production of target chemicals. This review explores the historical findings on product efflux, regardless of passive or active transport, in fermentation engineering, focusing on Corynebacterium species, and highlights the potential of multidrug transporters as valuable screening sources for efflux improvement. Furthermore, the review emphasizes the importance of understanding the machinery of efflux transporters to optimize their functionality. Molecular dynamics simulations are a promising tool for exploring novel strategies to advance fermentation-related processes. These insights provide a framework for overcoming current challenges in membrane transport engineering of product efflux and improving industrial-scale bioproduction. KEY POINTS: • Review of strategies to enhance product efflux in Corynebacterium species. • Multidrug transporters are key tools for optimizing metabolite efflux. • Efflux transporter mechanisms analyzed to improve microbial productivity. • Molecular dynamics simulations employed for understanding transporter mechanisms.

Channel Engineering of a Glutamate Exporter

Mechanosensitive channel MscCG2 is involved in glutamate excretion in most C. glutamicum strains. Improving the excretion efficiency of MscCG2 is beneficial to the production of glutamate. In this study, structure-based rational design was carried out to obtain an improved efflux ability of exporter MscCG2 and its mechanistic advance via two strategies: widening the channel entrance for smoother entry of glutamate and reducing the electronegativity at the entrance of the channels to minimize the rejection of negatively charged glutamate entry. The designed variants were found to enhance glutamate excretion by 2 to 3.3-fold in the early phase and 1.1-fold to 1.5-fold in the late phase of fermentation. The enhanced glutamate excretion was further confirmed by using glutamate toxic analog 4-fluoroglutamate (4-FG) and Glu-Glu peptide uptake and glutamate export assay. Molecular dynamic (MD) simulations revealed that the amino acid substitutions indeed enlarged the channel entrance and reduced the repulsion of glutamate when entering the channel. The finding of this study is important for understanding the underlying structure-function relationship and the mechanism of glutamate secretion to improve glutamate efflux efficiency of glutamate exporter.

Evolving Nonphosphorylative Metabolism for Improving Production of 2-Oxoglutarate Derivatives

The bioconversion of lignocellulosic biomass into value-added products provides an alternative solution to environmental and economic challenges. Nonphosphorylative metabolism can convert pentoses and d-galacturonate into 2-oxoglutarate (2-KG) in a few steps, facilitating the production of 2-KG derivatives. However, the efficiency of the Weimberg pathway from Caulobacter crescentus, a type of nonphosphorylative metabolism, is constrained by the low activity of CcXylX, 2-keto-3-deoxy-d-xylonate dehydratase. To overcome this limitation, we engineered CcXylX through directed evolution. A resulting CcXylX mutant exhibited a 3-fold higher kcat value and notably enhanced the production of 2-KG derivatives from d-xylose, a major component of lignocellulosic hydrolysates, including a 32% increase in l-glutamate titer (8.3 g/L) and a 79% increase in l-proline titer (4.3 g/L) compared with the wild-type CcXylX. This research holds promise for advancing lignocellulosic biotechnology and provides insights into economically viable production of other 2-KG derivatives besides l-glutamate and l-proline.

Engineering the next-generation synthetic cell factory driven by protein engineering

Synthetic cell factory offers substantial advantages in economically efficient production of biofuels, chemicals, and pharmaceutical compounds. However, to create a high-performance synthetic cell factory, precise regulation of cellular material and energy flux is essential. In this context, protein components including enzymes, transcription factor-based biosensors and transporters play pivotal roles. Protein engineering aims to create novel protein variants with desired properties by modifying or designing protein sequences. This review focuses on summarizing the latest advancements of protein engineering in optimizing various aspects of synthetic cell factory, including: enhancing enzyme activity to eliminate production bottlenecks, altering enzyme selectivity to steer metabolic pathways towards desired products, modifying enzyme promiscuity to explore innovative routes, and improving the efficiency of transporters. Furthermore, the utilization of protein engineering to modify protein-based biosensors accelerates evolutionary process and optimizes the regulation of metabolic pathways. The remaining challenges and future opportunities in this field are also discussed.

Molecular modification and biotechnological applications of microbial aspartic proteases

The growing preference for incorporating microbial aspartic proteases in industries is due to their high catalytic function and high degree of substrate selectivity. These properties, however, are attributable to molecular alterations in their structure and a variety of other characteristics. Molecular tools, functional genomics, and genome editing technologies coupled with other biotechnological approaches have aided in improving the potential of industrially important microbial proteases by addressing some of their major limitations, such as: low catalytic efficiency, low conversion rates, low thermostability, and less enzyme yield. However, the native folding within their full domain is dependent on a surrounding structure which challenges their functionality in substrate conversion, mainly due to their mutual interactions in the context of complex systems. Hence, manipulating their structure and controlling their expression systems could potentially produce enzymes with high selectivity and catalytic functions. The proteins produced by microbial aspartic proteases are industrially capable and far-reaching in regulating certain harmful distinctive industrial processes and the benefits of being eco-friendly. This review provides: an update on current trends and gaps in microbial protease biotechnology, exploring the relevant recombinant strategies and molecular technologies widely used in expression platforms for engineering microbial aspartic proteases, as well as their potential industrial and biotechnological applications.