Redox-initiated hydrogel system for detection and real-time imaging of cellulolytic enzyme activity

High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering

Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma. Typical enhancements sought in enzyme engineering and in vitro evolution campaigns include improved folding stability, catalytic activity, and/or substrate specificity. Despite significant progress in recent years in the areas of high-throughput screening and DNA sequencing, our ability to explore the vast space of functional enzyme sequences remains severely limited. Here, we review the currently available suite of modern methods for enzyme engineering, with a focus on novel readout systems based on enzyme cascades, and new approaches to reaction compartmentalization including single-cell hydrogel encapsulation techniques to achieve a genotype–phenotype link. We further summarize systematic scanning mutagenesis approaches and their merger with deep mutational scanning and massively parallel next-generation DNA sequencing technologies to generate mutability landscapes. Finally, we discuss the implementation of machine learning models for computational prediction of enzyme phenotypic fitness from sequence. This broad overview of current state-of-the-art approaches for enzyme engineering and evolution will aid newcomers and experienced researchers alike in identifying the important challenges that should be addressed to move the field forward.

Enzyme engineering is an important biotechnological process capable of generating tailored biocatalysts for applications in industrial chemical conversion and biopharma.

An Ingestible Self-Polymerizing System for Targeted Sampling of Gut Microbiota and Biomarkers

A proof-of-concept for the fabrication of a self-polymerizing system for sampling of gut microbiome in the upper gastrointestinal (GI) tract is presented. An orally ingestible microdevice is loaded with the self-polymerizing reaction mixture to entrap gut microbiota and biomarkers. This polymerization reaction is activated in the aqueous environment, like fluids in the intestinal lumen, and causes site-specific microsampling in the gastrointestinal tract. The sampled microbiota and protein biomarkers can be isolated and analyzed via high-throughput multiomic analyses. The study utilizes a hollow microdevice (Su-8, ca. 250 μm), loaded with an on-board reaction mixture (iron chloride, ascorbic acid, and poly(ethylene glycol) diacrylate monomers) for diacrylate polymerization in the gut of an animal model. An enteric-coated rat capsule was used to orally gavage these microdevices in a rat model, thereby, protecting the microdevices in the stomach (pH 2), but releasing them in the intestine (pH 6.6). Upon capsule disintegration, the microdevices were released in the presence of luminal fluids (in the small intestine region), where iron chloride reacts with ascorbic acid, to initiate poly(ethylene glycol) diacrylate polymerization via a free radical mechanism. Upon retrieval of the microdevices, gut microbiota was found to be entrapped in the polymerized hydrogel matrix, and genomic content was analyzed via 16s rRNA amplicon sequencing. Herein, the results show that the bacterial composition recovered from the microdevices closely resemble the bacterial composition of the gut microenvironment to which the microdevice is exposed. Further, histological assessment showed no signs of local tissue inflammation or toxicity. This study lays a strong foundation for the development of untethered, non-invasive microsampling technologies in the gut and advances our understanding of host-gut microbiome interactions, leading to a better understanding of their commensal behavior and associated GI disease progression in the near future.

Thread-Like Radical-Polymerization via Autonomously Propelled (TRAP) Bots

Micromotor-mediated synthesis of thread-like hydrogel microstructures in an aqueous environment is presented. The study utilizes a catalytic micromotor assembly (owing to the presence of a Pt layer), with an on-board chemical reservoir (i.e., polymerization mixture), toward thread-like radical-polymerization via autonomously propelled bots (i.e., TRAP bots). Synergistic coupling of catalytically active Pt layer, together with radical initiators (H₂ O₂ and FeCl₃ (III)), and PEGDA monomers preloaded into the TRAP bot, results in the polymerization of monomeric units into elongated thread-like hydrogel polymers coupled with self-propulsion. Interestingly, polymer generation via TRAP bots can also be triggered in the absence of hydrogen peroxide for cellular/biomedical application. The resulting polymeric hydrogel microstructures are able to entrap living cells (NIH 3T3 fibroblast cells), and are easily separable via a centrifugation or magnetic separation (owing to the presence of a Ni layer). The cellular biocompatibility of TRAP bots is established via a LIVE/DEAD assay and MTS cell proliferation assay (7 days observation). This is the first study demonstrating real-time in situ hydrogel polymerization via an artificial microswimmer, capable of enmeshing biotic/abiotic microobjects in its reaction environment, and lays a strong foundation for advanced applications in cell/tissue engineering, drug delivery, and cleaner technologies.

Atomic Force Microscopy Meets Biophysics, Bioengineering, Chemistry, and Materials Science

Briefly, herein the use of atomic force microscopy (AFM) in the characterization of molecules and (bioengineered) materials related to chemistry, materials science, chemical engineering, and environmental science and biotechnology is reviewed. First, the basic operations of standard AFM, Kelvin probe force microscopy, electrochemical AFM, and tip-enhanced Raman microscopy are described. Second, several applications of these techniques to the characterization of single molecules, polymers, biological membranes, films, cells, hydrogels, catalytic processes, and semiconductors are provided and discussed.

Nanoscale Engineering of Designer Cellulosomes

Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.