Evolution of Phosphorylases from N-Acetylglucosaminide Hydrolases in Family GH3

Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening

Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.

Evolution of Phosphorylase Activity in an Ancestral Glycosyltransferase

The reconstruction of ancestral sequences can offer a glimpse into the fascinating process of molecular evolution by exposing the adaptive pathways that shape the proteins found in nature today. Here, we track the evolution of the carbohydrate-active enzymes responsible for the synthesis and turnover of mannogen, a critical carbohydrate reserve in Leishmania parasites. Biochemical characterization of resurrected enzymes demonstrated that mannoside phosphorylase activity emerged in an ancestral bacterial mannosyltransferase, and later disappeared in the process of horizontal gene transfer and gene duplication in Leishmania. By shuffling through plausible historical sequence space in an ancestral mannosyltransferase, we found that mannoside phosphorylase activity could be toggled on through various combinations of mutations at positions outside of the active site. Molecular dynamics simulations showed that such mutations can affect loop rigidity and shield the active site from water molecules that disrupt key interactions, allowing α-mannose 1-phosphate to adopt a catalytically productive conformation. These findings highlight the importance of subtle distal mutations in protein evolution and suggest that the vast collection of natural glycosyltransferases may be a promising source of engineering templates for the design of tailored phosphorylases.

Building mutational bridges between carbohydrate-active enzymes

The commercial value of specialty carbohydrates and glycosylated compounds has sparked considerable interest in the synthetic potential of carbohydrate-active enzymes (CAZymes). Protein engineering methods have proven to be highly successful in expanding the range of glycosylation reactions that these enzymes can perform efficiently and cost-effectively. The past few years have witnessed meaningful progress in this area, largely due to a sharper focus on the understanding of structure-function relationships and mechanistic intricacies. Here, we summarize recent studies that demonstrate how protein engineers have become much better at traversing the fitness landscape of CAZymes through mutational bridges that connect the different activity types.

Synthesis and application of phosphorylated saccharides in researching carbohydrate-based drugs

Phosphorylated saccharides are valuable targets in glycochemistry and glycobiology, which play an important role in various physiological and pathological processes. The current research on phosphorylated saccharides primarily focuses on small molecule inhibitors, glycoconjugate vaccines and novel anti-tumour targeted drug carrier materials. It can maximise the pharmacological effects and reduce the toxicity risk caused by nonspecific off-target reactions of drug molecules. However, the number and types of natural phosphorylated saccharides are limited, and the complexity and heterogeneity of their structures after extraction and separation seriously restrict their applications in pharmaceutical development. The increasing demands for the research on these molecules have extensively promoted the development of carbohydrate synthesis. Numerous innovative synthetic methodologies have been reported regarding the continuous expansion of the potential building blocks, catalysts, and phosphorylation reagents. This review summarizes the latest methods for enzymatic and chemical synthesis of phosphorylated saccharides, emphasizing their breakthroughs in yield, reactivity, regioselectivity, and application scope. Additionally, the anti-bacterial, anti-tumour, immunoregulatory and other biological activities of some phosphorylated saccharides and their applications were also reviewed. Their structure-activity relationship and mechanism of action were discussed and the key phosphorylation characteristics, sites and extents responsible for observed biological activities were emphasised. This paper will provide a reference for the application of phosphorylated saccharide in the research of carbohydrate-based drugs in the future.

Insertions and deletions in protein evolution and engineering

Protein evolution or engineering studies are traditionally focused on amino acid substitutions and the way these contribute to fitness. Meanwhile, the insertion and deletion of amino acids is often overlooked, despite being one of the most common sources of genetic variation. Recent methodological advances and successful engineering stories have demonstrated that the time is ripe for greater emphasis on these mutations and their understudied effects. This review highlights the evolutionary importance and biotechnological relevance of insertions and deletions (indels). We provide a comprehensive overview of approaches that can be employed to include indels in random, (semi)-rational or computational protein engineering pipelines. Furthermore, we discuss the tolerance to indels at the structural level, address how domain indels can link the function of unrelated proteins, and feature studies that illustrate the surprising and intriguing potential of frameshift mutations.

Computer Simulation to Rationalize “Rational” Engineering of Glycoside Hydrolases and Glycosyltransferases

Glycoside hydrolases and glycosyltransferases are the main classes of enzymes that synthesize and degrade carbohydrates, molecules essential to life that are a challenge for classical chemistry. As such, considerable efforts have been made to engineer these enzymes and make them pliable to human needs, ranging from directed evolution to rational design, including mechanism engineering. Such endeavors fall short and are unreported in numerous cases, while even success is a necessary but not sufficient proof that the chemical rationale behind the design is correct. Here we review some of the recent work in CAZyme mechanism engineering, showing that computational simulations are instrumental to rationalize experimental data, providing mechanistic insight into how native and engineered CAZymes catalyze chemical reactions. We illustrate this with two recent studies in which (i) a glycoside hydrolase is converted into a glycoside phosphorylase and (ii) substrate specificity of a glycosyltransferase is engineered toward forming O-, N-, or S-glycosidic bonds.

Discovery of a Kojibiose Hydrolase by Analysis of Specificity-Determining Correlated Positions in Glycoside Hydrolase Family 65

The Glycoside Hydrolase Family 65 (GH65) is an enzyme family of inverting α-glucoside phosphorylases and hydrolases that currently contains 10 characterized enzyme specificities. However, its sequence diversity has never been studied in detail. Here, an in-silico analysis of correlated mutations was performed, revealing specificity-determining positions that facilitate annotation of the family’s phylogenetic tree. By searching these positions for amino acid motifs that do not match those found in previously characterized enzymes from GH65, several clades that may harbor new functions could be identified. Three enzymes from across these regions were expressed in E. coli and their substrate profile was mapped. One of those enzymes, originating from the bacterium Mucilaginibacter mallensis, was found to hydrolyze kojibiose and α-1,2-oligoglucans with high specificity. We propose kojibiose glucohydrolase as the systematic name and kojibiose hydrolase or kojibiase as the short name for this new enzyme. This work illustrates a convenient strategy for mapping the natural diversity of enzyme families and smartly mining the ever-growing number of available sequences in the quest for novel specificities.