An endo-N-acetyl-beta-D-glucosaminidase, acting on the di-N-acetylchitobiosyl part of N-linked glycans, is secreted during sporulation of Myxococcus xanthus

Myxobacteria: Versatile cell factories of novel commercial enzymes for bio-manufacturing

Microbial cell factories for the production of high-quality commercial-grade enzymes have accelerated the development of advanced bio-manufacturing approaches, which in turn are environmentally friendly and sustainable. Myxobacteria, a term commonly used to refer to a group within the Myxococcota phylum, are of great interest for their biotechnological applications due to their ability to synthesize a wide range of natural products and lytic enzymes. These traits are essential for the development of robust expression systems. However, myxobacteria have remained an underexploited resource with industrial relevance. Nevertheless, a growing number of food and industrial enzymes have been identified, highlighting myxobacteria as suitable platforms for exploring enzymes with commercial applications, including biomass conversion. Yet, the discovered lytic enzymes are just the tip of the iceberg given their large genomes and diversity across myxobacteria taxa. Despite holding much promise, challenges in genetic engineering, slow growth, and limitations in metabolic remodeling and expression strategies have limited the construction of myxobacterial cell factories. In this review, we highlight recent advances in the discovery of new myxobacterial enzymes and biomass conversion resources, focusing on their potential applications in agriculture and industry. We describe how myxobacteria and their enzymes can be identified through bioprospecting and computational approaches and summarize current biotechnological applications and synthetic biology strategies for bio-manufacturing. Finally, we discuss the promising potential of myxobacteria as industrial cell factories and address open research questions and future directions.

Editing a mushroom with high-digestibility using a novel endo-N-acetyl-β-D-glucosaminidase

Fungi comprise approximately 2 % of the Earth's biomass; however, the human gastrointestinal tract has a limited capacity to digest fungal biomass. In this study, a novel endo-N-acetyl-β-D-glucosaminidase, Endo CM, was characterized in the mushroom-forming fungus Cordyceps militaris, where it plays a role in maintaining the integrity of the fungal cell wall. Through gene editing, the Endo CM promoter was engineered to remove the binding site of the CmCreA carbon catabolite repressor, and the transformant was named CmT. After 12 h of treatment with simulated digestive fluids, the residual mycelial biomass of CmT was reduced to 50.00 ± 1.57 %, compared with 69.47 ± 0.97 % (p = 0.00005) for the parent strain. CmT also released more amino acids during the simulated digestion, suggesting that the expression level of Endo CM affects the accessibility of mycelial biomass to digestive enzymes. Additionally, CmT produced fruiting bodies with improved flavor but impaired appearance. This study highlights the production of alternative proteins with high digestibility and provides a sustainable approach for breeding mushrooms with improved digestibility and absorption properties.

Cell-Free Synthetic Glycobiology: Designing and Engineering Glycomolecules Outside of Living Cells

Glycans and glycosylated biomolecules are directly involved in almost every biological process as well as the etiology of most major diseases. Hence, glycoscience knowledge is essential to efforts aimed at addressing fundamental challenges in understanding and improving human health, protecting the environment and enhancing energy security, and developing renewable and sustainable resources that can serve as the source of next-generation materials. While much progress has been made, there remains an urgent need for new tools that can overexpress structurally uniform glycans and glycoconjugates in the quantities needed for characterization and that can be used to mechanistically dissect the enzymatic reactions and multi-enzyme assembly lines that promote their construction. To address this technology gap, cell-free synthetic glycobiology has emerged as a simplified and highly modular framework to investigate, prototype, and engineer pathways for glycan biosynthesis and biomolecule glycosylation outside the confines of living cells. From nucleotide sugars to complex glycoproteins, we summarize here recent efforts that harness the power of cell-free approaches to design, build, test, and utilize glyco-enzyme reaction networks that produce desired glycomolecules in a predictable and controllable manner. We also highlight novel cell-free methods for shedding light on poorly understood aspects of diverse glycosylation processes and engineering these processes toward desired outcomes. Taken together, cell-free synthetic glycobiology represents a promising set of tools and techniques for accelerating basic glycoscience research (e.g., deciphering the "glycan code") and its application (e.g., biomanufacturing high-value glycomolecules on demand).

Up-regulation of carbon metabolism-related glyoxylate cycle and toxin production in Beauveria bassiana JEF-007 during infection of bean bug, Riptortus pedestris (Hemiptera: Alydidae)

Beauveria bassiana (Bb) is used as an environment-friendly biopesticide. However, the molecular mechanisms of Bb-host interactions are not well understood. Herein, RNA isolated from B. bassiana (Bb JEF-007) and Riptortus pedestris (Hemiptera: Alydidae) infected with this strain were firstly subjected to high-throughput next generation sequencing (NGS) to analyze and compare transcriptomes. Due to lack of fungal and host genome information, fungal transcriptome was processed to partially exclude non-infection specific genes and host-flora. Differentially Expressed Gene (DEG) analysis showed that 2381 genes were up-regulated and 2303 genes were down-regulated upon infection. Most DEGs were classified into the categories of single-organism, cellular and metabolism processes by Gene Ontology analysis. Most DEGs were involved in metabolic pathways based on Kyoto Encyclopedia of Genes and Genomes pathway mapping. Carbon metabolism-related enzymes in the glyoxylate cycle were significantly up-regulated, suggesting a possible role for them in Bb growth in the host. Additionally, transcript levels of several fungal genes were dramatically increased after infection, such as cytotoxic lectin-like protein, bacterial-like toxin, proteins related to cell wall formation, hyphal growth, nutrient uptake, and halogenated compound synthesis. This work provides insight into how entomopathogenic B. bassiana grows in agriculturally harmful bean bug at 6 d post infection.

Advances in Enzymatic Glycoside Synthesis

A robust platform for facile defined glycan synthesis does not exist. Yet the need for such technology has never been greater as researchers seek to understand the full scope of carbohydrate function, stretching beyond the classical roles of structure and energy storage to encompass highly nuanced cell signaling events. To comprehensively explore and exploit the full diversity of carbohydrate functions, we must first be able to synthesize them in a controlled manner. Toward this goal, traditional chemical syntheses are inefficient while nature's own synthetic enzymes, the glycosyl transferases, can be challenging to express and expensive to employ on scale. Glycoside hydrolases represent a pool of glycan processing enzymes that can be either used in a transglycosylation mode or, better, engineered to function as "glycosynthases," mutant enzymes capable of assembling glycosides. Glycosynthases grant access to valuable glycans that act as functional and structural probes or indeed as inhibitors and therapeutics in their own right. The remodelling of glycosylation patterns in therapeutic proteins via glycoside hydrolases and their mutants is an exciting frontier in both basic research and industrial scale processes.

How hydrophobicity and the glycosylation site of glycans affect protein folding and stability: a molecular dynamics simulation

Glycosylation is one of the most common post-translational modifications in the biosynthesis of protein, but its effect on the protein conformational transitions underpinning folding and stabilization is poorly understood. In this study, we present a coarse-grained off-lattice 46-β barrel model protein glycosylated by glycans with different hydrophobicity and glycosylation sites to examine the effect of glycans on protein folding and stabilization using a Langevin dynamics simulation, in which an H term was proposed as the index of the hydrophobicity of glycan. Compared with its native counterpart, introducing glycans of suitable hydrophobicity (0.1 < H < 0.4) at flexible peptide residues of this model protein not only facilitated folding of the protein but also increased its conformation stability significantly. On the contrary, when glycans were introduced at the restricted peptide residues of the protein, only those hydrophilic (H = 0) or very weak hydrophobic (H < 0.2) ones contributed slightly to protein stability but hindered protein folding due to increased free energy barriers. The glycosylated protein retained the two-step folding mechanism in terms of hydrophobic collapse and structural rearrangement. Glycan chains located in a suitable site with an appropriate hydrophobicity facilitated both collapse and rearrangement, whereas others, though accelerating collapse, hindered rearrangement. In addition to entropy effects, that is, narrowing the space of the conformations of the unfolded state, the presence of glycans with suitable hydrophobicity at suitable glycosylation site strengthened the folded state via hydrophobic interaction, that is, the enthalpy effect. The simulations have shown both the stabilization and the destabilization effects of glycosylation, as experimentally reported in the literature, and provided molecular insight into glycosylated proteins. The understanding of the effects of glycans with different hydrophobicities on the folding and stability of protein, as attempted by the present work, is helpful not only to explain the stabilization and destabilization effect of real glycoproteins but also to design protein-polymer conjugates for biotechnological purposes.

The two endo-β-N-acetylglucosaminidase genes from Arabidopsis thaliana encode cytoplasmic enzymes controlling free N-glycan levels

Endo-β-N-acetylglucosaminidases (ENGases) cleave N-glycans from proteins and/or peptides by hydrolyzing the O-glycosidic linkage between the two core-N-acetylglucosamine (GlcNAc) residues. Although, two homologous genes potentially encoding ENGases have been identified in Arabidopsis thaliana, their respective substrate specificity, their subcellular and their organ specific localization was hitherto unknown. In order to investigate the role of ENGases in this model plant species, we transiently expressed the two A. thaliana genes in Nicotiana benthamiana and determined the substrate specificities, as well as the Km values, of the purified recombinant enzymes. The assumed predominantly cytosolic localisation of both enzymes, here referred to as AtENGase85A and AtENGase85B, was determined by confocal microscopy of plant leaves expressing the respective GFP-fusion constructs. For the individual characterization of the two enzymes expression patterns in planta, single knock-out plants were selected for both genes. Although both enzymes are present in most organs, only AtENGase85A (At5g05460) was expressed in stems and no ENGase activity was detected in siliques. A double knock-out was generated by crossing but-like single knock-out plants-no apparent phenotype was observed. In contrast, in this double knock-out, free N-glycans carrying a single GlcNAc at the reducing end are completely absent and their counterparts with two GlcNAc-visible only at a trace level in wild type-accumulated dramatically.

Endo-N-acetyl-beta-D-glucosaminidases and their potential substrates: structure/function relationships

Endo-N-acetyl-beta-D-glucosaminidases (ENGases) have been defined as the enzymes that hydrolyse the glycosidic bond between an N-acetyl-beta-D-glucosamine residue and the adjacent (partner) monosaccharide within an oligosaccharide chain. Three types of enzymes have been distinguished according to this definition: ENGases acting on murein (type I), those acting on chitin (type II) and, finally, those acting on N-glycans (type III). Considering that N-acetylmuramic acid is a derivative of N-acetylglucosamine (3-O-substituted by a lactyl group), only ENGases acting between two N-acetylglucosamine residues are actually known despite the fact that other possibilities of partner monosaccharides for N-acetyl-beta-D-glucosamine are reported. Similarities in the amino acid sequences were found to occur only between chitin-ENGases and N-glycan-ENGases, but the substrate specificities of these two types of enzymes are different. However, it is possible that certain enzymes are able to cleave more than one type of substrate, and this could in particular explain why the N-glycan-ENGases are largely produced by bacteria in which no potential substrate for this type of enzymes was identified. Further study in this area is expected.

Secretion kinetics of endo-N-acetyl-beta-D-glucosaminidase during vegetative growth of Myxococcus xanthus

It was recently demonstrated that endo-N-acetyl-beta-D-glucosaminidases (ENGase) acting on N-glycosylproteins are produced by myxobacteria. In this study, it was shown that the secretion of ENGase during vegetative growth of Myxococcus xanthus was cell-density-dependent. The activity produced per cell increased up to 6 x 10(8) cells/ml and stabilized thereafter (maximum level). Two of the developmental mutants used in this study (bsgA and csgA) were locked for ENGase secretion into the maximum level regardless of cell density. To explain the pattern of ENGase secretion, we postulated the presence of a molecule that induces the enzyme until it reaches a proper concentration threshold. Although the chemical structure of this cell density signal was not determined during this study, its occurrence during vegetative growth of M. xanthus was strongly suggested by the results.

Are there biological functions for bacterial endo-N-acetyl-beta-D-glucosaminidases?

The endo-N-acetyl-beta-D-glucosaminidases (ENGase) acting on the N-N'-diacetylchitobiosyl core of N-glycosylproteins are essential reagents for the investigation of the structure and the functions of glycoproteins. These enzymes were largely studied with the aim of offering more tools with new and broader substrate specificities to the community of glycobiologist. Conversely, little attention was given to their potential role in the physiology of bacteria, even though it had been shown that ENGases are important enzymes for the physiology of animal and plant cells. In this brief review, we present the main characteristics of the bacterial ENGases and confine our discussion to biological aspects of their action in bacterial systems.

Do de-N-glycosylation enzymes have an important role in plant cells?

In this review de-N-glycosylation was defined as the removal of the glycan(s) from a N-glycosylprotein, by means of enzymes acting on the di-N-acetylchitobiosyl part of the invariant pentasaccharide inner-core of N-glycosylproteins. Peptide-N4-(N-acetyl-beta-D-glucosaminyl) asparagine amidases (PNGase) and endo-N-acetyl-beta-D-glucosaminidases (ENGase) were both considered as de-N-glycosylation enzymes. A detailed description of the characterization and the function of plant PNGases and ENGases is presented, together with a brief presentation on the occurrence and the current knowledge on the function of microbial and animal enzymes. De-N-glycosylation of plant glycoproteins was proposed as a possible mechanism for the release of oligosaccharides displaying biological activities and the removal of N-glycans could also explain the regulation of protein activity. Each enzyme seems to have a specific function during germination and post-germinative development. All the arguments concur that de-N-glycosylation enzymes have an important role in plant cells and confirm that the N-glycosylation/de-N-glycosylation system should occur more commonly than presently recognized in living organisms.