Suzanne Jansen

Nature Biotechnology, Published online: 11 August 2023; doi:10.1038/s41587-023-01913-6

US approves ‘no kill’ meat for sale

Clovibactin, a new antibiotic isolated from soil bacteria, blocks bacterial cell wall synthesis by targeting essential peptidoglycan precursors, allowing it to kill drug-resistant bacterial pathogens without detectable resistance.

Nature Reviews Methods Primers, Published online: 20 July 2023; doi:10.1038/s43586-023-00238-7

Aptamers offer the specificity and affinity normally expected of antibodies but in small, chemically synthesized molecules free from cell culture-derived contaminants. In this Primer, DeRosa et al. provide guidance on the experimental design and data analysis of aptamers as well as considerations for improving reproducibility in experiments.

As antibiotic resistance soars, a journalist revisits an often overlooked antimicrobial strategy

Nature Chemical Biology, Published online: 13 July 2023; doi:10.1038/s41589-023-01387-2

Tian et al. developed a bacterial orthogonal DNA replication system by harnessing the temperate phage GIL16 DNA replication machinery, which provides a powerful tool for continuous evolution in prokaryotic cells.

A method is reported for sensitive enrichment of antigenic bioorthogonal peptides from APCs using click-antigens. Aha-containing peptides are captured on an alkynyl-functionalized solid support. Stringent washing removes a-specifically bound background molecules, prior to peptide retrieval by acid-mediated release. Femtomole amounts of click-antigen are identified from a full proteome digest, showing enrichment of rare Aha-containing peptides from complex mixtures.

Abstract

Uptake and processing of antigens by antigen presenting cells (APCs) is a key step in the initiation of the adaptive immune response. Studying these processes is complex as the identification of low abundant exogenous antigens from complex cell extracts is difficult. Mass-spectrometry based proteomics – the ideal analysis tool in this case – requires methods to retrieve such molecules with high efficiency and low background. Here, we present a method for the selective and sensitive enrichment of antigenic peptides from APCs using click-antigens; antigenic proteins expressed with azidohomoalanine (Aha) in place of methionine residues. We here describe the capture of such antigens using a new covalent method namely, alkynyl functionalized PEG-based Rink amide resin, that enables capture of click-antigens via copper-catalyzed azide-alkyne [2 + 3] cycloaddition (CuAAC). The covalent nature of the thus formed linkage allows stringent washing to remove a-specific background material, prior to retrieval peptides by acid-mediated release. We successfully identified peptides from a tryptic digest of the full APC proteome containing femtomole amounts of Aha-labelled antigen, making this a promising approach for clean and selective enrichment of rare bioorthogonally modified peptides from complex mixtures.

Nature Biotechnology, Published online: 15 February 2023; doi:10.1038/s41587-023-01694-y

First bee vaccine

Nature Biotechnology, Published online: 26 January 2023; doi:10.1038/s41587-022-01618-2

A generative deep-learning model designs artificial proteins with desired enzymatic activities.

Iterative rounds of directed evolution of PETase were performed employing a novel high-throughput fluorescence screening assay with a newly designed substrate BHET-OH. The generated DepoPETase enabled complete depolymerization of untreated PET wastes at mild temperature. The identified substitutions stabilized the loops around the active sites and transmitted the stabilization effect to the active sites through enhancing inter-loop interactions network.

Abstract

PETase displays great potential in PET depolymerization. Directed evolution has been limited to engineer PETase due to the lack of high-throughput screening assay. In this study, a novel fluorescence-based high-throughput screening assay employing a newly designed substrate, bis (2-hydroxyethyl) 2-hydroxyterephthalate (termed BHET-OH), was developed for PET hydrolases. The best variant DepoPETase produced 1407-fold more products towards amorphous PET film at 50 °C and showed a 23.3 °C higher T _m value than the PETase WT. DepoPETase enabled complete depolymerization of seven untreated PET wastes and 19.1 g PET waste (0.4 % W_enzyme/W_PET) in liter-scale reactor, suggesting that it is a potential candidate for industrial PET depolymerization processes. The molecular dynamic simulations revealed that the distal substitutions stabilized the loops around the active sites and transmitted the stabilization effect to the active sites through enhancing inter-loop interactions network.

A single-cell approach integrating D₂O-labeled Raman spectroscopy, advanced multivariate analysis and genotypic profiling was developed to in situ track the highly heterogeneous and dynamic physiological evolution trajectory of bacteria toward antibiotic resistance. The physiological diversification of single cells into four subpopulations preceding resistance from an isogeneic population was sensitively captured and their dynamic shift was tracked.

Abstract

Understanding evolution of antibiotic resistance is vital for containing its global spread. Yet our ability to in situ track highly heterogeneous and dynamic evolution is very limited. Here, we present a new single-cell approach integrating D₂O-labeled Raman spectroscopy, advanced multivariate analysis, and genotypic profiling to in situ track physiological evolution trajectory toward resistance. Physiological diversification of individual cells from isogenic population with cyclic ampicillin treatment is captured. Advanced multivariate analysis of spectral changes classifies all individual cells into four subsets of sensitive, intrinsic tolerant, evolved tolerant and resistant. Remarkably, their dynamic shifts with evolution are depicted and spectral markers of each state are identified. Genotypic analysis validates the phenotypic shift and provides insights into the underlying genetic basis. The new platform advances rapid phenotyping resistance evolution and guides evolution control.

Nature Catalysis, Published online: 23 January 2023; doi:10.1038/s41929-022-00904-1

Albicidin is a peptide antibiotic that has shown great promise for inhibiting DNA topoisomerase of fluoroquinolone-resistant Gram-negative pathogens, but its mode of action is not fully clear. Now, cryoelectron microscopy structures of albicidin–gyrase complexes provide detailed insights into the mechanism of this natural product.

We made a metagenome library and discovered urethanases that can hydrolyse a broad range of industrially relevant dicarbamates resulting from glycolysis of polyether-polyurethanes. This enables a two-step chemo-enzymatic recycling procedure consisting of glycolysis followed by enzymatic hydrolysis, allowing both the polyether polyols and the aromatic diamines to be recovered from polyether-polyurethane foams.

Abstract

Enzymatic degradation and recycling can reduce the environmental impact of plastics. Despite decades of research, no enzymes for the efficient hydrolysis of polyurethanes have been reported. Whereas the hydrolysis of the ester bonds in polyester-polyurethanes by cutinases is known, the urethane bonds in polyether-polyurethanes have remained inaccessible to biocatalytic hydrolysis. Here we report the discovery of urethanases from a metagenome library constructed from soil that had been exposed to polyurethane waste for many years. We then demonstrate the use of a urethanase in a chemoenzymatic process for polyurethane foam recycling. The urethanase hydrolyses low molecular weight dicarbamates resulting from chemical glycolysis of polyether-polyurethane foam, making this strategy broadly applicable to diverse polyether-polyurethane wastes.

Nature Chemical Biology, Published online: 02 January 2023; doi:10.1038/s41589-022-01223-z

A machine-learning method called MetalNet was developed to systematically predict metal-binding sites in proteomes using sequence co-evolution, which enabled the identification of new metalloproteins.

Uttamapinant et al. reported the discovery of new polyethylene terephthalate (PET) degrading enzymes from aquatic and human saliva metagenomes. Their catalytic performance is up to 83 times higher than known PETases. Site-specific incorporation of an unnatural amino acid results in a stable acyl-enzyme intermediate and a PET-enzyme conjugate which can be imaged via confocal microscopy.

Abstract

The discovery and engineering of new plastic degrading enzymes is an important challenge in chemical biotechnology to enable transition to a more sustainable and circular plastics economy. This field has so far yielded a range of enzymes and microbial pathways for the recycling and valorization of plastic waste. New research from Uttamapinant et al. reports the discovery of a novel polyethylene terephthalate (PET) hydrolase from the human saliva metagenome that displays improved properties and catalytic performance over previously characterized PET hydrolases (PETases). The authors also demonstrate the site-specific incorporation of a photocaged unnatural amino acid, 2,3-diaminopropionic acid (DAP), which upon photodecaging enables covalent binding of DAP to the PET surface. Thus, this work highlights metagenomic datasets as an untapped source of new PET degrading enzymes and the chemical modification of PETases via genetic code expansion, enabling new biotechnologies for the circular plastics economy.

Publication date: 9 February 2023

Source: Chem, Volume 9, Issue 2

Author(s): Cong Guo, Li-Qun Zhang, Wenjun Jiang