Title: A universal glycoenzyme biosynthesis pipeline that enables efficient cell-free remodeling of glycans
Abstract The ability to reconstitute natural glycosylation pathways or prototype entirely new ones from scratch is hampered by the limited availability of functional glycoenzymes, many of which are membrane proteins that fail to express in heterologous hosts. Here, we describe a strategy for topologically converting membrane-bound glycosyltransferases (GTs) into water soluble biocatalysts, which are expressed at high levels in the cytoplasm of living cells with retention of biological activity. We demonstrate the universality of the approach through facile production of 98 difficult-to-express GTs, predominantly of human origin, across several commonly used expression platforms. Using a subset of these water-soluble enzymes, we perform structural remodeling of both free and protein-linked glycans including those found on the monoclonal antibody therapeutic trastuzumab. Overall, our strategy for rationally redesigning GTs provides an effective and versatile biosynthetic route to large quantities of diverse, enzymatically active GTs, which should find use in structure-function studies as well as in biochemical and biomedical applications involving complex glycomolecules. more »« less
Zabotina, Olga A.; Zhang, Ning; Weerts, Richard
(, Frontiers in Plant Science)
null
(Ed.)
Glycosyltransferases (GTs) are enzymes that catalyze reactions attaching an activated sugar to an acceptor substrate, which may be a polysaccharide, peptide, lipid, or small molecule. In the past decade, notable progress has been made in revealing and cloning genes encoding polysaccharide-synthesizing GTs. However, the vast majority of GTs remain structurally and functionally uncharacterized. The mechanism by which they are organized in the Golgi membrane, where they synthesize complex, highly branched polysaccharide structures with high efficiency and fidelity, is also mostly unknown. This review will focus on current knowledge about plant polysaccharide-synthesizing GTs, specifically focusing on protein-protein interactions and the formation of multiprotein complexes.
Goverde, Casper A; Pacesa, Martin; Goldbach, Nicolas; Dornfeld, Lars J; Balbi, Petra_E M; Georgeon, Sandrine; Rosset, Stéphane; Kapoor, Srajan; Choudhury, Jagrity; Dauparas, Justas; et al
(, Nature)
Abstract De novo design of complex protein folds using solely computational means remains a substantial challenge1. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors2, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
Peruzzi, Justin A.; Jacobs, Miranda L.; Vu, Timothy Q.; Wang, Kenneth S.; Kamat, Neha P.
(, Angewandte Chemie International Edition)
Abstract Targeted vesicle fusion is a promising approach to selectively control interactions between vesicle compartments and would enable the initiation of biological reactions in complex aqueous environments. Here, we explore how two features of vesicle membranes, DNA tethers and phase‐segregated membranes, promote fusion between specific vesicle populations. Membrane phase‐segregation provides an energetic driver for membrane fusion that increases the efficiency of DNA‐mediated fusion events. The orthogonality provided by DNA tethers allows us to direct fusion and delivery of DNA cargo to specific vesicle populations. Vesicle fusion between DNA‐tethered vesicles can be used to initiate in vitro protein expression to produce model soluble and membrane proteins. Engineering orthogonal fusion events between DNA‐tethered vesicles provides a new strategy to control the spatiotemporal dynamics of cell‐free reactions, expanding opportunities to engineer artificial cellular systems.
Flores, Judith; Brea, Roberto J.; Lamas, Alejandro; Fracassi, Alessandro; Salvador‐Castell, Marta; Xu, Cong; Baiz, Carlos R.; Sinha, Sunil K.; Devaraj, Neal K.
(, Angewandte Chemie International Edition)
Abstract Cell membranes define the boundaries of life and primarily consist of phospholipids. Living organisms assemble phospholipids by enzymatically coupling two hydrophobic tails to a soluble polar head group. Previous studies have taken advantage of micellar assembly to couple single‐chain precursors, forming non‐canonical phospholipids. However, biomimetic nonenzymatic coupling of two alkyl tails to a polar head‐group remains challenging, likely due to the sluggish reaction kinetics of the initial coupling step. Here we demonstrate rapid de novo formation of biomimetic liposomes in water using dual oxime bond formation between two alkyl chains and a phosphocholine head group. Membranes can be generated from non‐amphiphilic, water‐soluble precursors at physiological conditions using micromolar concentrations of precursors. We demonstrate that functional membrane proteins can be reconstituted into synthetic oxime liposomes from bacterial extracts in the absence of detergent‐like molecules.
Ranaweera, I; Shrestha, U; Ranjana, KC; Varela, M
(, Trends in Cell & Molecular Biology)
The biological membrane is an efficient barrier against water-soluble substances. Solute transporters circumvent this membrane barrier by transporting water-soluble solutes across the membrane to the other sides. These transport proteins are thus required for all living organisms. Microorganisms, such as bacteria, effectively exploit solute transporters to acquire useful nutrients for growth or to expel substances that are inhibitory to their growth. Overall, there are distinct types of related solute transporters that are grouped into families or superfamilies. Of these various transporters, the major facilitator superfamily (MFS) represents a very large and constantly growing group and are driven by solute- and ion-gradients, making them passive and secondary active transporters, respectively. Members of the major facilitator superfamily transport an extreme variety of structurally different substrates such as antimicrobial agents, amino acids, sugars, intermediary metabolites, ions, and other small molecules. Importantly, bacteria, especially pathogenic ones, have evolved multidrug efflux pumps which belong to the major facilitator superfamily. Furthermore, members of this important superfamily share similar primary sequences in the form of highly conserved sequence motifs that confer useful functional properties during transport. The transporters of the superfamily also share similarities in secondary structures, such as possessing 12- or 14-membrane spanning α-helices and the more recently described 3-helix structure repeat element, known as the MFS fold. The three-dimensional structures of bacterial multidrug efflux pumps have been determined for only a few members of the superfamily, all drug pumps of which are surprisingly from Escherichia coli. This review briefly summarizes the structural properties of the bacterial multidrug efflux pumps of the major facilitator superfamily in a comparative manner and provides future directions for study.
Jaroentomeechai, Thapakorn, Kwon, Yong Hyun, Liu, Yiwen, Young, Olivia, Bhawal, Ruchika, Wilson, Joshua D., Li, Mingji, Chapla, Digantkumar G., Moremen, Kelley W., Jewett, Michael C., Mizrachi, Dario, and DeLisa, Matthew P.
"A universal glycoenzyme biosynthesis pipeline that enables efficient cell-free remodeling of glycans". Nature Communications 13 (1). Country unknown/Code not available: Nature Publishing Group. https://doi.org/10.1038/s41467-022-34029-7.https://par.nsf.gov/biblio/10376877.
@article{osti_10376877,
place = {Country unknown/Code not available},
title = {A universal glycoenzyme biosynthesis pipeline that enables efficient cell-free remodeling of glycans},
url = {https://par.nsf.gov/biblio/10376877},
DOI = {10.1038/s41467-022-34029-7},
abstractNote = {Abstract The ability to reconstitute natural glycosylation pathways or prototype entirely new ones from scratch is hampered by the limited availability of functional glycoenzymes, many of which are membrane proteins that fail to express in heterologous hosts. Here, we describe a strategy for topologically converting membrane-bound glycosyltransferases (GTs) into water soluble biocatalysts, which are expressed at high levels in the cytoplasm of living cells with retention of biological activity. We demonstrate the universality of the approach through facile production of 98 difficult-to-express GTs, predominantly of human origin, across several commonly used expression platforms. Using a subset of these water-soluble enzymes, we perform structural remodeling of both free and protein-linked glycans including those found on the monoclonal antibody therapeutic trastuzumab. Overall, our strategy for rationally redesigning GTs provides an effective and versatile biosynthetic route to large quantities of diverse, enzymatically active GTs, which should find use in structure-function studies as well as in biochemical and biomedical applications involving complex glycomolecules.},
journal = {Nature Communications},
volume = {13},
number = {1},
publisher = {Nature Publishing Group},
author = {Jaroentomeechai, Thapakorn and Kwon, Yong Hyun and Liu, Yiwen and Young, Olivia and Bhawal, Ruchika and Wilson, Joshua D. and Li, Mingji and Chapla, Digantkumar G. and Moremen, Kelley W. and Jewett, Michael C. and Mizrachi, Dario and DeLisa, Matthew P.},
}
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