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1.
Nat Protoc ; 2024 Jun 12.
Article de Anglais | MEDLINE | ID: mdl-38867073

RÉSUMÉ

Catalytic mechanism-based, light-activated traps have recently been developed to identify the substrates of cysteine or serine hydrolases. These traps are hydrolase mutants whose catalytic cysteine or serine are replaced with genetically encoded 2,3-diaminopropionic acid (DAP). DAP-containing hydrolases specifically capture the transient thioester- or ester-linked acyl-enzyme intermediates resulting from the first step of the proteolytic reaction as their stable amide analogs. The trapped substrate fragments allow the downstream identification of hydrolase substrates by mass spectrometry and immunoblotting. In this protocol, we provide a detailed step-by-step guide for substrate capture and identification of the peptidase domain of the large tegument protein deneddylase (UL36USP) from human herpesvirus 1, both in mammalian cell lysate and live mammalian cells. Four procedures are included: Procedure 1, DAP-mediated substrate trapping in mammalian cell lysate (~8 d); Procedure 2, DAP-mediated substrate trapping in adherent mammalian cells (~6 d); Procedure 3, DAP-mediated substrate trapping in suspension mammalian cells (~5 d); and Procedure 4, substrate identification and validation (~12-13 d). Basic skills to perform protein expression in bacteria or mammalian cells, affinity enrichment and proteomic analysis are required to implement the protocol. This protocol will be a practical guide for identifying substrates of serine or cysteine hydrolases either in a complex mixture, where genetic manipulation is challenging, or in live cells such as bacteria, yeasts and mammalian cells.

2.
Nature ; 625(7995): 603-610, 2024 Jan.
Article de Anglais | MEDLINE | ID: mdl-38200312

RÉSUMÉ

The genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1-3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4-6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs-this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-L-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs in Escherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several ß-amino acids, α,α-disubstituted-amino acids and ß-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of ß-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers.


Sujet(s)
Acides aminés , Amino acyl-tRNA synthetases , Escherichia coli , Code génétique , ARN de transfert , Acylation , Acides aminés/composition chimique , Acides aminés/métabolisme , Amino acyl-tRNA synthetases/composition chimique , Amino acyl-tRNA synthetases/génétique , Amino acyl-tRNA synthetases/métabolisme , Code génétique/génétique , Hydroxyacides/composition chimique , Hydroxyacides/métabolisme , ARN de transfert/composition chimique , ARN de transfert/génétique , ARN de transfert/métabolisme , Spécificité du substrat , Ribosomes/métabolisme , Escherichia coli/enzymologie , Escherichia coli/génétique , Escherichia coli/métabolisme
3.
Science ; 383(6681): 421-426, 2024 Jan 26.
Article de Anglais | MEDLINE | ID: mdl-38271510

RÉSUMÉ

The evolution of new function in living organisms is slow and fundamentally limited by their critical mutation rate. Here, we established a stable orthogonal replication system in Escherichia coli. The orthogonal replicon can carry diverse cargos of at least 16.5 kilobases and is not copied by host polymerases but is selectively copied by an orthogonal DNA polymerase (O-DNAP), which does not copy the genome. We designed mutant O-DNAPs that selectively increase the mutation rate of the orthogonal replicon by two to four orders of magnitude. We demonstrate the utility of our system for accelerated continuous evolution by evolving a 150-fold increase in resistance to tigecycline in 12 days. And, starting from a GFP variant, we evolved a 1000-fold increase in cellular fluorescence in 5 days.


Sujet(s)
Réplication de l'ADN , Évolution moléculaire dirigée , Protéines Escherichia coli , Escherichia coli , Évolution moléculaire , Réplicon , DNA-directed DNA polymerase/génétique , DNA-directed DNA polymerase/métabolisme , Escherichia coli/effets des médicaments et des substances chimiques , Escherichia coli/génétique , Protéines Escherichia coli/génétique , Évolution moléculaire dirigée/méthodes , Protéines à fluorescence verte/génétique , Tigecycline/pharmacologie , Antibactériens/pharmacologie , Résistance bactérienne aux médicaments/génétique , Fluorescence
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