Blog


Isolation through unity: creating orthogonal ribosomes through tethered subunit assembly
By Patrick Ginther & Jason Ray
For several decades, polyethers, such as polyethylene glycol (PEG) have garnered tremendous interest as functional biomaterials due to their biocompatible nature.
Sequence-defined Multifunctional Polyethers
By Joshua A. Walker
For several decades, polyethers, such as polyethylene glycol (PEG) have garnered tremendous interest as functional biomaterials due to their biocompatible nature.
Cell-free protein synthesis
By Fred Ward
Cell-free protein synthesis (CFPS) is a powerful way to explore the synthesis of proteins and other polymers outside of the cellular environment.
EvolvR: where precision meets diversity
By Omer Ad & Patrick Ginther

EvolvR, a tool developed in UC Berkeley and the Innovative Genomics Institute (IGI), set out to solve one grand challenge – the ability to completely diversify all of the nucleotides at a user-defined location in an organism’s genome in a continuous fashion [1]. EvolvR relies on a fusion of two proteins. The first, nCas9 creates a single-stranded nick in an “editing window” and the second enzyme, a nick-translating low-fidelity DNA polymerase I (PolI3M), then proceeds to diversify the “editing window” through substitution, deletion, and insertions of bases. The work focused on engineering and optimizing the components of the protein chimera such that the mutation rate and base mutation window were increased, as well as identifying mutations that enable improved dissociation of nCas9 from its DNA target [1].

Mitigating translation arrest caused by D-α-amino acids
By Jason Ray

A recent study by Ruben L. Gonzalez Jr. and coworkers [1] provides insight into how to improve the incorporation of D-α-amino acids into proteins. It has already been shown that D-α-amino acids can be incorporated at the C-terminus of a growing peptide chain by wild type E. coli ribosomes [2] but at a cost: they halt translation in a fraction of the incorporating ribosomes. The proportion of ribosomes that stall out during translation depends on the identity of the D-α-amino acid at the C-terminus of the peptidyl-D-aminoacyl-tRNA.

Driving orthogonality between variant pyrrolysyl-tRNA synthetase/tRNA pairs
By Patrick Ginther

In a recent 2018 Nature news & views, the work of Jason Chin and co-workers was highlighted for the lab’s extraordinary work on developing new tools for synthetic biology [1]. Specifically, Chin and co-workers successfully generated a variant of the pyrrolysyl-tRNA synthetase/tRNA pair (PylRS/pyltRNA) derived from Methanomethylophilus alvus (Ma) that was mutually orthogonal to the commonly used Methanosarcina mazei (Mm) and methanosarcina barkeri (Mb) PylRS/pyltRNA pairs [2].

Ronald Breaker’s "Riboswitches and Translation Control"
By Kyle Hoffman

Ronald Breaker’s recent review on riboswitches and translation control, published in Cold Spring Harbor Perspectives in Biology,[1], describes the fascinating mechanisms of RNA regulation of gene expression. Riboswitches are defined as RNA structures, typically found in the 5’ untranslated region (5’UTR) of mRNA, that sense and respond to small molecules, metabolites, or coenzymes to regulate transcription and translation. While he speculates that many riboswitch classes likely remain to be discovered, the article nicely highlights a number of riboswitch mechanisms that have been elucidated.

Ribosome assembly revealed by cryo-EM
By Fred Ward

Ribosome assembly is a remarkably complex cellular process. In the yeast large subunit (60S) alone, it requires the ordered association and folding of 3 rRNAs and 46 r-proteins as the nascent ribosomes move from the nucleolus, to the nucleus, and finally to the cytoplasm. Like workers building a house, there are over 200 proteins, knows as assembly factors (AFs), that coordinate the construction of these gigantic cellular machines. ...

Replacement of a histidine by a non-canonical amino acid to generate a dependent organism
By Pol Arranz Gibert

In a recent paper in JACS, Schultz and co-workers present a strategy where replacing a key amino acid of an enzyme by a non-standard amino acid (nsAA) produces an organism that requires this nsAA for survival. ...

Addition by subtraction
By Omer Ad

Posttranslational modifications (PTMs) are responsible for some of the most exotic ribosomally synthesized peptide backbones in biology. Examples include manipulations to generate D-amino acids, thioether linkages, and even formation amino acids with sp2 hybridized α-carbons [1]. In a recent publication by Jörn Piel’s research group in Science, bacteria are capable of making another unusual PTM - α-keto-β-amino amide formation [2].

More peptides with backbone modifications from wild type ribosomes in vitro
By Kyle Hoffman

In the most recent issue of Organic and Biomolecular Chemistry, a paper from Matthew Hartman’s lab highlights the use of an editing-deficient valine-tRNA synthetase (ValRS T222P) to incorporate 11 non-canonical amino acids (ncAAs) into peptides synthesized in vitro [1].

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