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Suppression of amber stop codons impairs pathogenicity in Salmonella.
FEBS Lett
December 2024
Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA.
Translation terminates at UAG (amber), UGA (opal), and UAA (ochre) stop codons. In nature, readthrough of stop codons can be substantially enhanced by suppressor tRNAs. Stop-codon suppression also provides powerful tools in synthetic biology and disease treatment.
View Article and Find Full Text PDFDirected Evolution of Pyrrolysyl-tRNA Synthetase for the Genetic Incorporation of Two Different Noncanonical Amino Acids in One Protein.
ACS Bio Med Chem Au
October 2024
Texas A&M Drug Discovery Center and Department of Chemistry, College of Arts and Sciences, Texas A&M University, College Station, Texas 77843, United States.
The genetic code expansion technique is a powerful chemical biology tool to install noncanonical amino acids (ncAAs) in proteins. As a key enzyme for this technique, pyrrolysyl-tRNA synthetase (PylRS), coupled with its cognate amber suppressor tRNA, has been engineered for the genetic incorporation of more than 200 ncAAs. Using PylRS clones from different archaeal origins, two ncAAs have also been genetically encoded in one protein.
View Article and Find Full Text PDFA conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses.
bioRxiv
August 2024
Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Alphaviruses are enveloped, single-stranded, positive-sense RNA viruses that often require transmission between arthropod and vertebrate hosts for their sustained propagation. Most alphaviruses encode an opal (UGA) termination codon in nonstructural protein 3 (nsP3) upstream of the viral polymerase, nsP4. The selective constraints underlying the conservation of the opal codon are poorly understood.
View Article and Find Full Text PDFComprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR.
Int J Cancer
November 2023
Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance.
View Article and Find Full Text PDFPI3Kβ controls immune evasion in PTEN-deficient breast tumours.
Nature
May 2023
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
Loss of the PTEN tumour suppressor is one of the most common oncogenic drivers across all cancer types. PTEN is the major negative regulator of PI3K signalling. The PI3Kβ isoform has been shown to play an important role in PTEN-deficient tumours, but the mechanisms underlying the importance of PI3Kβ activity remain elusive.
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