Mechanisms and clinical importance of bacteriophage resistance

JE Egido, AR Costa… - FEMS microbiology …, 2022 - academic.oup.com
We are in the midst of a golden age of uncovering defense systems against bacteriophages.
Apart from the fundamental interest in these defense systems, and revolutionary applications …

[HTML][HTML] Evolutionary plasticity and functional versatility of CRISPR systems

EV Koonin, KS Makarova - PLoS Biology, 2022 - journals.plos.org
The principal biological function of bacterial and archaeal CRISPR systems is RNA-guided
adaptive immunity against viruses and other mobile genetic elements (MGEs). These …

COG database update: focus on microbial diversity, model organisms, and widespread pathogens

MY Galperin, YI Wolf, KS Makarova… - Nucleic acids …, 2021 - academic.oup.com
Abstract The Clusters of Orthologous Genes (COG) database, also referred to as the
Clusters of Orthologous Groups of proteins, was created in 1997 and went through several …

Cyclic nucleotide-induced helical structure activates a TIR immune effector

G Hogrel, A Guild, S Graham, H Rickman, S Grüschow… - Nature, 2022 - nature.com
Cyclic nucleotide signalling is a key component of antiviral defence in all domains of life.
Viral detection activates a nucleotide cyclase to generate a second messenger, resulting in …

[HTML][HTML] Precise transcript targeting by CRISPR-Csm complexes

D Colognori, M Trinidad, JA Doudna - Nature biotechnology, 2023 - nature.com
Robust and precise transcript targeting in mammalian cells remains a difficult challenge
using existing approaches due to inefficiency, imprecision and subcellular …

Craspase is a CRISPR RNA-guided, RNA-activated protease

C Hu, SPB van Beljouw, KH Nam, G Schuler, F Ding… - Science, 2022 - science.org
The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated
with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided …

Alternative functions of CRISPR–Cas systems in the evolutionary arms race

P Mohanraju, C Saha, P van Baarlen… - Nature Reviews …, 2022 - nature.com
CRISPR–Cas systems of bacteria and archaea comprise chromosomal loci with typical
repetitive clusters and associated genes encoding a range of Cas proteins. Adaptation of …

RNA-targeting CRISPR–Cas systems

SPB van Beljouw, J Sanders… - Nature Reviews …, 2023 - nature.com
CRISPR–Cas is a widespread adaptive immune system in bacteria and archaea that
protects against viral infection by targeting specific invading nucleic acid sequences …

Cyclic nucleotide signaling in phage defense and counter-defense

JS Athukoralage, MF White - Annual review of virology, 2022 - annualreviews.org
Advances in our understanding of prokaryotic antiphage defense mechanisms in the past
few years have revealed a multitude of new cyclic nucleotide signaling molecules that play a …

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

JL Weissman, S Hou… - Proceedings of the …, 2021 - National Acad Sciences
Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders
of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth …