A 3′ terminal sugar-specific polymerase for terminator-free single-nucleotide extension of RNA oligonucleotides

Extant single-nucleotide extension (SNE) methods for oligonucleotide synthesis rely on terminator-modified substrates, which require complex nucleotide synthesis and induce side reactions that comprom...

researchsquare.com

Analog intrinsic recoding measures RNA dynamics without chemical conversion

Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...

biorxiv.org

A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins

Abstract. Efficient purification of specific RNAs from lysates remains a major challenge. Existing methods, such as MS2 tagging or oligonucleotide hybridiz

doi.org

High-precision binary trait association on phylogenetic trees

Traditional methods for identifying associations between genomic features and traits, or between pairs of genomic traits, struggle when applied to bacterial genomes. While several microbial genome-wid...

microbiologyresearch.org

DNA polymerization activates RNA cleavage of a reverse transcriptase–like antiviral enzyme

Defense-associated reverse transcriptases (DRTs) transcribe noncoding RNAs (ncRNAs) for antiviral defense, but the mechanisms of ncRNA-independent DRTs remain unclear. In this work, we show that a sin...

science.org

Complexity Postdoctoral Fellowship - Santa Fe Institute

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Animated E. coli Bacteria Drawing

Alt: Animated E. coli Bacteria Drawing

static.klipy.com

Mobility shapes plasmid GC content evolution

Plasmids are frequently AT-rich relative to their bacterial hosts. Despite this tendency towards lower GC content, plasmid and host chromosome GC content are positively correlated across diverse collections of plasmid-host pairs. However, the evolutionary processes underlying this pattern remain unclear. The classic model of amelioration predicts that horizontally acquired DNA gradually converges on host nucleotide composition. However, because plasmids can repeatedly transfer between bacterial hosts, the opportunity for such host-associated evolution may depend on their transmission dynamics. Using 50,936 plasmid-host pairs from a public sequence database, we found that the apparent global correlation between plasmid and host chromosome GC content was largely driven by differences between bacterial species rather than within species. We therefore accounted for plasmid and host population structure when testing how plasmid mobility shaped host-associated compositional evolution. We compared two contrasting regimes: a population of 3,682 Enterobacterales plasmids distributed across diverse host backgrounds, and six long-term host-associated plasmids from a Rhizobium leguminosarum lineage with INSeq-determined gene essentiality data. In the Enterobacterales population, GC content variation was overwhelmingly explained by plasmid lineage rather than host phylogeny, and conjugative plasmids showed greater similarity to their host chromosomes than mobilisable or non-mobilisable plasmids. In the Rhizobium leguminosarum plasmids, synonymous-site composition was more similar to the host chromosome among genes required across multiple host life stages. Together, these results support a model in which plasmid mobility influences the opportunity for host-associated evolutionary processes to alter nucleotide composition. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 319534/Z/24/Z St. John's College, University of Oxford, UK

doi.org

The planktonic microbiome of the Great Barrier Reef - Nature

The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...

nature.com

Step by mutational step

New bacterial regulatory interactions can evolve more readily than previously appreciated, providing new insights into the evolution of gene regulation.

elifesciences.org

CRISPR–Cas regulates expression of embedded anti-phage defence systems - Nature

CRISPR–Cas systems transcriptionally tune diverse innate defences using CRISPR RNA-like guides to balance antiviral protection with fitness, and hyperactivate these defences when compromised, establis...

nature.com

Research Professional I, Ecology & Evolutionary Biology (Extended Temporary)

Conducting scientific research, including:Maintaining bacterial glycerol stocks and managing common bacterial supplies (e.g., bacterial media, glycero...

arizona.csod.com

Doctoral and Postdoctoral Researcher Positions in the Cluster of Excellence ‘Microbes for Climate’

stellenangebote.uni-marburg.de

Chromosome topology gates productive RecA homology search

In homologous recombination, DNA repair depends on recombinase filaments finding homologous templates on chromosomes whose topology is continually remodeled by replication and transcription. How dynam...

biorxiv.org

Immune safeguarding as a conserved principle of antiviral defence - Nature Reviews Microbiology

All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death. Recent research increasingly shows...

nature.com

2027 Multi-Drug Efflux Systems Conference GRC

The 2027 Gordon Research Conference on Multi-Drug Efflux Systems will be held in Ventura, California. Apply today to reserve your spot.

grc.org

A family of lanthipeptides with anti-phage function

Shomar, Guillaume, et al. report the genomics-driven discovery of a family of more than 2,000 lanthipeptide biosynthetic gene clusters with anti-phage potential. They experimentally demonstrate anti-p...

cell.com