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The authors describe BoltzNet, a neural network that learns the energy of transcription factor (TF)-DNA binding from genomic data and can be used to design new binding sites. They report the in vivo mapping and BoltzNet modeling of 139 E. coli TFs.

A suite of bridged rhodamine dyes (BriDyes) offers excellent brightness, solubility, photostability, and tunable cell permeability along with resistance to photoblueing, making them exceptional all-pu...

Internal promoters in operons are critical in genome-wide stress responses, compensating for frequent premature RNAP falloffs.

The mechanisms underlying bacterial chromosome configuration are not fully understood. Here, Spahn et al. show that the Escherichia coli nucleoid adopts a condensed, membrane-proximal configuration du...

Nature Physics - Oscillatory Min protein patterns prevent abnormal bacterial cell division. Now it is shown that Min pattern formation is resource efficient and involves wavelength-invariant...

The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal mul...

Yellow fluorescent proteins (YFPs) photobleach rapidly, restricting microscopy experiments. Here, the authors report mGold2s and mGold2t, YFPs that extend imaging durations up to 25 times longer than ...

Adhikashreni et al. use quantitative live-cell imaging to track cell-cycle dynamics in hundreds of individual bacteria. They observe nutrient-dependent regulation of replication elongation rates that ...

DNA replication initiation is orchestrated in many prokaryotes by the replication initiator DnaA. Two models for regulation of DnaA activity in Escherichia coli have been proposed: the switch between ...

The DNA of bacterial cells is organized in a highly dynamic chromosome structure. To guarantee its propagation, the chromosome must replicate, segregate, and accommodate other biological processes lik...

A high number of genetic fitness peaks does not impair adaptive evolution in a large empirical fitness landscape.