Volume 15 Issue 2, February 2019

Two protein circuit systems, split-protease-cleavable orthogonal coiled-coil logic (SPOC logic) and circuits of hacked orthogonal modular proteases (CHOMP), have been developed to permit rapid and logic function-based control of mammalian cellular signaling.

The carboxyl-terminal domain (CTD) of RNA polymerase II (Pol II) is post-translationally modified during gene expression. A recent study has identified a CTD kinase, Hrr25, that regulates the termination of noncoding RNA genes by recruiting Rtt103, a key termination factor.

Faster-than-transcription control of cellular activities is an important but challenging engineering target. Using split ferredoxins and induced dimerization or conformational changes, newly developed metalloprotein switches provide a fast method to control electron flux.

A collection of genetically encoded tools, each with their own capabilities, limitations and performance characteristics, are available for monitoring and manipulating neuronal activity that could allow visualizing the brain at single-cell resolution.

Transcription factor decoys, DNA molecules designed to mimic regulatory DNAs and prevent repressors binding to their DNA targets, are used to achieve de-repression of silent biosynthetic gene clusters, resulting in production of new natural products.

Protease-cleavable orthogonal-coiled-coil-based (SPOC) systems, in which split viral proteases are activated by small molecules and cleave coiled-coil protease substrates, reprogram signaling with rapid kinetics in mammalian cells.

Ten new RNA polymerase II kinases were identified, of these Hrr25 was engineered to enable covalent and noncovalent chemical inhibition in vivo, revealing that this kinase regulates polymerase function at noncoding snoRNA genes.

Structural analysis of the human MePCE methyltransferase domain in complex with 7SK in the presence of SAH or SAM reveals that MePCE has higher affinity for capped 7SK and holds it for subsequent assembly of 7SK RNP.

A mass-spectrometry-based approach to identify E. coli targets of ppGpp finds 56 putative targets including enzymes involved in nucleotide synthesis, such as PurF, which is directly inhibited by ppGpp, regulating adenosine and guanine nucleotide synthesis.

A NO delivery system that depends on the hydrolysis of an alkyl-galactose-conjugated NO prodrug by an engineered galactosidase developed using a ‘bump-and-hole’ strategy enabled targeted delivery of NO to specific tissues.

A combination of elicitor screening to induce expression of silent biosynthetic gene clusters with imaging mass spectrometry to visualize the resulting metabolome enables the discovery of nine cryptic natural products.

Screening with a small-molecule reactive-oxygen-species generator identifies the serine hydrolase enzyme ABHD12 as a lipase for the proapoptotic oxidized phoshatidylserine (ox-PS) lipids, which trigger production of proinflammatory cytokines.

A cell-based phenotypic screen identifying inhibitors of Notch signaling led to the discovery of NVS-ZP7-4, which blocks the activity of the zinc transporter SLC39a7 (ZIP7) and induces cell death through an ER stress mechanism.

Designed split ferredoxins, fused to protein fragments that associate under certain conditions such as the presence of rapamycin, enable transcriptional and post-translational control over electron transfer in Escherichia coli cells and lysates.

A directed evolution approach was applied to optimize a set of 12 small-molecule-responsive biosensors, which led to the engineering of “Marionette” strains of Escherichia coli incorporating these sensors for biotechnological applications.