How mutations affect function.

A new study reveals how naturally occurring mutations affect the biophysical properties of nucleocapsid proteins in SARS-CoV-2.

Synthesis, insertion, and characterization of SARS-CoV-2 membrane protein within lipid bilayers.

Throughout history, coronaviruses have posed challenges to both public health and the global economy; nevertheless, methods to combat them remain rudimentary, primarily due to the absence of experiments to understand the function of various viral components. Among these, membrane (M) proteins are one of the most elusive because of their small size and challenges with expression. Here, we report the development of an expression system to produce tens to hundreds of milligrams of M protein per liter of culture.

Repetitive DNA regulates gene expression.

Short tandem repeats affect gene expression by binding regulatory proteins.

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity.

Here, a protocol is outlined to perform live, real-time imaging of transposable element activity in live bacterial cells using a suite of fluorescent reporters coupled to transposition. In particular, it demonstrates how real-time imaging can be used to assess the effects of the accessory protein TnpB on the activity of the transposable element IS608, a member of the IS200/IS605 family of transposable elements. The IS200/IS605 family of transposable elements are abundant mobile elements connected with one of the most innumerable genes found in nature, tnpB.

Tracking structural solvent reorganization and recombination dynamics following e photoabstraction from aqueous I with femtosecond x-ray spectroscopy and scattering.

We present a sub-picosecond resolved investigation of the structural solvent reorganization and geminate recombination dynamics following 400 nm two-photon excitation and photodetachment of a valence p electron from the aqueous atomic solute, I(aq). The measurements utilized time-resolved X-ray Absorption Near Edge Structure (TR-XANES) spectroscopy and X-ray Solution Scattering (TR-XSS) at the Linac Coherent Light Source x-ray free electron laser in a laser pump/x-ray probe experiment. The XANES measurements around the L-edge of the generated nascent iodine atoms (I) yield an average electron ejection distance from the iodine parent of 7.

Targeted insertion of large genetic payloads using cas directed LINE-1 reverse transcriptase.

A difficult genome editing goal is the site-specific insertion of large genetic constructs. Here we describe the GENEWRITE system, where site-specific targetable activity of Cas endonucleases is coupled with the reverse transcriptase activity of the ORF2p protein of the human retrotransposon LINE-1. This is accomplished by providing two RNAs: a guide RNA targeting Cas endonuclease activity and an appropriately designed payload RNA encoding the desired insertion.

with a Tunable Point Mutation Rate for Evolution Experiments.

The mutation rate and mutations' effects on fitness are crucial to evolution. Mutation rates are under selection due to linkage between mutation rate modifiers and mutations' effects on fitness. The linkage between a higher mutation rate and more beneficial mutations selects for higher mutation rates, while the linkage between a higher mutation rate and more deleterious mutations selects for lower mutation rates.

Tuning and Tracking of Coherent Shear Waves in Molecular Films.

We have determined the time-dependent displacement fields in molecular sub-micrometer thin films as response to femtosecond and picosecond laser pulse heating by time-resolved X-ray diffraction. This method allows a direct absolute determination of the molecular displacements induced by electron-phonon interactions, which are crucial for, for example, charge transport in organic electronic devices. We demonstrate that two different modes of coherent shear motion can be photoexcited in a thin film of organic molecules by careful tuning of the laser penetration depth relative to the thickness of the film.

Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell.

Phylogenetic evidence suggests that the invasion and proliferation of retroelements, selfish mobile genetic elements that copy and paste themselves within a host genome, was one of the early evolutionary events in the emergence of eukaryotes. Here we test the effects of this event by determining the pressures retroelements exert on simple genomes. We transferred two retroelements, human LINE-1 and the bacterial group II intron Ll.

Environment determines evolutionary trajectory in a constrained phenotypic space.

Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration.

Effect of Genomic Integration Location on Heterologous Protein Expression and Metabolic Engineering in E. coli.

Chromosomal integration offers a selection-free alternative to DNA plasmids for expression of foreign proteins and metabolic pathways. Episomal plasmid DNA is convenient but has drawbacks including increased metabolic burden and the requirement for selection in the form of antibiotics. E.

Real-time transposable element activity in individual live cells.

The excision and reintegration of transposable elements (TEs) restructure their host genomes, generating cellular diversity involved in evolution, development, and the etiology of human diseases. Our current knowledge of TE behavior primarily results from bulk techniques that generate time and cell ensemble averages, but cannot capture cell-to-cell variation or local environmental and temporal variability. We have developed an experimental system based on the bacterial TE IS608 that uses fluorescent reporters to directly observe single TE excision events in individual cells in real time.

Ribosome biogenesis in replicating cells: Integration of experiment and theory.

Ribosomes-the primary macromolecular machines responsible for translating the genetic code into proteins-are complexes of precisely folded RNA and proteins. The ways in which their production and assembly are managed by the living cell is of deep biological importance. Here we extend a recent spatially resolved whole-cell model of ribosome biogenesis in a fixed volume [Earnest et al.

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells.

Live cell RNA imaging using genetically encoded fluorescent labels is an important tool for monitoring RNA activities. A recently reported RNA aptamer-fluorogen system, the Spinach, in which an RNA aptamer binds and induces the fluorescence of a GFP-like 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) ligand, can be readily tagged to the RNA of interest. Although the aptamer-fluorogen system is sufficient for imaging highly abundant non-coding RNAs (tRNAs, rRNAs, etc.

An Integrated System for Precise Genome Modification in Escherichia coli.

We describe an optimized system for the easy, effective, and precise modification of the Escherichia coli genome. Genome changes are introduced first through the integration of a 1.3 kbp Landing Pad consisting of a gene conferring resistance to tetracycline (tetA) or the ability to metabolize the sugar galactose (galK).

Automated single cell microbioreactor for monitoring intracellular dynamics and cell growth in free solution.

We report an automated microfluidic-based platform for single cell analysis that allows for cell culture in free solution with the ability to control the cell growth environment. Using this approach, cells are confined by the sole action of gentle fluid flow, thereby enabling non-perturbative analysis of cell growth away from solid boundaries. In addition, the single cell microbioreactor allows for precise and time-dependent control over cell culture media, with the combined ability to observe the dynamics of non-adherent cells over long time scales.

The non-ergodic nature of internal conversion.

The absorption of light by molecules can induce ultrafast dynamics and coupling of electronic and nuclear vibrational motion. The ultrafast nature in many cases rests on the importance of several potential energy surfaces in guiding the nuclear motion-a concept of central importance in many aspects of chemical reaction dynamics. This Minireview focuses on the non-ergodic nature of internal conversion, that is, on the concept that the nuclear dynamics only sample a reduced phase space, potentially resulting in localization of the dynamics in real space.

DNA-binding-protein inhomogeneity in E. coli modeled as biphasic facilitated diffusion.

We have recently shown that nonspecifically bound lac repressors are spatially inhomogeneous in E. coli cells and depends upon the location of its encoding gene and the DNA compaction state [Kuhlman and Cox, Mol. Syst.

Symmetry, vibrational energy redistribution and vibronic coupling: the internal conversion processes of cycloketones.

In this paper, we discern two basic mechanisms of internal conversion processes; one direct, where immediate activation of coupling modes leads to fast population transfer and one indirect, where internal vibrational energy redistribution leads to equidistribution of energy, i.e., ergodicity, and slower population transfer follows.

Between ethylene and polyenes--the non-adiabatic dynamics of cis-dienes.

Using Ab Initio Multiple Spawning (AIMS) with a Multi-State Multi-Reference Perturbation theory (MS-MR-CASPT2) treatment of the electronic structure, we have simulated the non-adiabatic excited state dynamics of cyclopentadiene (CPD) and 1,2,3,4-tetramethyl-cyclopentadiene (Me4-CPD) following excitation to S1. It is observed that torsion around the carbon-carbon double bonds is essential in reaching a conical intersection seam connecting S1 and S0. We identify two timescales; the induction time from excitation to the onset of population transfer back to S0 (CPD: -25 fs, Me4-CPD: -71 fs) and the half-life of the subsequent population transfer (CPD: -28 fs, Me4-CPD: -48 fs).

Surprising intrinsic photostability of the disulfide bridge common in proteins.

For a molecule to survive evolution and to become a key building block in nature, photochemical stability is essential. The photolytically weak S-S bond does not immediately seem to possess that ability. We mapped the real-time motion of the two sulfur radicals that result from disulfide photolysis on the femtosecond time scale and found the reason for the existence of the S-S bridge as a natural building block in folded structures.

Gene location and DNA density determine transcription factor distributions in Escherichia coli.

The diffusion coefficient of the transcription factor LacI within living Escherichia coli has been measured directly by in vivo tracking to be D = 0.4 μm(2)/s. At this rate, simple models of diffusion lead to the expectation that LacI and other proteins will rapidly homogenize throughout the cell.

Coherent motion reveals non-ergodic nature of internal conversion between excited states.

We found that specific nuclear motion along low-frequency modes is effective in coupling electronic states and that this motion prevail in some small molecules. Thus, in direct contradiction to what is expected based on the standard models, the internal conversion process can proceed faster for smaller molecules. Specifically, we focus on the S(2) →S(1) internal conversion in cyclobutanone, cyclopentanone, and cyclohexanone.