Environmental Perturbations Lift the Degeneracy of the Genetic Code to Regulate Protein Levels in Bacteria

The genetic code underlying protein synthesis is a canonical example of a degenerate biological system. Degeneracies in physical and biological systems can be lifted by external perturbations, thus allowing degenerate systems to exhibit a wide range of behaviors. Here we show that the degeneracy of the genetic code is lifted by environmental perturbations to regulate protein levels in living cells. By measuring protein synthesis rates from a synthetic reporter library in Escherichia coli, we find that environmental perturbations, such as reduction of cognate amino acid supply, lift the degeneracy of the genetic code by splitting codon families into a hierarchy of robust and sensitive synonymous codons. Rates of protein synthesis associated with robust codons are up to 100-fold higher than those associated with sensitive codons under these conditions. We find that the observed hierarchy between synonymous codons is not determined by usual rules associated with tRNA abundance and codon usage. Rather, competition among tRNA isoacceptors for aminoacylation underlies the robustness of protein synthesis. Remarkably, the hierarchy established using the synthetic library also explains the measured robustness of synthesis for endogenous proteins in E. coli. We further found that the same hierarchy is reflected in the fitness cost of synonymous mutations in amino acid biosynthesis genes and in the transcriptional control of σ-factor genes. Our study suggests that organisms can exploit degeneracy lifting as a general strategy to adapt protein synthesis to their environment.Molecular and Cellular Biolog

Entanglement entropy and multifractality at localization transitions

The von Neumann entanglement entropy is a useful measure to characterize a quantum phase transition. We investigate the non-analyticity of this entropy at disorder-dominated quantum phase transitions in non-interacting electronic systems. At these critical points, the von Neumann entropy is determined by the single particle wave function intensity which exhibits complex scale invariant fluctuations. We find that the concept of multifractality is naturally suited for studying von Neumann entropy of the critical wave functions. Our numerical simulations of the three dimensional Anderson localization transition and the integer quantum Hall plateau transition show that the entanglement at these transitions is well described using multifractal analysis.Comment: v3, 5 pages, published versio

Boundary criticality and multifractality at the 2D spin quantum Hall transition

Multifractal scaling of critical wave functions at a disorder-driven (Anderson) localization transition is modified near boundaries of a sample. Here this effect is studied for the example of the spin quantum Hall plateau transition using the supersymmetry technique for disorder averaging. Upon mapping of the spin quantum Hall transition to the classical percolation problem with reflecting boundaries, a number of multifractal exponents governing wave function scaling near a boundary are obtained exactly. Moreover, additional exact boundary scaling exponents of the localization problem are extracted, and the problem is analyzed in other geometries.Comment: v2, 17 pages, 10 figures, published versio

A serine sensor for multicellularity in a bacterium

We report the discovery of a simple environmental sensing mechanism for biofilm formation in the bacterium Bacillus subtilis that operates without the involvement of a dedicated RNA or protein. Certain serine codons, the four TCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these TCN codons with AGC or AGT impaired biofilm formation and gene expression. Conversely, switching AGC or AGT to TCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosome density was higher at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome occupancy and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, reduced translation speed at serine codons may be exploited by other microbes in adapting to stationary phase. DOI: http://dx.doi.org/10.7554/eLife.01501.00