We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mechanisms are still poorly understood. A collection of contributions to a recent interdisciplinary CECAM (Center Européen de Calcul Atomique et Moléculaire) workshop is used hereto provide an overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems. The main conceptual frameworks instrumental in driving the field are discussed. We illustrate the role of these frameworks in illuminating molecular mechanisms and explaining cellular processes, and describe some of their promising practical applications in engineering molecular sensors and informing drug design efforts.

Protein acetylation emerged as a key regulatory mechanism for many cellular processes. We used genetic analysis of Saccharomyces cerevisiae to identify Esa1 as a histone acetyltransferase required for autophagy. We further identified the autophagy signaling component Atg3 as a substrate for Esa1. Specifically, acetylation of K19 and K48 of Atg3 regulated autophagy by controlling Atg3 and Atg8 interaction and lipidation of Atg8. Starvation induced transient K19-K48 acetylation through spatial and temporal regulation of the localization of acetylase Esa1 and the deacetylase Rpd3 on pre-autophagosomal structures (PASs) and their interaction with Atg3. Attenuation of K19-K48 acetylation was associated with attenuation of autophagy. Increased K19-K48 acetylation after deletion of the deacetylase Rpd3 caused increased autophagy. Thus, protein acetylation contributes to control of autophagy.

Oxidant-mediated antibacterial response systems are broadly used to control bacterial proliferation. Hypochlorite (HOCl) is an important component of the innate immune system produced in neutrophils and specific epithelia. Its antimicrobial activity is due to damaging cellular macromolecules. Little is known about how bacteria escape HOCl-inflicted damage. Recently, the transcription factor YjiE was identified that specifically protects Escherichia coli from HOCl killing. According to its function, YjiE is now renamed HypT (hypochlorite-responsive transcription factor). Here we unravel that HypT is activated by methionine oxidation to methionine sulfoxide. Interestingly, so far only inactivation of cellular proteins by methionine oxidation has been reported. Mutational analysis revealed three methionines that are essential to confer HOCl resistance. Their simultaneous substitution by glutamine, mimicking the methionine sulfoxide state, increased the viability of E. coli cells upon HOCl stress. Triple glutamine substitution generates a constitutively active HypT that regulates target genes independently of HOCl stress and permanently down-regulates intracellular iron levels. Inactivation of HypT depends on the methionine sulfoxide reductases A/B. Thus, microbial protection mechanisms have evolved along the evolution of antimicrobial control systems, allowing bacteria to survive within the host environment.

Background: Hypochlorite is strongly bactericidal and used as disinfectant; yet, a response regulator allowing adaptation to the inflicted stress is so far unknown. Results: The transcription factor YjiE specifically confers hypochlorite resistance and is an atypical dodecameric regulator that undergoes DNA-induced dissociation to dimers and tetramers. Conclusion: YjiE protects cells from hypochlorite-induced oxidative damage by triggering a specific stress response. Significance: This is the first described hypochlorite-specific regulator.

We introduce a numerical scheme to evolve functional elastic materials that can accomplish a specified mechanical task. In this scheme, the number of solutions, their spatial architectures, and the correlations among them can be computed. As an example, we consider an "allosteric" task, which requires the material to respond specifically to a stimulus at a distant active site. We find that functioning materials evolve a less-constrained trumpetshaped region connecting the stimulus and active sites, and that the amplitude of the elastic response varies nonmonotonically along the trumpet. As previously shown for some proteins, we find that correlations appearing during evolution alone are sufficient to identify key aspects of this design. Finally, we show that the success of this architecture stems from the emergence of soft edge modes recently found to appear near the surface of marginally connected materials. Overall, our in silico evolution experiment offers a window to study the relationship between structure, function, and correlations emerging during evolution. disordered materials | proteins | evolution P roteins are long polymers that can fold in a reproducible way and achieve a specific function. Often, the activity of the main functional site depends on the binding of an effector on a distant site (1, 2). Such an allosteric behavior can occur over large distances, such as 20 residues or more (3), and often involves only a sparse subset of residues in the protein (3, 4). Allosteric regulation offers an appealing target for drug design (5), and there is considerable interest in predicting allosteric pathways (6, 7). One central difficulty is that the physical mechanisms allowing such an "action at a distance" remain elusive. In some cases, allostery can be understood as the modulation of a hinge connecting two extended rigid parts of the protein (8, 9), but, often, the displacement field induced by the binding of the effector cannot be described in these terms (4, 10, 11). Another route, statistical coupling analysis (12), considers correlations within sequences of proteins of the same family to infer allosteric pathways (4, 7). The generality of this elegant approach is, however, debated (13).From a physical viewpoint, specific response at a distance is surprising. The structure of proteins is similar to randomly packed spheres (14). Generically, the response of such systems is nonspecific and decays rapidly in space (in a manner similar to a continuum medium) at distances larger than the particle size; this is true, except close to a critical point where the number of constraints coming from strongly interacting particles is just sufficient to match the number of degrees of freedom of the particles (15). There, the elastic response becomes heterogeneous on all scales (16,17). This point is illustrated in Fig. 1A, showing the rapidly decaying response of a random spring network to a stimulus. However, as shown in Fig. 1B (and independently found in ref. 18 using a different algorithm), springs can be move...

Respiratory viral infections are associated with an increased risk of asthma, but how acute Th1 antiviral immune responses lead to chronic inflammatory Th2 disease remains undefined. We define a novel pathway that links transient viral infection to chronic lung disease with dendritic cell (DC) expression of the high-affinity IgE receptor (FcεRIα). In a mouse model of virus-induced chronic lung disease, in which Sendai virus triggered a switch to persistent mucous cell metaplasia and airway hyperreactivity after clearance of replicating virus, we found that FceRIa−/− mice no longer developed mucous cell metaplasia. Viral infection induced IgE-independent, type I IFN receptor–dependent expression of FcεRIα on mouse lung DCs. Cross-linking DC FcεRIα resulted in the production of the T cell chemoattractant CCL28. FceRIa−/− mice had decreased CCL28 and recruitment of IL-13–producing CD4+ T cells to the lung after viral infection. Transfer of wild-type DCs to FceRIa−/− mice restored these events, whereas blockade of CCL28 inhibited mucous cell metaplasia. Therefore, lung DC expression of FcεRIα is part of the antiviral response that recruits CD4+ T cells and drives mucous cell metaplasia, thus linking antiviral responses to allergic/asthmatic Th2 responses.

Models for confluent biological tissues often describe the network formed by cells as a triplejunction network, similar to foams. However, higher-order vertices or multicellular rosettes are prevalent in developmental and in vitro processes and have been recognized as crucial in many important aspects of morphogenesis, disease, and physiology. In this work, we study the influence of rosettes on the mechanics of a confluent tissue. We find that the existence of rosettes in a tissue can greatly influence its rigidity. Using a generalized vertex model and the effective medium theory, we find a fluid-to-solid transition driven by rosette density and intracellular tensions. This transition exhibits several hallmarks of a second-order phase transition such as a growing correlation length and a universal critical scaling in the vicinity of a critical point. Furthermore, we elucidate the nature of rigidity transitions in dense biological tissues and other cellular structures using a generalized Maxwell constraint counting approach, which answers a long-standing puzzle of the origin of solidity in these systems.