Structural insights into amino acid binding and gene control by a lysine riboswitch

In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches. One of the important regulatory circuits involves lysine-specific riboswitches, which direct the biosynthesis and transport of lysine and precursors common for lysine and other amino acids. To understand the molecular basis of amino acid recognition by riboswitches, here we present the crystal structure of the 174-nucleotide sensing domain of the Thermotoga maritima lysine riboswitch in the lysine-bound (1.9 ?ngstr?m (A)) and free (3.1 A) states. The riboswitch features an unusual and intricate architecture, involving three-helical and two-helical bundles connected by a compact five-helical junction and stabilized by various long-range tertiary interactions. Lysine interacts with the junctional core of the riboswitch and is specifically recognized through shape-complementarity within the elongated binding pocket and through several direct and K(+)-mediated hydrogen bonds to its charged ends. Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements. We have also determined several structures of the riboswitch bound to different lysine analogues, including antibiotics, in an effort to understand the ligand-binding capabilities of the lysine riboswitch and understand the nature of antibiotic resistance. Our results provide insights into a mechanism of lysine-riboswitch-dependent gene control at the molecular level, thereby contributing to continuing efforts at exploration of the pharmaceutical and biotechnological potential of riboswitches.     

Spatio-temporal correlations and visual signalling in a complete neuronal population

Statistical dependencies in the responses of sensory neurons govern both the amount of stimulus information conveyed and the means by which downstream neurons can extract it. Although a variety of measurements indicate the existence of such dependencies, their origin and importance for neural coding are poorly understood. Here we analyse the functional significance of correlated firing in a complete population of macaque parasol retinal ganglion cells using a model of multi-neuron spike responses. The model, with parameters fit directly to physiological data, simultaneously captures both the stimulus dependence and detailed spatio-temporal correlations in population responses, and provides two insights into the structure of the neural code. First, neural encoding at the population level is less noisy than one would expect from the variability of individual neurons: spike times are more precise, and can be predicted more accurately when the spiking of neighbouring neurons is taken into account. Second, correlations provide additional sensory information: optimal, model-based decoding that exploits the response correlation structure extracts 20% more information about the visual scene than decoding under the assumption of independence, and preserves 40% more visual information than optimal linear decoding. This model-based approach reveals the role of correlated activity in the retinal coding of visual stimuli, and provides a general framework for understanding the importance of correlated activity in populations of neurons.     

A light carbon reservoir recorded in zircon-hosted diamond from the Jack Hills

The recent discovery of diamond-graphite inclusions in the Earth's oldest zircon grains (formed up to 4,252 Myr ago) from the Jack Hills metasediments in Western Australia provides a unique opportunity to investigate Earth's earliest known carbon reservoir. Here we report ion microprobe analyses of the carbon isotope composition of these diamond-graphite inclusions. The observed delta(13)C(PDB) values (expressed using the PeeDee Belemnite standard) range between -5 per mil and -58 per mil with a median of -31 per mil. This extends beyond typical mantle values of around -6 per mil to values observed in metamorphic and some eclogitic diamonds that are interpreted to reflect deep subduction of low-delta(13)C(PDB) biogenic surface carbon. Low delta(13)C(PDB) values may also be produced by inorganic chemical reactions, and therefore are not unambiguous evidence for life on Earth as early as 4,250 Myr ago. Regardless, our results suggest that a low-delta(13)C(PDB) reservoir may have existed on the early Earth.     

Structure of the 30S translation initiation complex

Translation initiation, the rate-limiting step of the universal process of protein synthesis, proceeds through sequential, tightly regulated steps. In bacteria, the correct messenger RNA start site and the reading frame are selected when, with the help of initiation factors IF1, IF2 and IF3, the initiation codon is decoded in the peptidyl site of the 30S ribosomal subunit by the fMet-tRNA(fMet) anticodon. This yields a 30S initiation complex (30SIC) that is an intermediate in the formation of the 70S initiation complex (70SIC) that occurs on joining of the 50S ribosomal subunit to the 30SIC and release of the initiation factors. The localization of IF2 in the 30SIC has proved to be difficult so far using biochemical approaches, but could now be addressed using cryo-electron microscopy and advanced particle separation techniques on the basis of three-dimensional statistical analysis. Here we report the direct visualization of a 30SIC containing mRNA, fMet-tRNA(fMet) and initiation factors IF1 and GTP-bound IF2. We demonstrate that the fMet-tRNA(fMet) is held in a characteristic and precise position and conformation by two interactions that contribute to the formation of a stable complex: one involves the transfer RNA decoding stem which is buried in the 30S peptidyl site, and the other occurs between the carboxy-terminal domain of IF2 and the tRNA acceptor end. The structure provides insights into the mechanism of 70SIC assembly and rationalizes the rapid activation of GTP hydrolysis triggered on 30SIC-50S joining by showing that the GTP-binding domain of IF2 would directly face the GTPase-activated centre of the 50S subunit.     

Freiberg and the Frontier: Louis Janin,German Engineering,and ‘Civilisation’ in the American West

Mining companies after the Gold Rush depended heavily on foreign expertise, and yet historians of mining have glorified ‘German engineering’ in America. The application of German technology in America was fraught with difficulties, and most advances were micro- rather than macro-innovations, such as Philip Deidesheimer's famous square-set timbering on the Comstock Lode. The problem began at German mining schools, such as the Freiberg Mining Academy, where Americans like Louis and Henry Janin, while they acquired advanced training and adopted an engineering ethos, struggled to learn about Mexican and American mining. Having complemented their course of study to remedy this deficiency, the brothers returned to the US intending to modernize mining on the frontier. Louis attempted the ‘Freiberg Process’ of amalgamation on the Comstock Lode, but locally developed methods proved more feasible, and the experiment failed. He came to apply his training rather toward the micro-level problem of how to reprocess amalgamation waste heaps.     

T cells become licensed in the lung to enter the central nervous system

The blood–brain barrier (BBB) and the environment of the central nervous system (CNS) guard the nervous tissue from peripheral immune cells. In the autoimmune disease multiple sclerosis, myelin-reactive T-cell blasts are thought to transgress the BBB and create a pro-inflammatory environment in the CNS, thereby making possible a second autoimmune attack that starts from the leptomeningeal vessels and progresses into the parenchyma. Using a Lewis rat model of experimental autoimmune encephalomyelitis, we show here that contrary to the expectations of this concept, T-cell blasts do not efficiently enter the CNS and are not required to prepare the BBB for immune-cell recruitment. Instead, intravenously transferred T-cell blasts gain the capacity to enter the CNS after residing transiently within the lung tissues. Inside the lung tissues, they move along and within the airways to bronchus-associated lymphoid tissues and lung-draining mediastinal lymph nodes before they enter the blood circulation from where they reach the CNS. Effector T cells transferred directly into the airways showed a similar migratory pattern and retained their full pathogenicity. On their way the T cells fundamentally reprogrammed their gene-expression profile, characterized by downregulation of their activation program and upregulation of cellular locomotion molecules together with chemokine and adhesion receptors. The adhesion receptors include ninjurin 1, which participates in T-cell intravascular crawling on cerebral blood vessels. We detected that the lung constitutes a niche not only for activated T cells but also for resting myelin-reactive memory T cells. After local stimulation in the lung, these cells strongly proliferate and, after assuming migratory properties, enter the CNS and induce paralytic disease. The lung could therefore contribute to the activation of potentially autoaggressive T cells and their transition to a migratory mode as a prerequisite to entering their target tissues and inducing autoimmune disease.     

The limits of the nuclear landscape

In 2011, 100 new nuclides were discovered. They joined the approximately 3,000 stable and radioactive nuclides that either occur naturally on Earth or are synthesized in the laboratory. Every atomic nucleus, characterized by a specific number of protons and neutrons, occupies a spot on the chart of nuclides, which is bounded by 'drip lines' indicating the values of neutron and proton number at which nuclear binding ends. The placement of the neutron drip line for the heavier elements is based on theoretical predictions using extreme extrapolations, and so is uncertain. However, it is not known how uncertain it is or how many protons and neutrons can be bound in a nucleus. Here we estimate these limits of the nuclear 'landscape' and provide statistical and systematic uncertainties for our predictions. We use nuclear density functional theory, several Skyrme interactions and high-performance computing, and find that the number of bound nuclides with between 2 and 120 protons is around 7,000. We find that extrapolations for drip-line positions and selected nuclear properties, including neutron separation energies relevant to astrophysical processes, are very consistent between the models used.