Research articles

The thermodynamically uphill uptake of glutamate from the synaptic cleft into the cytoplasm of glia and neuronal cells is carried out by glutamate transporters. The conformational transition of the transporters between outward and inward facing states is crucial for this process to occur. Here, the crystal structure of a double cysteine mutant of a bacterial homologue of glutamate transporters, trapped in the inward facing state by cysteine crosslinking, is described.

It is notoriously difficult to target transcription factors with aberrant activity in cancer. Inappropriate activation of the NOTCH complex of transcription factors is directly implicated in the pathogenesis of several disease states, including T-cell acute lymphoblastic leukaemia. The design of synthetic, cell-permeable, stabilized α-helical peptides that disrupt protein–protein interactions in NOTCH is now described.

Overexpression of certain transcription factors can reprogram somatic cells into induced pluripotent stem (iPS) cells; however, only a minority of donor somatic cells can be reprogrammed to pluripotency. Here, this reprogramming is shown to be a continuous stochastic process where almost all mouse donor cells eventually give rise to iPS cells on continued growth and transcription factor expression; changing certain parameters results in accelerated iPS cell formation.

The plant hormone abscisic acid (ABA) is a regulator of plant growth, development and responses to environmental stresses. Recently, the PYR/PYL/RCAR family of START proteins was found to bind ABA and mediate inactivation of downstream effectors. The crystal structures of apo and ABA-bound receptors as well as a ternary PYL2–ABA–PP2C complex is now reported and analysed, revealing a gate–latch–lock mechanism underlying ABA signalling.

The precise patterns of gene expression required for development are primarily controlled by transcription factors binding to cis-regulatory modules; however, decoding this regulatory landscape remains challenging. Here, a novel approach is used to predict spatio-temporal cis-regulatory activity based only on in vivo transcription factor binding and enhancer activity data, and is then applied to Drosophila mesoderm development.

Many transcription factors bind to regulatory DNA elements that are distant from gene promoters. These distal binding sites are thought to regulate transcription through long-range chromatin interactions, but, until now, the impact of chromatin interactions on transcription regulation has not been investigated in a genome-wide manner. A new strategy — chromatin interaction analysis by paired-end tag sequencing — is now described for the de novo detection of global chromatin interactions.

Drugs that are chemically quite similar often bind to biologically diverse protein targets, and it is unclear how selective many of these compounds are. Because many drug–target combinations exist, it would be useful to explore possible interactions computationally. Here, 3,665 drugs are tested against hundreds of targets; chemical similarities between drugs and ligand sets are found to predict thousands of unanticipated associations.

The question of how proteins recognize specific DNA sequences in the face of vastly higher concentrations of non-specific DNA remains unclear. One suggested mechanism involves the formation of hydrogen bonds with specific bases, primarily in the major groove. The comprehensive analysis of the three-dimensional structures of protein–DNA complexes now shows that the binding of arginine residues to narrow minor grooves is a widely used mode for protein–DNA recognition.

Specialized urea transporters have evolved to achieve rapid and selective urea permeation in the mammalian kidney, a process ultimately necessary for water re-absorption. Here, the X-ray crystal structure of a functional urea transporter from the bacterium Desulfovibrio vulgaris is presented and analysed; the results establish that the urea transporter operates by a channel-like mechanism and reveal the physical and chemical basis of urea selectivity.

The plant hormone abscisic acid (ABA) is a regulator of plant growth, development and responses to environmental stresses. Within plants, the PYR/PYL/RCAR family of START proteins receives ABA to inhibit the phosphatase activity of the group-A protein phophatases 2C (PP2Cs). Here, the crystal structures of ABA bound to its receptor PYL1 and a complex formed between ABA, PYL1 and the PP2C protein ABI1 are presented, shedding light on the structural basis of ABA signalling.

The tumour microenvironment has an important role in tumorigenesis. Here, the genetic inactivation of Pten in stromal fibroblasts of mouse mammary glands is shown to accelerate the initiation, progression and malignant transformation of mammary epithelial tumours. The data presented suggest that the Pten–Ets2 axis — Ets2 being a transcription factor activated by the loss of Pten — is a critical stroma-specific signalling pathway that suppresses mammary epithelial tumours.

Here, in order to gain insight into the relationship between rates of genomic evolution and organismal adaptation, genomes sampled through 40,000 generations are sequenced from a laboratory population of Escherichia coli. The results indicate that the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment, with beneficial mutations surprisingly uniform over time whereas neutral substitutions were highly variable.

As we navigate, spatial information is encoded in both rate and temporal codes by place cells located in the hippocampus. To investigate the origin of these codes, the intracellular dynamics of place cells are now measured in vivo in awake mice navigating a virtual-reality environment. Three subthreshold signatures of place fields are identified that underlie the primary features of place-cell rate and temporal codes.

Radial glia progenitors divide asymmetrically in the ventricular zone (VZ) of the developing neocortex to produce both self-renewing radial glia and differentiating cells. The latter will then leave the VZ whereas the renewing radial glia progenitors stay to divide further, but the mechanisms underlying these differences in behaviour are unclear. Asymmetric inheritance of centrosomes is now shown to regulate the differential behaviour of renewing progenitors in the embryonic mouse neocortex.

DNA cytosine methylation has essential roles in a number of cellular processes. Here, the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome — from both human embryonic stem cells and fetal fibroblasts — are presented, along with analyses of the transcriptome, histone modifications, and sites of DNA–protein interaction for several regulatory factors. The results reveal key differences in methylation patterns between the two genomes.

During DNA metabolism, single-stranded DNA intermediates are often generated that are protected from degradation by binding of ssDNA-binding (SSB) proteins. Bacterial SSB protein forms a tetramer that wraps ssDNA using its four subunits. Here it is shown that tetrameric SSB protein can spontaneously migrate along ssDNA; this diffusional movement introducing a new model for the redistribution of the SSB protein, while remaining bound to ssDNA during recombination and repair processes.

Transcription of eukaryotic protein-coding genes is initiated by RNA polymerase II (Pol II) in a complex with transcription factors including the transcription factor IIB (B). The crystal structure of the complete Pol II–B complex is now presented with complementary functional data. The results shed light on the mechanism of transcription initiation, including the transition to RNA elongation.

The Argonaute (Ago) family of proteins provides the slicer activity of the RNA-induced silencing complex, with the Ago component of the complex providing the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here, the crystal structures of ternary complexes of Thermus thermophilus Ago catalytic mutants are reported and analysed.

Much genetic variation among humans can be accounted for by structural DNA differences that are greater than 1 kilobase in size. Here, using tiling oligonucleotide arrays and HapMap samples, a map of 11,700 copy number variations (CNVs) bigger than 443 base pairs has been generated. About half of these CNVs were also genotyped in individuals of different ancestry. The results offer insight into the relative prevalence of mechanisms that generate CNVs, their evolution, and their contribution to complex genetic diseases.

Closely related species often have different sex-chromosome systems, but it is not known whether sex-chromosome turnover contributes to the evolution of reproductive isolation between species. Here, a neo-sex chromosome is identified in only one member of a sympatric species pair of stickleback fish in Japan. The newly evolved sex chromosome is found to contain genes that contribute to speciation, suggesting that sex-chromosome turnover might have a greater role in speciation than was previously appreciated.