This Week in Science

Science  10 Feb 2012:
Vol. 335, Issue 6069, pp. 633
  1. Wrapped DNA

    CREDIT: JON BOGDANOVE

    TAL effectors are proteins that bacterial pathogens inject into plant cells that bind to host DNA to activate expression of plant genes. The DNA-binding domain of TAL proteins is composed of tandem repeats within which a repeat-variable diresidue sequence confers nucleotide specificity. Deng et al. (p. 720, published online 5 January) report the structure of the TAL effector dHax3, containing 11.5 repeats, in DNA-free and DNA-bound states, and Mak et al. (p. 716, published online 5 January) report the structure of the PthXo1 TAL effector, containing 22 repeats, bound to its DNA target. Together, the structures reveal the conformational changes involved in DNA binding and provide the structural basis of DNA recognition.

  2. Spring Bloom

    The spring bloom of plankton in northern seas develops apparently in response to increasing light and to winter weather, which make nutrients available at the surface. This seasonality is important on a global scale because it reflects a tipping point, driven by phytoplankton growth, between CO2 production and carbon storage. The phenomenon is thus of particular interest in this era of carbon excess. Giovannoni and Vergin (p. 671) review what is known about the dynamics of these highly ordered microbial plankton communities, discuss the specialist roles of certain taxa, and reflect on predictions for anthropogenic changes to the oceans and what these might mean for geochemical cycles driven by ocean microbiota.

  3. Earthquakes from Above

    Preparing for risks and hazards associated with large earthquakes requires detailed understanding of their mechanical properties. In addition to pinpointing the location and magnitude of earthquakes, postmortem analyses of the extent of rupture and amount of deformation are key quantities, but are not simply available from seismological data alone. Using a type of optical remote sensing, Light Detection and Ranging (LiDAR), Oskin et al. (p. 702) surveyed the surrounding area that ruptured during the 2010 Mw 7.2 El Mayor–Cucapah earthquake in Northern Mexico. Because this area had also been analyzed in 2006, a comparative analysis revealed slip rate and strain release on the shallow fault zone and a number of previously unknown faults. As remote imaging becomes cheaper and more common, differential analyses will continue to provide fault-related deformation data that complements modern seismological networks.

  4. Edging In on MoS2

    CREDIT: KARUNADASA ET AL.

    Molybdenum disulfide is a widely used catalyst in the petrochemical industry that has recently shown promise for water-splitting applications. Its activity appears to be confined to edge sites with exposed disulfide groups, although the precise geometric details underlying the chemistry remain uncertain. Karunadasa et al. (p. 698) prepared a molecular complex modeling one of these edge sites, in which a triangular Mo-S-S unit is supported by metal coordination to five tethered pyridine rings. The molecule was characterized crystallographically and proved robustly active toward electrochemical generation of hydrogen from water, even when applied to crudely filtered seawater.

  5. Challenging the Mushroom Bodies

    Early memory is labile and is gradually consolidated over time into long-lasting, stable memory. In several species, including mammals, memory consolidation depends on protein synthesis. In Drosophila, long-term memory is produced by spaced repetitive training, which induces cyclic adenosine monophosphate (cAMP)–response element–binding protein (CREB)–dependent gene transcription and de novo protein synthesis. Using a large number of genetic tools, Chen et al. (p. 678; see the Perspective by Dubnau) localized this CREB-dependent induction of de novo protein synthesis to two dorsal-anterior-lateral neurons in the adult brain. Importantly, protein synthesis was not required within the mushroom bodies, which are usually considered to be the site of associative learning and memory in insects.

  6. Maintaining Equilibrium

    Na+/Ca2+ exchangers (NCX) are membrane transporters that maintain the homeostasis of cytosolic Ca2+ and play an essential role in Ca2+ signaling. Despite a long history of physiological work and a large body of functional data, the structural basis underlying the ion exchange mechanism of NCX is poorly understood. Liao et al. (p. 686; see the Perspective by Abramson et al.) present a high-resolution crystal structure of an NCX from Methanococcus jannaschii and demonstrate that this archaeal NCX catalyzes Na+/Ca2+-exchange reactions similar to its eukaryotic counterpart. The structure clarifies the mechanism of ion exchange proteins and reveals the basis for the stoichiometry, cooperativity, and bidirectionality of the reaction.

  7. Too Much Tolerance?

    In the immune system, loss of tolerance to self can have devastating consequences, such as the development of autoimmune diseases. In some cases, however, we may wish to be able to break tolerance, for example, to activate immune cells to fight tumors. Schietinger et al. (p. 723, published online 19 January; see the Perspective by Lee and Jameson) used a combination of genetic mouse models and adoptive immune cell transfers to better understand the mechanisms regulating tolerance in T lymphocytes. In contrast to the prevailing paradigm, the maintenance of T lymphocyte tolerance did not require the continuous presence of antigen. Tolerance was able to be broken when previously tolerized cells were placed in an environment depleted of immune cells. However, when lymphocyte numbers were restored, cells were once again tolerized, even in the absence of antigen. These data, together with gene expression profiling, suggest that tolerance is associated with a specific gene expression program that, although possible to override temporarily, is reimposed by epigenetic mechanisms.

  8. Be My Guests

    For a range of applications, including medical diagnostics or drug delivery, it is necessary to encapsulate one or more components into a microcapsule. While there are many methods that can do this, most either produce a range of capsule size or are not easily scalable for making large quantities. J. Zhang et al. (p. 690) developed a microfluidic-based system for making capsules using host-guest chemistry. Cucurbit[8]uril, which readily forms complexes in water, was used as the host molecule and could accommodate two different guest molecules. Rapid complexation was observed of methyl viologen–modified gold nanoparticles and a naphthol-containing copolymer.

  9. Ties That Bind

    Almost by definition, effective catalysts bind their substrates for a very short time—releasing them quickly after helping them react and then moving on to bind new, as yet unreacted, substrates. This property engenders an efficient cycle, but it hinders study of the binding motif. Garand et al. (p. 694, published online 19 January; see the Perspective by Zwier) devised a technique to extract bound complexes from solution and freeze their conformations in cold, gas-phase clusters. Probing these clusters by vibrational spectroscopy in conjunction with theoretical calculations then allowed the sites of hydrogen bonding that hold the complexes together to be pinpointed.

  10. Close-Up of DNA Methylation

    CREDIT: SONG ET AL.

    In eukaryotes, maintenance of genomic CpG methylation patterns is required for imprinting, retrotransposon silencing, and X-chromosome inactivation. The epigenetic mark needs to be faithfully maintained and propagated during repeated cell divisions in somatic cells by selective methylation of hemimethylated CpG dinucleotides following DNA replication, which is carried out by the enzyme DNMT1. Song et al. (p. 709) determined the crystal structure of mouse DNMT1 bound to a DNA duplex containing a hemimethylated CpG on the parental strand, such as would be found immediately after DNA replication. Together with a previous structure of the autoinhibited structure, the findings suggest that a combination of active and auto-inhibitory mechanisms ensures the high fidelity of DNMT1-mediated maintenance of DNA methylation.

  11. Before Tohoku-Oki

    Recordings by Japan's dense seismic network in the days and weeks before the 2011 Mw 9.0 Tohoku-Oki earthquake provide an opportunity to interrogate what caused the dynamic rupture of one of the largest earthquakes on record. Using a method to extract small earthquakes that are often obscured by overlapping seismic waves, Kato et al. (p. 705, published online 19 January) identified over a thousand small repeating earthquakes that migrated slowly toward the hypocenter of the main rupture. Based on the properties of these foreshocks, the plate interface experienced two sequences of slow slip, the second of which probably contributed a substantial amount of stress and may have initiated the nucleation of the main shock.

  12. Keeping a Kinase in Check

    Cyclic adenosine monophosphate (cAMP)–dependent protein kinase (PKA) is involved in the regulation of several key metabolic pathways. It exists in mammalian cells as an inactive tetramer composed of a regulatory (R) subunit dimer and two catalytic (C) subunits. cAMP binding causes activation by releasing the C subunits. Insight into PKA regulation has come from structures of R and C subunit heterodimers; however, further understanding requires knowledge of the holoenzyme structure. P. Zhang et al. (p. 712) report a high-resolution structure of the RIIβ2:C2 tetramer. The structure reveals interactions at an interface between the two RC heterodimers and provides insight into the mechanism of allosteric activation upon cAMP binding.

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