[Working Life] En pointe

Author: Elisabeth Pain

[New Products] New Products

A weekly roundup of information on newly offered instrumentation, apparatus, and laboratory materials of potential interest to researchers.

[Report] Direct observation of structure-function relationship in a nucleic acid–processing enzyme

The relationship between protein three-dimensional structure and function is essential for mechanism determination. Unfortunately, most techniques do not provide a direct measurement of this relationship. Structural data are typically limited to static pictures, and function must be inferred. Conversely, functional assays usually provide little information on structural conformation. We developed a single-molecule technique combining optical tweezers and fluorescence microscopy that allows for both measurements simultaneously. Here we present measurements of UvrD, a DNA repair helicase, that directly and unambiguously reveal the connection between its structure and function. Our data reveal that UvrD exhibits two distinct types of unwinding activity regulated by its stoichiometry. Furthermore, two UvrD conformational states, termed “closed” and “open,” correlate with movement toward or away from the DNA fork.
Authors: Matthew J. Comstock, Kevin D. Whitley, Haifeng Jia, Joshua Sokoloski, Timothy M. Lohman, Taekjip Ha, Yann R. Chemla

[This Week in Science] Will the real mutation please stand up?

Author: Yevgeniya Nusinovich

[Report] Anthropogenic environmental changes affect ecosystem stability via biodiversity

Human-driven environmental changes may simultaneously affect the biodiversity, productivity, and stability of Earth’s ecosystems, but there is no consensus on the causal relationships linking these variables. Data from 12 multiyear experiments that manipulate important anthropogenic drivers, including plant diversity, nitrogen, carbon dioxide, fire, herbivory, and water, show that each driver influences ecosystem productivity. However, the stability of ecosystem productivity is only changed by those drivers that alter biodiversity, with a given decrease in plant species numbers leading to a quantitatively similar decrease in ecosystem stability regardless of which driver caused the biodiversity loss. These results suggest that changes in biodiversity caused by drivers of environmental change may be a major factor determining how global environmental changes affect ecosystem stability.
Authors: Yann Hautier, David Tilman, Forest Isbell, Eric W. Seabloom, Elizabeth T. Borer, Peter B. Reich

[This Week in Science] Stem cells can sort mitochondria by age

Author: L. Bryan Ray

[Report] Dilution limits dissolved organic carbon utilization in the deep ocean

Oceanic dissolved organic carbon (DOC) is the second largest reservoir of organic carbon in the biosphere. About 72% of the global DOC inventory is stored in deep oceanic layers for years to centuries, supporting the current view that it consists of materials resistant to microbial degradation. An alternative hypothesis is that deep-water DOC consists of many different, intrinsically labile compounds at concentrations too low to compensate for the metabolic costs associated to their utilization. Here, we present experimental evidence showing that low concentrations rather than recalcitrance preclude consumption of a substantial fraction of DOC, leading to slow microbial growth in the deep ocean. These findings demonstrate an alternative mechanism for the long-term storage of labile DOC in the deep ocean, which has been hitherto largely ignored.
Authors: Jesús M. Arrieta, Eva Mayol, Roberta L. Hansman, Gerhard J. Herndl, Thorsten Dittmar, Carlos M. Duarte

[This Week in Science] Gaze into my eyes

Author: Sacha Vignieri

[Report] The weakening summer circulation in the Northern Hemisphere mid-latitudes

Rapid warming in the Arctic could influence mid-latitude circulation by reducing the poleward temperature gradient. The largest changes are generally expected in autumn or winter, but whether significant changes have occurred is debated. Here we report significant weakening of summer circulation detected in three key dynamical quantities: (i) the zonal-mean zonal wind, (ii) the eddy kinetic energy (EKE), and (iii) the amplitude of fast-moving Rossby waves. Weakening of the zonal wind is explained by a reduction in the poleward temperature gradient. Changes in Rossby waves and EKE are consistent with regression analyses of climate model projections and changes over the seasonal cycle. Monthly heat extremes are associated with low EKE, and thus the observed weakening might have contributed to more persistent heat waves in recent summers.
Authors: Dim Coumou, Jascha Lehmann, Johanna Beckmann

[Research Article] The complete structure of the 55S mammalian mitochondrial ribosome

Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of the porcine 55S mitoribosome at 3.8 angstrom resolution by cryo–electron microscopy and chemical cross-linking/mass spectrometry. The structure of the 28S subunit in the complex was resolved at 3.6 angstrom resolution by focused alignment, which allowed building of a detailed atomic structure including all of its 15 mitoribosomal-specific proteins. The structure reveals the intersubunit contacts in the 55S mitoribosome, the molecular architecture of the mitoribosomal messenger RNA (mRNA) binding channel and its interaction with transfer RNAs, and provides insight into the highly specialized mechanism of mRNA recruitment to the 28S subunit. Furthermore, the structure contributes to a mechanistic understanding of aminoglycoside ototoxicity.
Authors: Basil J. Greber, Philipp Bieri, Marc Leibundgut, Alexander Leitner, Ruedi Aebersold, Daniel Boehringer, Nenad Ban