Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes

A decisive step in the biosynthesis of many proteins is their partial or complete translocation across the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. Most of these proteins are translocated through a protein-conducting channel that is formed by a conserved, heterotrimeric membrane-protein complex, the Sec61 or SecY complex. Depending on channel binding partners, polypeptides are moved by different mechanisms: the polypeptide chain is transferred directly into the channel by the translating ribosome, a ratcheting mechanism is used by the endoplasmic reticulum chaperone BiP, and a pushing mechanism is used by the bacterial ATPase SecA. Structural, genetic and biochemical data show how the channel opens across the membrane, releases hydrophobic segments of membrane proteins laterally into lipid, and maintains the membrane barrier for small molecules.     

Evolution of increased complexity in a molecular machine

Many cellular processes are carried out by molecular 'machines'-assemblies of multiple differentiated proteins that physically interact to execute biological functions. Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking. Here we use ancestral gene resurrection and manipulative genetic experiments to determine how the complexity of an essential molecular machine--the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump--increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.     

Distribution of phenylalanine transaminase and phenylalanine ammonia-lyase activities in etiolated and light irradiated radish seedlings (Raphanus sativus L.).

In dark-grown Raphanus sativus seedlings the level of phenylalanine transaminase is higher in cotyledons than in root and hypocotyl. The maximum activity of phenylalanine ammonia-lyase (PAL) is found in the root. Only PAL is significantly increased by light.     

Additive Biclustering: A Comparison of One New and Two Existing ALS Algorithms

The additive biclustering model for two-way two-mode object by variable data implies overlapping clusterings of both the objects and the variables together with a weight for each bicluster (i.e., a pair of an object and a variable cluster). In the data analysis, an additive biclustering model is fitted to given data by means of minimizing a least squares loss function. To this end, two alternating least squares algorithms (ALS) may be used: (1) PENCLUS, and (2) Baier’s ALS approach. However, both algorithms suffer from some inherent limitations, which may hamper their performance. As a way out, based on theoretical results regarding optimally designing ALS algorithms, in this paper a new ALS algorithm will be presented. In a simulation study this algorithm will be shown to outperform the existing ALS approaches.     

Disruptive coloration and background pattern matching

Effective camouflage renders a target indistinguishable from irrelevant background objects. Two interrelated but logically distinct mechanisms for this are background pattern matching (crypsis) and disruptive coloration: in the former, the animal's colours are a random sample of the background; in the latter, bold contrasting colours on the animal's periphery break up its outline. The latter has long been proposed as an explanation for some apparently conspicuous coloration in animals, and is standard textbook material. Surprisingly, only one quantitative test of the theory exists, and one experimental test of its effectiveness against non-human predators. Here we test two key predictions: that patterns on the body's outline should be particularly effective in promoting concealment and that highly contrasting colours should enhance this disruptive effect. Artificial moth-like targets were exposed to bird predation in the field, with the experimental colour patterns on the 'wings' and a dead mealworm as the edible 'body'. Survival analysis supported the predictions, indicating that disruptive coloration is an effective means of camouflage, above and beyond background pattern matching.     

A structural basis for allosteric control of DNA recombination by lambda integrase

Site-specific DNA recombination is important for basic cellular functions including viral integration, control of gene expression, production of genetic diversity and segregation of newly replicated chromosomes, and is used by bacteriophage lambda to integrate or excise its genome into and out of the host chromosome. lambda recombination is carried out by the bacteriophage-encoded integrase protein (lambda-int) together with accessory DNA sites and associated bending proteins that allow regulation in response to cell physiology. Here we report the crystal structures of lambda-int in higher-order complexes with substrates and regulatory DNAs representing different intermediates along the reaction pathway. The structures show how the simultaneous binding of two separate domains of lambda-int to DNA facilitates synapsis and can specify the order of DNA strand cleavage and exchange. An intertwined layer of amino-terminal domains bound to accessory (arm) DNAs shapes the recombination complex in a way that suggests how arm binding shifts the reaction equilibrium in favour of recombinant products.     

A Systems Approach for Engaging Groups in Global Complexity: Capacity Building Through an Online Course

Sustainability is not simply about changing practices but more centrally about agreeing to change practices together. To achieve such an end, groups need to improve processes for making complex decisions together. An online course was designed and tested linking students in the United States and in Australia. Students engaged in a re-enactment of deliberations based on Hasan Ozbekhan’s “Predicament of Mankind,” which was constructed originally under assignment from the founders of the Club of Rome in 1970. This re-enactment included contemporary research for examples of a set of 49 continuous critical problems of mankind, asynchronous clarification of these problems using a wiki, pair-wise construction of a systems view of problems assessed to be of highest priority by the class, narrative analysis of the structure, and creative suggestions for resolving the systems problem based on resources available today. This report comments on the strengths and challenges identified in an initial application of an approach for building collaborative and systems thinking skills through an online course in a general education curriculum. Findings are particularly meaningful for contemporary policy makers as well as online educators.