Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models

With recent advances in single-molecule manipulation techniques, it is now possible to measure the mechanical resistance of proteins to external pulling forces applied at specific positions. Remarkably, such recent studies demonstrated that the pulling/stretching forces required to initiate unfolding vary considerably depending on the location of the application of the forces, unraveling residue/position-specific response of proteins to uniaxial tension. Here we show that coarse-grained elastic network models based on the topology of interresidue contacts in the native state can satisfactory explain the relative sizes of such stretching forces exerted on different residue pairs. Despite their simplicity, such models presumably capture a fundamental property that dominates the observed behavior: deformations that can be accommodated by the relatively lower frequency modes of motions intrinsically favored by the structure require weaker forces and vice versa. The mechanical response of proteins to external stress is therefore shown to correlate with the anisotropic fluctuation dynamics intrinsically accessible in the folded state. The dependence on the overall fold implies that evolutionarily related proteins sharing common structural features tend to possess similar mechanical properties. However, the theory cannot explain the differences observed in a number of structurally similar but sequentially distant domains, such as the fibronectin domains.     

Overexpression of the lemon basil alpha-zingiberene synthase gene increases both mono- and sesquiterpene contents in tomato fruit

alpha-Zingiberene synthase (ZIS), a sesquiterpene synthase gene that was isolated from lemon basil (Ocimum basilicum L.), encodes an enzyme that catalyzes the formation of alpha-zingiberene, and other sesquiterpenes, from farnesyl diphosphate. Transgenic tomato fruits overexpressing ZIS under the control of the fruit ripening-specific tomato polygalacturonase promoter (PG) accumulated high levels of alpha-zingiberene (224-1000 ng g(-1) fresh weight) and other sesquiterpenes, such as alpha-bergamotene, 7-epi-sesquithujene, beta-bisabolene and beta-curcumene, whereas no sesquiterpenes were detected in non-transformed control fruits. The ZIS-transgenic fruits also produced monoterpenes, such as alpha-thujene, alpha-pinene, beta-phellandrene and gamma-terpinene (1-22 ng g(-1) fresh weight), which were either not detected or were found only in minute concentrations in control fruits. Recombinant ZIS overexpressed in Escherichia coli catalyzed the formation of these monoterpenes from geranyl diphosphate. As the ZIS protein apparently lacks a transit peptide, and is localized in the cytosol, the production of monoterpenes in the transgenic tomatoes suggests that a pool of geranyl diphosphate is available in the cytosol. The phenotype of the ZIS-transgenic tomatoes was the same as that for wild-type tomatoes, with regard to plant vigor and shape, but transgenic plants exhibited a small decrease in lycopene content. This study thus showed that the synthesis of both mono- and sesquiterpenes can be enhanced by the ectopic expression of a single transgene in tomato fruit, and it further demonstrated the interconnection between the pools of terpenoid precursors in the plastids and the cytosol.     

Enhanced Levels of the Aroma and Flavor Compound S-Linalool by Metabolic Engineering of the Terpenoid Pathway in Tomato Fruits

The aromas of fruits, vegetables, and flowers are mixtures of volatile metabolites, often present in parts per billion levels or less. We show here that tomato (Lycopersicon esculentum Mill.) plants transgenic for a heterologous Clarkia breweri S-linalool synthase (LIS) gene, under the control of the tomato late-ripening-specific E8 promoter, synthesize and accumulate S-linalool and 8-hydroxylinalool in ripening fruits. Apart from the difference in volatiles, no other phenotypic alterations were noted, including the levels of other terpenoids such as gamma- and alpha-tocopherols, lycopene, beta-carotene, and lutein. Our studies indicate that it is possible to enhance the levels of monoterpenes in ripening fruits by metabolic engineering.     

The Effect of Male Competition on the Courtship Song of Drosophila melanogaster

The courtship song of Drosophila has been extensively used as a model system for studies of sexual selection and species recognition. Traditionally, the courtship song has been recorded from males placed individually with a female. However, under natural conditions females are exposed to multiple courting males, and the effect of their joint signal on mate recognition by the female is not yet understood. Here, we recorded the courtship behavior of D. melanogaster males singing either individually to a female lpar;1:1) or in the presence of an additional male lpar;2:1). We compared the structure of the male song in the two experimental designs. Our results show that when two males courted a female their songs could overlap each other. Males produced a significantly different signal in the presence of competition; the duration of each song component was significantly shorter and the rate of singing was markedly lower. The present study demonstrates that male competition can dramatically alter the acoustic signal detected by the female.     

Robust Prediction of Expression Differences among Human Individuals Using Only Genotype Information

Many genetic variants that are significantly correlated to gene expression changes across human individuals have been identified, but the ability of these variants to predict expression of unseen individuals has rarely been evaluated. Here, we devise an algorithm that, given training expression and genotype data for a set of individuals, predicts the expression of genes of unseen test individuals given only their genotype in the local genomic vicinity of the predicted gene. Notably, the resulting predictions are remarkably robust in that they agree well between the training and test sets, even when the training and test sets consist of individuals from distinct populations. Thus, although the overall number of genes that can be predicted is relatively small, as expected from our choice to ignore effects such as environmental factors and trans sequence variation, the robust nature of the predictions means that the identity and quantitative degree to which genes can be predicted is known in advance. We also present an extension that incorporates heterogeneous types of genomic annotations to differentially weigh the importance of the various genetic variants, and we show that assigning higher weights to variants with particular annotations such as proximity to genes and high regional G/C content can further improve the predictions. Finally, genes that are successfully predicted have, on average, higher expression and more variability across individuals, providing insight into the characteristics of the types of genes that can be predicted from their cis genetic variation.     

A case study of a shared/buy-in computing ecosystem

Many research institutions are deploying computing clusters based on a shared/buy-in paradigm. Such clusters combine shared computers, which are free to be used by all users, and buy-in computers, which are computers purchased by users for semi-exclusive use. The purpose of this paper is to characterize the typical behavior and performance of a shared/buy-in computing cluster, using data traces from the Shared Computing Cluster (SCC) at Boston University that runs under this paradigm as a case study. Among our main findings, we show that the semi-exclusive policy, which allows any SCC user to use idle buy-in resources for a limited time, increases the utilization of buy-in resources by 17.4%, thus significantly improving the performance of the system as a whole. We find that jobs allowed to run on idle buy-in resources arrive more frequently and run for a shorter time than other jobs. Finally, we identify the run time limit (i.e., the maximum time during which a job is allowed to use resources) and the type of parallel environment as two factors that have a significant impact on the different performance experienced by shared and buy-in jobs.     

When TRBP leaves Dicer at the alt‐’ER

The principle underlying miRNA silencing seems rather simple: Dicer is required for the biogenesis of endogenous miRNAs, and mature miRNAs at the RNA‐induced silencing complex, RISC, bind to targets by sequence complementary, inhibiting protein expression. However, research shows that there are many degrees of complexity to miRNA regulation. A new study by Antoniou et al 1 that is published in this issue of EMBO Reports explores an interesting neuron‐specific facet of miRNA biogenesis. We learn that in neuronal dendrites, the endoplasmic reticulum (ER) acts as a regulatory domain for the dynamic encounter of TRBP and Dicer, two proteins required for the biogenesis of miRNAs, thus affecting neuron morphogenesis.