Smaug assembles an ATP-dependent stable complex repressing nanos mRNA translation at multiple levels.

The nanos (nos) mRNA encodes the posterior determinant of the Drosophila embryo. Translation of the RNA is repressed throughout most of the embryo by the protein Smaug binding to Smaug recognition elements (SREs) in the 3' UTR. Translation is locally activated at the posterior pole by Oskar. This paper reports that the SREs govern the time- and ATP-dependent assembly of an exceedingly stable repressed ribonucleoprotein particle (RNP) in embryo extract. Repression can be virtually complete. Smaug and its co-repressor Cup as well as Trailer hitch and the DEAD box protein Me31B are part of the repressed RNP. The initiation factor eIF4G is specifically displaced, and 48S pre-initiation complex formation is inhibited. However, later steps in translation initiation are also sensitive to SRE-dependent inhibition. These data confirm several previously untested predictions of a current model for Cup-dependent repression but also suggest that the Cup model by itself is insufficient to explain translational repression of the nos RNA. In the embryo extract, recombinant Oskar relieves translational repression and deadenylation by preventing Smaug's binding to the SREs.

An ancient oxidoreductase making differential use of its cofactors.

Abstract Many transcription factors contribute to cellular homeostasis by integrating multiple signals. Signaling via the yeast Gal80 protein, a negative regulator of the prototypic transcription activator Gal4, is primarily regulated by galactose. ScGal80 from Saccharomyces cerevisiae has been reported to bind NAD(P). Here, we show that the ability to bind these ligands is conserved in KlGal80, a Gal80 homolog from the distantly related yeast Kluyveromyces lactis. However, the homologs apparently have diverged with respect to response to the dinucleotide. Strikingly, ScGal80 binds NAD(P) and NAD(P)H with more than 50-fold higher affinity than KlGal80. In contrast to ScGal80, where NAD is neutral, NAD and NADP have a negative effect in KlGal80 on its interaction with a KlGal4-peptide in vitro. Swapping a loop in the NAD(P) binding Rossmann-fold of ScGal80 into KlGal80 increases the affinity for NAD(P) and has a significant impact on KlGal4 regulation in vivo. Apparently, dinucleotide binding allows coupling of the metabolic state of the cell to regulation of the GAL/LAC genes. The particular sequences involved in binding determine how exactly the metabolic state is sensed and integrated by Gal80 to regulate Gal4.

Asymmetric mating behavior of isogamous budding yeast.

Anisogamy, the size difference between small male and large female gametes, is known to enable selection for sexual dimorphism and behavioral differences between sexes. Nevertheless, even isogamous species exhibit molecular asymmetries between mating types, which are known to ensure their self-incompatibility. Here, we show that different properties of the pheromones secreted by the MATa and MATα mating types of budding yeast lead to asymmetry in their behavioral responses during mating in mixed haploid populations, which resemble behavioral asymmetries between gametes in anisogamous organisms. MATa behaves as a random searcher that is stimulated in proportion to the fraction of MATα partner cells within the population, whereas MATα behaves as a short-range directional distance sensor. Mathematical modeling suggests that the observed asymmetric responses can enhance efficiency of mating and might thus provide a selective advantage. Our results demonstrate that the emergence of asymmetric mating behavior did not require anisogamy-based sexual selection.

Design of a MAPK signalling cascade balances energetic cost versus accuracy of information transmission.

Cellular processes are inherently noisy, and the selection for accurate responses in presence of noise has likely shaped signalling networks. Here, we investigate the trade-off between accuracy of information transmission and its energetic cost for a mitogen-activated protein kinase (MAPK) signalling cascade. Our analysis of the pheromone response pathway of budding yeast suggests that dose-dependent induction of the negative transcriptional feedbacks in this network maximizes the information per unit energetic cost, rather than the information transmission capacity itself. We further demonstrate that futile cycling of MAPK phosphorylation and dephosphorylation has a measurable effect on growth fitness, with energy dissipation within the signalling cascade thus likely being subject to evolutionary selection. Considering optimization of accuracy versus the energetic cost of information processing, a concept well established in physics and engineering, may thus offer a general framework to understand the regulatory design of cellular signalling systems.

A System for Gene Expression Noise Control in Yeast.

Gene expression noise arises from stochastic variation in the synthesis and degradation of mRNA and protein molecules and creates differences in protein numbers across populations of genetically identical cells. Such variability can lead to imprecision and reduced performance of both native and synthetic networks. In principle, gene expression noise can be controlled through the rates of transcription, translation and degradation, such that different combinations of those rates lead to the same protein concentrations but at different noise levels. Here, we present a "noise tuner" which allows orthogonal control over the transcription and the mRNA degradation rates by two different inducer molecules. Combining experiments with theoretical analysis, we show that in this system the noise is largely determined by the transcription rate, whereas the mean expression is determined by both the transcription rate and mRNA stability and can thus be decoupled from the noise. This noise tuner enables 2-fold changes in gene expression noise over a 5-fold range of mean protein levels. We demonstrated the efficacy of the noise tuner in a complex regulatory network by varying gene expression noise in the mating pathway of Saccharomyces cerevisiae, which allowed us to control the output noise and the mutual information transduced through the pathway. The noise tuner thus represents an effective tool of gene expression noise control, both to interrogate noise sensitivity of natural networks and enhance performance of synthetic circuits.

Sensory input attenuation allows predictive sexual response in yeast.

Animals are known to adjust their sexual behaviour depending on mate competition. Here we report similar regulation for mating behaviour in a sexual unicellular eukaryote, the budding yeast Saccharomyces cerevisiae. We demonstrate that pheromone-based communication between the two mating types, coupled to input attenuation by recipient cells, enables yeast to robustly monitor relative mate abundance (sex ratio) within a mixed population and to adjust their commitment to sexual reproduction in proportion to their estimated chances of successful mating. The mechanism of sex-ratio sensing relies on the diffusible peptidase Bar1, which is known to degrade the pheromone signal produced by mating partners. We further show that such a response to sexual competition within a population can optimize the fitness trade-off between the costs and benefits of mating response induction. Our study thus provides an adaptive explanation for the known molecular mechanism of pheromone degradation in yeast.

Predicted alterations in tertiary structure of the N-terminus of Na(+)/K(+)-ATPase alpha-subunit caused by phosphorylation or acidic replacement of the PKC phosphorylation site Ser-23.

The protein kinase C (PKC)-mediated phosphorylation of the Na(+)/K(+)-ATPase alpha-subunit has been shown to play an important role in regulation of the Na(+)/K(+)-ATPase activity. In the rat alpha1-subunit, phosphorylation occurs at Ser-23 and results in inhibition of the transport function of the Na(+)/K(+)-ATPase, which is mimicked by replacing the Ser-23 by the negatively charged glutamic acid or by aspartic acid. Using comparative molecular modeling, we investigated whether phosphorylation or acidic replacement at position 23 causes a dramatic change in the molecular electrostatic potential at position 23 as a result of insertion of a negative charge of the phosphoryl group or Glu per se, or whether, alternatively, the modification causes larger-scale conformational changes in the N-terminus of the alpha-subunit. The results predict a considerable conformational change of the 30-residue stretch around Ser-23 when mutated to the residues carrying a net negative charge or being phosphorylated. The structural rearrangements occur within the N-terminal helix-loop-helix motif with a set of charged residues. This motif has structural homology with one in the Ca(2+)-ATPase and may form a function-related structural site in the P-type ATPases. Comparative molecular modeling indicates a lengthening of the interhelical loop and an order-to-disorder transition by disrupting a helix at position 23 because of posphorylation.

Evolutionary aspects of a genetic network: studying the lactose/galactose regulon of Kluyveromyces lactis.

The budding yeast Kluyveromyces lactis has diverged from the Saccharomyces lineage before the whole-genome duplication and its genome sequence reveals lower redundancy of many genes. Moreover, it shows lower preference for fermentative carbon metabolism and a broader substrate spectrum making it a particularly rewarding system for comparative and evolutionary studies of carbon-regulated genetic networks. The lactose/galactose regulon of K. lactis, which is regulated by the prototypic transcription activator Gal4 exemplifies important aspects of network evolution when compared with the model GAL regulon of Saccharomyces cerevisiae. Differences in physiology relate to different subcellular compartmentation of regulatory components and, importantly, to quantitative differences in protein-protein interactions rather than major differences in network architecture. Here, we introduce genetic and biochemical tools to study K. lactis in general and the lactose/galactose regulon in particular. We present methods to quantify relevant protein-protein interactions in that network and to visualize such differences in simple plate assays allowing for genetic approaches in further studies.

The galactose switch in Kluyveromyces lactis depends on nuclear competition between Gal4 and Gal1 for Gal80 binding.

The Gal4 protein represents a universally functional transcription activator, which in yeast is regulated by protein-protein interaction of its transcription activation domain with the inhibitor Gal80. Gal80 inhibition is relieved via galactose-mediated Gal80-Gal1-Gal3 interaction. The Gal4-Gal80-Gal1/3 regulatory module is conserved between Saccharomyces cerevisiae and Kluyveromyces lactis. Here we demonstrate that K. lactis Gal80 (KlGal80) is a nuclear protein independent of the Gal4 activity status, whereas KlGal1 is detected throughout the entire cell, which implies that KlGal80 and KlGal1 interact in the nucleus. Consistently KlGal1 accumulates in the nucleus upon KlGAL80 overexpression. Furthermore, we show that the KlGal80-KlGal1 interaction blocks the galactokinase activity of KlGal1 and is incompatible with KlGal80-KlGal4-AD interaction. Thus, we propose that dissociation of KlGal80 from the AD forms the basis of KlGal4 activation in K. lactis. Quantitation of the dissociation constants for the KlGal80 complexes gives a much lower affinity for KlGal1 as compared with Gal4. Mathematical modeling shows that with these affinities a switch based on competition between Gal1 and Gal4 for Gal80 binding is nevertheless efficient provided two monomeric Gal1 molecules interact with dimeric Gal80. Consistent with such a mechanism, analysis of the sedimentation behavior by analytical ultracentrifugation demonstrates the formation of a heterotetrameric KlGal80-KlGal1 complex of 2:2 stoichiometry.

Magneto-structural correlations in Cu(tn)Cl2 (tn = 1,3-diaminopropane): two-dimensional spatially anisotropic triangular magnet formed by hydrogen bonds.

A novel polymeric one-dimensional compound Cu(tn)Cl2 (tn = 1,3-diaminopropane) was prepared and structurally characterized, and its spectral, magnetic, thermodynamic, and thermal properties were studied. The unique structure shows ladderlike chains composed of Cu(II) atoms and chloro bridging ligands [Cu(-mu(3)-Cl-)Cu2] running along the crystallographic c axis. The coordination geometry about copper (4 + 2) approximates that of a strongly elongated octahedron. The equatorial plane of the coordination octahedron is formed by a chelate N-bonded tn ligand and two chloro ligands. One of the chloro ligands is terminal, and the other one, mu3-Cl-, forms two additional longer bonds to the neighboring copper atoms and thus occupies the axial octahedral positions. The electronic ground state of the Cu(II) ion is of d(z)2 symmetry and suggests the activation of intraladder and interladder Cl...H-N hydrogen bonds as exchange paths that form a two-dimensional pattern of a triangular symmetry. The interaction due to the hydrogen bonds seems to play an important role in molecular packing and magnetic coupling. The studies of magneto-structural correlations including electron paramagnetic resonance measurements and thermodynamic and magnetic properties revealed a two-dimensional character of magnetic correlations with the effective intralayer exchange coupling J/k(B) approximately -3 K. No phase transition to the ordered state has been observed down to 60 mK. Cu(tn)Cl2 with the interlayer coupling J' approximately 10(-3)J and moderate intralayer interaction represents an excellent example of a two-dimensional magnetic system.