Between genotype and phenotype: protein chaperones and evolvability

Chaperonin overexpression promotes genetic variation and enzyme evolution

Most protein mutations, and mutations that alter protein functions in particular, undermine stability and are therefore deleterious. Chaperones, or heat-shock proteins, are often implicated in buffering mutations, and could thus facilitate the acquisition of neutral genetic diversity and the rate of adaptation. We examined the ability of the Escherichia coli GroEL/GroES chaperonins to buffer destabilizing and adaptive mutations. Here we show that mutational drifts performed in vitro with four different enzymes indicated that GroEL/GroES overexpression doubled the number of accumulating mutations, and promoted the folding of enzyme variants carrying mutations in the protein core and/or mutations with higher destabilizing effects (destabilization energies of >3.5 kcal mol(-)(1), on average, versus approximately 1 kcal mol(-)(1) in the absence of GroEL/GroES). The divergence of modified enzymatic specificity occurred much faster under GroEL/GroES overexpression, in terms of the number of adapted variants (>or=2-fold) and their improved specificity and activity (>or=10-fold). These results indicate that protein stability is a major constraint in protein evolution, and buffering mechanisms such as chaperonins are key in alleviating this constraint.

Selection for chaperone-like mediated genetic robustness at low mutation rate: impact of drift, epistasis and complexity

Genetic robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Overexpression of chaperones, to assist the folding of proteins carrying deleterious mutations, is so far one of the most accepted molecular mechanisms enhancing genetic robustness. Most theories on the evolution of robustness have focused on the implications of high mutation rate. Here we show that genetic drift, which is modulated by population size, organism complexity, and epistasis, can be a sufficient force to select for chaperone-mediated genetic robustness. Using an exact analytical solution, we also show that selection for costly genetic robustness leads to a paradox: the decrease of population fitness on long timescales and the long-term dependency on robustness mechanisms. We suggest that selection for genetic robustness could be universal and not restricted to high mutation rate organisms such as RNA viruses. The evolution of the endosymbiont Buchnera illustrates this selection mechanism and its paradox: the increased dependency on chaperones mediating genetic robustness. Our model explains why most chaperones might have become essential even in optimal growth conditions.

Clair D, He L. Prenatal malnutrition and adult schizophrenia: further evidence from the 1959-1961 Chinese famine

OBJECTIVE

Evidence from the 1944-1995 Dutch Hunger Winter and the 1959-1961 Chinese famines suggests that those conceived or in early gestation during famines, have a 2-fold increased risk of developing schizophrenia in adult life. We tested the hypothesis in a second Chinese population and also determined whether risk differed between urban and rural areas.

METHOD

The risk of schizophrenia was examined in Liuzhou prefecture of Guangxi autonomous region. Rates were compared among those conceived before, during, and after the famine years. Based on the decline in birth rates, we predicted that those born in 1960 and 1961 would have been exposed to the famine during conception or early gestation. All psychiatric case records in Liuzhou psychiatric hospital for the years 1971 through 2001 were examined and clinical/sociodemographic data extracted by psychiatrists blind to exposure status. Data on births and deaths in the famine years were also available, and cumulative mortality was estimated from later demographic surveys. Evidence of famine was verified, and results were adjusted for mortality. Relative risks (RRs) for schizophrenia were calculated for the region as a whole and for urban and rural areas separately.

RESULTS

Mortality-adjusted RR for schizophrenia was 1.5 (1960) and 2.05 (1961), respectively. However, the effect was exclusively from the rural areas RR = 1.68 (1960) and RR = 2.25 (1961).

CONCLUSIONS

We observe a 2-fold increased risk of schizophrenia among those conceived or in early gestation at the height of famine with risk related to severity of famine conditions.

Over-expression of heat shock protein 70 in mice is associated with growth retardation, tumor formation, and early death

Experiments in lower organisms, such as worms and flies, indicate that the molecular chaperone protein heat shock protein 70 (HSP70) is a longevity factor. In contrast, we demonstrate here that mice overexpressing HSP70 display growth retardation and early death. HSP70 transgenic mice displayed increased levels of serum corticosterone and weaker expression and activity of the glucocorticoid receptor in the liver. Serum insulin-like growth factor-1 (IGF-1) concentrations in the transgenic mice were 50% lower than in the control mice, leading to growth retardation. HSP70 transgenic mice showed decreased expression of Casp9, which encodes caspase-9, and increased expression of the anti-apoptotic Bcl-2 gene, indicating that apoptosis is suppressed. Consequently, most of the transgenic animals died before the age of 18 months from tumors in their lungs and lymph nodes. We suggest that the proinflammatory and antiapoptotic effects of HSP70 might be responsible for the growth retardation, tumor formation, and early death observed in the HSP70 transgenic mice.

Nucleotide diversity in the Hsp90 gene in natural populations of Drosophila melanogaster from Australia

Hsp90 is regarded as one of the best candidates for an evolved mechanism that regulates the expression of genetic and phenotypic variability. We examined nucleotide diversity in both the promoter and coding regions of Hsp90, the gene which encodes Hsp90 in Drosophila, in natural populations of Drosophila melanogaster from eastern Australia. We found that Hsp90 is polymorphic for only two nonsynonymous changes in the coding region, both of which are deletions of a lysine residue. One of these lysine deletions was in complete linkage disequilibrium with the inversion In(3L)P, and showed a significant association with latitude. The other lysine deletion reported here for the first time varied from 0 to 15% in natural populations, but did not show a clinal pattern. The regulatory and coding regions of Hsp90 showed very low nucleotide diversity compared to other nuclear genes, and chromosomes containing In(3L)P had lower levels of nucleotide diversity than the standard arrangements. Non-neutral evolution of Hsp90 was not supported by analyses of either the regulatory or coding regions of the gene. These results are discussed within the context of Hsp90 variation being involved in thermotolerance as well as the expression of genetic and phenotypic variability.

Diversify or Die: Generation of Diversity in Response to Stress

When challenged with unfavorable conditions, microorganisms can develop a stress response that allows them to adapt to or survive in the new environment. A common feature of the numerous specific stress response pathways that have been described in a wide range of bacteria is that they are energy demanding and therefore often transient. In addition, stress responses may come too late or be insufficient to protect the cell or the population against very sudden or severe stresses. However, it seems that microorganisms can also enhance their chances of survival under stress by increasing the generation of diversity at the population level. This can be achieved either by creating genetic diversity by a variety of mechanisms involving for example constitutive or transient mutators and contingency loci, or by revealing phenotypic diversity that remained dormant due to a mechanism called genetic buffering. This review gives an overview of these emerging diversity-generating mechanisms, which seem to play an important role in the ability of microbial populations to overcome stress challenges.

Alleviation of deleterious effects of protein mutation through inactivation of molecular chaperones

Molecular chaperones recognize and bind destabilized proteins. This can be especially important for proteins whose stability is reduced by mutations. We focused our study on a major chaperone system, RAC-Ssb, which assists folding of newly synthesized polypeptides in the yeast cytosol. A sensitive phenotypic assay, the red color of Ade2 mutants, was used to screen for variants with metabolic activity dependent on RAC-Ssb. None of the Ade2 mutants were found to exhibit lower metabolic activity after inactivation of RAC-Ssb. In order to explicitly test the relationship between protein instability and activity of chaperones, a series of temperature sensitive Ade2 mutants were tested in the presence or absence of RAC-Ssb. The growth of Ade2(ts) mutants at elevated temperatures was enhanced if chaperones were missing. Similar pattern was found for thermally sensitive mutants of several other genes. Because RAC-Ssb normally supports the folding of proteins, it appears paradoxical that catabolic activity of mutants is reduced when these chaperones are present. We suggest that under non-stressful conditions, molecular chaperones are tuned to support folding of native proteins, but not that of mutated ones.

Heat shock inhibits caspase-1 activity while also preventing its inflammasome-mediated activation by anthrax lethal toxin

Anthrax lethal toxin (LT) rapidly kills macrophages from certain mouse strains in a mechanism dependent on the breakdown of unknown protein(s) by the proteasome, formation of the Nalp1b (NLRP1b) inflammasome and subsequent activation of caspase-1. We report that heat-shocking LT-sensitive macrophages rapidly protects them against cytolysis by inhibiting caspase-1 activation without upstream effects on LT endocytosis or cleavage of the toxin's known cytosolic substrates (mitogen-activated protein kinases). Heat shock protection against LT occurred through a mechanism independent of de novo protein synthesis, HSP90 activity, p38 activation or proteasome inhibition and was downstream of mitogen-activated protein kinase cleavage and degradation of an unknown substrate by the proteasome. The heat shock inhibition of LT-mediated caspase-1 activation was not specific to the Nalp1b (NLRP1b) inflammasome, as heat shock also inhibited Nalp3 (NLRP3) inflammasome-mediated caspase-1 activation in macrophages. We found that heat shock induced pro-caspase-1 association with a large cellular complex that could prevent its activation. Additionally, while heat-shocking recombinant caspase-1 did not affect its activity in vitro, lysates from heat-shocked cells completely inhibited recombinant active caspase-1 activity. Our results suggest that heat shock inhibition of active caspase-1 can occur independently of an inflammasome platform, through a titratable factor present within intact, functioning heat-shocked cells.

Staying in the fold: The SGT1/chaperone machinery in maintenance and evolution of leucine-rich repeat proteins

The conserved eukaryotic protein SGT1 (suppressor of G(2) allele of skp1) participates in diverse physiological processes such as cell cycle progression in yeast, plant immunity against pathogens and plant hormone signalling. Recent genetic and biochemical studies suggest that SGT1 functions as a novel co-chaperone for cytosolic/nuclear HSP90 and HSP70 molecular chaperones in the folding and maturation of substrate proteins. Since proteins containing the leucine-rich repeat (LRR) protein-protein interaction motif are overrepresented in SGT1-dependent phenomena, we consider whether LRR-containing proteins are preferential substrates of an SGT1/HSP70/HSP90 complex. Such a chaperone organisation is reminiscent of the HOP/HSP70/HSP90 machinery which controls maturation and activation of glucocorticoid receptors in animals. Drawing on this parallel, we discuss the possible contribution of an SGT1-chaperone complex in the folding and maturation of LRR-containing proteins and its evolutionary consequences for the emergence of novel LRR interaction surfaces.

The evolution of fungal drug resistance: modulating the trajectory from genotype to phenotype

The emergence of drug resistance in pathogenic microorganisms provides an excellent example of microbial evolution that has had profound consequences for human health. The widespread use of antimicrobial agents in medicine and agriculture exerts strong selection for the evolution of drug resistance. Selection acts on the phenotypic consequences of resistance mutations, which are influenced by the genetic variation in particular genomes. Recent studies have revealed a mechanism by which the molecular chaperone heat shock protein 90 (Hsp90) can alter the relationship between genotype and phenotype in an environmentally contingent manner, thereby 'sculpting' the course of evolution. Harnessing Hsp90 holds great promise for treating life-threatening infectious diseases.

Subnuclear localization and mobility are key indicators of PAX3 dysfunction in Waardenburg syndrome

Mutations in the transcription factor PAX3 cause Waardenburg syndrome (WS) in humans and the mouse Splotch mutant, which display similar neural crest-derived defects. Previous characterization of disease-causing mutations revealed pleiotropic effects on PAX3 DNA binding and transcriptional activity. In this study, we evaluated the impact of disease alleles on PAX3 localization and mobility. Immunofluorescence analyses indicated that the majority of PAX3 occupies the interchromatin space, with only sporadic colocalization with sites of transcription. Interestingly, PAX3 disease alleles fell into two distinct categories when localization and dynamics in fluorescence recovery after photobleaching (FRAP) were assessed. The first group (class I), comprising N47H, G81A and V265F exhibit a diffuse distribution and markedly increased mobility when compared with wild-type PAX3. In contrast, the G42R, F45L, S84F, Y90H and R271G mutants (class II) display evidence of subnuclear compartmentalization and mobility intermediate between wild-type PAX3 and class I proteins. However, unlike class I mutants, which retain DNA binding, class II proteins are deficient for this activity, indicating that DNA binding is not a primary determinant of PAX3 distribution and movement. Importantly, class I properties prevail when combined with a class II mutation, which taken with the proximity of the two mutant classes within the PAX3 protein, suggests class I mutants act by perturbing PAX3 conformation. Together, these results establish that altered localization and dynamics play a key role in PAX3 dysfunction and that loss of the underlying determinants represents the principal defect for a subset of Waardenburg mutations.

HSP90 affects the expression of genetic variation and developmental stability in quantitative traits

Modulation of the activity of the molecular chaperone HSP90 has been extensively discussed as a means to alter phenotype in many traits and organisms. Such changes can be due to the exposure of cryptic genetic variation, which in some instances may also be accomplished by mild environmental alteration. Should such polymorphisms be widespread, natural selection may be more effective at producing phenotypic change in suboptimal environments. However, the frequency and identity of buffered polymorphisms in natural populations are unknown. Here, we employ quantitative genetic dissection of an Arabidopsis thaliana developmental response, hypocotyl elongation in the dark, to detail the underpinnings of genetic variation responsive to HSP90 modulation. We demonstrate that HSP90-dependent alleles occur in continuously distributed, environmentally responsive traits and are amenable to quantitative genetic mapping techniques. Furthermore, such alleles are frequent in natural populations and can have significant effects on natural phenotypic variation. We also find that HSP90 modulation has both general and allele-specific effects on developmental stability; that is, developmental stability is a phenotypic trait that can be affected by natural variation. However, effects of revealed variation on trait means outweigh effects of decreased developmental stability, and the HSP90-dependent trait alterations could be acted on by natural selection. Thus, HSP90 may centrally influence canalization, assimilation, and the rapid evolutionary alteration of phenotype through the concealment and exposure of cryptic genetic variation.

Molecular chaperones and selection against mutations

Background

Molecular chaperones help to restore the native states of proteins after their destabilization by external stress. It has been proposed that another function of chaperones is to maintain the activity of proteins destabilized by mutation, weakening the selection against suboptimal protein variants. This would allow for the accumulation of genetic variation which could then be exposed during environmental perturbation and facilitate rapid adaptation.

Results

We focus on studies describing interactions of chaperones with mutated polypeptides. There are some examples that chaperones can alleviate the deleterious effects of mutations through increased assistance of destabilized proteins. These experiments are restricted to bacteria and typically involve overexpression of chaperones. In eukaryotes, it was found that the malfunctioning of chaperones aggravated phenotypic aberrations associated with mutations. This effect could not be linked to chaperone-mediated stabilization of mutated proteins. More likely, the insufficient activity of chaperones inflicted a deregulation of multiple cellular systems, including those responsible for signaling and therefore important in development. As to why the assistance of mutated proteins by chaperones seems difficult to demonstrate, we note that chaperone-assisted folding can often co-exist with chaperone-assisted degradation. There is growing evidence that some chaperones, including those dependent on Hsp90, can detect potentially functional but excessively unstable proteins and direct them towards degradation instead of folding. This implies that at least some mutations are exposed rather than masked by the activity of molecular chaperones.

Conclusion

It is at present impossible to determine whether molecular chaperones are mostly helpers or examiners of mutated proteins because experiments showing either of these roles are very few. Depending on whether assistance or disposal prevails, molecular chaperones could speed up or slow down evolution of protein sequences. Similar uncertainties arise when the concept of chaperones (mostly Hsp90) as general regulators of evolvability is considered. If the two roles of chaperones are antagonistic, then any (even small) modification of the chaperone activities to save mutated polypeptides could lead to increased misfolding and aggregation of other proteins. This would be a permanent burden, different from the stochastic cost arising from indiscriminate buffering of random mutations of which many are maladaptive.

Reviewers

This article was reviewed by A. S. Kondrashov, J. Höhfeld (nominated by A. Eyre-Walker) and D. A. Drummond (nominated by C. Adami). For the full reviews, please go to the Reviewers' comments section.

The Hsp90 capacitor, developmental remodeling, and evolution: the robustness of gene networks and the curious evolvability of metamorphosis

Genetic capacitors moderate expression of heritable variation and provide a novel mechanism for rapid evolution. The prototypic genetic capacitor, Hsp90, interfaces stress responses, developmental networks, trait thresholds and expression of wide-ranging morphological changes in Drosophila and other organisms. The Hsp90 capacitor hypothesis, that stress-sensitive storage and release of genetic variation through Hsp90 facilitates adaptive evolution in unpredictable environments, has been challenged by the belief that Hsp90-buffered variation is unconditionally deleterious. Here we review recent results supporting the Hsp90 capacitor hypothesis, highlighting the heritability, selectability, and potential evolvability of Hsp90-buffered traits. Despite a surprising bias toward morphological novelty and typically invariable quantitative traits, Hsp90-buffered changes are remarkably modular, and can be selected to high frequency independent of the expected negative side-effects or obvious correlated changes in other, unselected traits. Recent dissection of cryptic signal transduction variation involved in one Hsp90-buffered trait reveals potentially dozens of normally silent polymorphisms embedded in cell cycle, differentiation and growth control networks. Reduced function of Hsp90 substrates during environmental stress would destabilize robust developmental processes, relieve developmental constraints and plausibly enables genetic network remodeling by abundant cryptic alleles. We speculate that morphological transitions controlled by Hsp90 may fuel the incredible evolutionary lability of metazoan life-cycles.

Linking Hsp90 function to micro-environmental and stochastic variation in floralorgans of Iris pumila L

Hsp90 is an environmentally responsive molecular chaperone that was found to play a key role in buffering against genetic and non-genetic perturbations in the model organisms Arabidopsis and Drosophila. Here we analyzed the buffering capacity of Hsp90 against two kinds of non-genetic factors - stochastic noise and micro-environmental varia?tion of floral organ traits in naturally growing Iris pumila plants. We found no statistical association between the endog?enous level of Hsp90 and the floral organ radial symmetry produced by stochastic developmental noise. Conversely, floral organ plasticity in response to micro-environmental variation tended to be greater with decrease in Hsp90b isoform expression.

RAR1 and HSP90 form a complex with Rac/Rop GTPase and function in innate-immune responses in rice

A rice (Oryza sativa) Rac/Rop GTPase, Os Rac1, is involved in innate immunity, but its molecular function is largely unknown. RAR1 (for required for Mla12 resistance) and HSP90 (a heat shock protein 90 kD) are important components of R gene-mediated disease resistance, and their function is conserved in several plant species. HSP90 has also recently been shown to be important in mammalian innate immunity. However, their functions at the molecular level are not well understood. In this study, we examined the functional relationships between Os Rac1, RAR1, and HSP90. Os RAR1-RNA interference (RNAi) rice plants had impaired basal resistance to a compatible race of the blast fungus Magnaporthe grisea and the virulent bacterial blight pathogen Xanthomonas oryzae. Constitutively active Os Rac1 complemented the loss of resistance, suggesting that Os Rac1 and RAR1 are functionally linked. Coimmunoprecipitation experiments with rice cell culture extracts indicate that Rac1 forms a complex with RAR1, HSP90, and HSP70 in vivo. Studies with Os RAR1-RNAi and treatment with geldanamycin, an HSP90-specific inhibitor, showed that RAR1 and HSP90 are essential for the Rac1-mediated enhancement of pathogen-associated molecular pattern-triggered immune responses in rice cell cultures. Furthermore, the function of HSP90, but not RAR1, may be essential for their association with the Rac1 complex. Os Rac1 also regulates RAR1 expression at both the mRNA and protein levels. Together, our results indicate that Rac1, RAR1, HSP90, and HSP70 form one or more protein complexes in rice cells and suggest that these proteins play important roles in innate immunity in rice.

Mutation rate variation in multicellular eukaryotes: causes and consequences

A basic knowledge about mutation rates is central to our understanding of a myriad of evolutionary phenomena, including the maintenance of sex and rates of molecular evolution. Although there is substantial evidence that mutation rates vary among taxa, relatively little is known about the factors that underlie this variation at an empirical level, particularly in multicellular eukaryotes. Here we integrate several disparate lines of theoretical and empirical inquiry into a unified framework to guide future studies that are aimed at understanding why and how mutation rates evolve in multicellular species.

Hsp90 and Developmental Networks

The most abundant cytoplasmic chaperone of eukaryotic cells, Hsp90 is a hub in developmental regulatory networks and the first example described of the phenomenon of molecular buffering. As a chaperone for many different signaling proteins, Hsp90 maintains the clarity and strength of communication within and between cells, concealing developmental and stochastic variations that otherwise cause abrupt morphological changes in a large variety of organisms, including Drosophila and Arabidopsis. The chapter provides a framework for understanding how Hsp90 controls the sudden appearance of novel morphologies. We start with a discussion of the longstanding problem of hidden polygenic variation and then introduce the idea of signal transduction thresholds in mediating the effect of Hsp90 on the expression of phenotypic variation. This leads to a discussion of the role of nonlinearity in creating thresholds for sudden changes in cellular responses to developmental signals. We end with speculation on the potentially pivotal role of Hsp90 in controlling the developmental networks that determine morphological stasis and change in evolution.

Phosphoglucose isomerase genotype affects running speed and heat shock protein expression after exposure to extreme temperatures in a montane willow beetle

Eastern Sierra Nevada populations of the willow beetle Chrysomela aeneicollis commonly experience stressfully high and low environmental temperatures that may influence survival and reproduction. Allele frequencies at the enzyme locus phosphoglucose isomerase (PGI) vary across a climatic latitudinal gradient in these populations, with PGI allele 1 being most common in cooler regions and PGI allele 4 in warmer ones. PGI genotypes differ in heat and cold tolerance and in expression of a 70 kDa heat shock protein. Here we examine genetic, behavioral and environmental factors affecting a performance character, running speed, for willow beetles, and assess effects of consecutive cold and heat exposure on running speed and expression of Hsp70 in the laboratory. In nature, running speed depends on air temperature and is higher for males than females. Mating beetles ran faster than single beetles, and differences among PGI genotypes in male running speed depended on the presence of females. In the laboratory, exposure to cold reduced subsequent running speed, but the amount of this reduction depended on PGI genotype and previous thermal history. Effects of exposure to heat also depended on life history stage and PGI genotype. Adults possessing allele 1 ran fastest after a single exposure to stressful temperature, whereas those possessing allele 4 ran faster after repeated exposure. Larvae possessing allele 4 ran fastest after a single stressful exposure, but running speed generally declined after a second exposure to stressful temperature. The ranking of PGI genotypes after the second exposure depended on whether a larva had been exposed to cold or heat. Effects of temperature on Hsp70 expression also varied among PGI genotypes and depended on type of exposure, especially for adults (single heat exposure, two cold exposures: PGI 1-1>1-4>4-4; other multiple extreme exposures: 4-4>1-4>1-1). There was no consistent association between alleles at other polymorphic enzyme loci and running speed or Hsp70 expression. These data suggest that variation at PGI is associated with considerable plasticity in running speed. Differences in Hsp70 expression among PGI genotypes suggest that the heat-shock response may buffer differences in thermal tolerance and performance among genotypes and help maintain the PGI polymorphism in a thermally variable environment.

Phenotypic plasticity in Drosophila pigmentation caused by temperature sensitivity of a chromatin regulator network

Phenotypic plasticity is the ability of a genotype to produce contrasting phenotypes in different environments. Although many examples have been described, the responsible mechanisms are poorly understood. In particular, it is not clear how phenotypic plasticity is related to buffering, the maintenance of a constant phenotype against genetic or environmental variation. We investigate here the genetic basis of a particularly well described plastic phenotype: the abdominal pigmentation in female Drosophila melanogaster. Cold temperature induces a dark pigmentation, in particular in posterior segments, while higher temperature has the opposite effect. We show that the homeotic gene Abdominal-B (Abd-B) has a major role in the plasticity of pigmentation in the abdomen. Abd-B plays opposite roles on melanin production through the regulation of several pigmentation enzymes. This makes the control of pigmentation very unstable in the posterior abdomen, and we show that the relative spatio-temporal expression of limiting pigmentation enzymes in this region of the body is thermosensitive. Temperature acts on melanin production by modulating a chromatin regulator network, interacting genetically with the transcription factor bric-à-brac (bab), a target of Abd-B and Hsp83, encoding the chaperone Hsp90. Genetic disruption of this chromatin regulator network increases the effect of temperature and the instability of the pigmentation pattern in the posterior abdomen. Colocalizations on polytene chromosomes suggest that BAB and these chromatin regulators cooperate in the regulation of many targets, including several pigmentation enzymes. We show that they are also involved in sex comb development in males and that genetic destabilization of this network is also strongly modulated by temperature for this phenotype. Thus, we propose that phenotypic plasticity of pigmentation is a side effect reflecting a global impact of temperature on epigenetic mechanisms. Furthermore, the thermosensitivity of this network may be related to the high evolvability of several secondary sexual characters in the genus Drosophila.

The phenotype of an individual is not fully controlled by its genes. Environmental conditions (food, light, temperature, pathogens, etc.) can also contribute to phenotypic variation. This phenomenon is called phenotypic plasticity. We investigate here the genetic basis of the phenotypic plasticity of pigmentation in the fruit fly Drosophila melanogaster. Drosophila pigmentation is strongly modulated by temperature, in particular in the posterior abdominal segments of females. The development of these segments is controlled by the homeotic gene Abdominal-B (Abd-B). Abd-B sensitizes pigmentation patterning in this region of the body by repressing several crucial pigmentation enzymes. It makes the regulation of their spatio-temporal expression in the posterior abdomen particularly sensitive to temperature variation. We show that temperature modulates the mechanisms regulating the dynamic structure of the chromosomes. Chromosomal domains can be compacted and transcriptionally silent, or opened and transcriptionally active. Temperature interacts with a network of chromatin regulators and affects not only the regulation of pigmentation enzymes but several traits under the control of this network. Thus, we conclude that the phenotypic plasticity of female abdominal pigmentation in Drosophila is a visible consequence for a particularly sensitive phenotype, of a general effect of temperature on the regulation of chromosome architecture.

The role of stress proteins in responses of a montane willow leaf beetle to environmental temperature variation

The heat shock response is a critical mechanism by which organisms buffer effects of variable and unpredictable environmental temperatures. Upregulation of heat shock proteins (Hsps) increases survival after exposure to stressful conditions in nature, although benefits of Hsp expression are often balanced by costs to growth and reproductive success. Hsp-assisted folding of variant polypeptides may prevent development of unfit phenotypes; thus, some differences in Hsp expression among natural populations of ectotherms may be due to interactions between enzyme variants (allozymes) and Hsps. In the Sierra willow leaf beetle Chrysomela aeneicollis, which lives in highly variable thermal habitats at the southern edge of their range in the Eastern Sierra Nevada, California, allele frequencies at the enzyme locus phosphoglucose isomerase (PGI) vary across a climatic latitudinal gradient. PGI allozymes differ in kinetic properties,and expression of a 70 kDa Hsp differs between populations, along elevation gradients,and among PGI genotypes. Differences in Hsp70 expression among PGI genotypes correspond to differences in thermal tolerance and traits important for reproductive success, such as running speed, survival and fecundity. Thus, differential Hsp expression among genotypes may allow functionally important genetic variation to persist, allowing populations to respond effectively to environmental change.

The theory of biological robustness and its implication in cancer

One of the essential issues in systems biology is to identify fundamental principles that govern living organisms at the system level. In this chapter, I argue that robustness is a fundamental feature of living systems where its relationship with evolution-trade-offs among robustness, fragility, resource demands, and performance-provides a possible framework for how biological systems have evolved and been organized. In addition, diseases can be con- sidered as a manifestation of fragility of the system. In some cases, such as cancer, the disease state establishes its own robustness against therapeutic interventions. Understanding robustness and its intrinsic properties will provide us with a more profound understanding of biological systems, their anomalies, and countermeasures.

A robustness-based approach to systems-oriented drug design

Many potential drugs that specifically target a particular protein considered to underlie a given disease have been found to be less effective than hoped, or to cause significant side effects. The intrinsic robustness of living systems against various perturbations is a key factor that prevents such compounds from being successful. By studying complex network systems and reformulating control and communication theories that are well established in engineering, a theoretical foundation for a systems-oriented approach to more effectively control the robustness of living systems, particularly at the cellular level, could be developed. Here, I use examples that are based on existing drugs to illustrate the concept of robustness, and then discuss how a greater consideration of the importance of robustness could influence the design of new drugs that will be intended to control complex systems.

Hsp90 selectively modulates phenotype in vertebrate development

Compromised heat shock protein 90 (Hsp90) function reveals cryptic phenotypes in flies and plants. These observations were interpreted to suggest that this molecular stress-response chaperone has a capacity to buffer underlying genetic variation. Conversely, the protective role of Hsp90 could account for the variable penetrance or severity of some heritable developmental malformations in vertebrates. Using zebrafish as a model, we defined Hsp90 inhibitor levels that did not induce a heat shock response or perturb phenotype in wild-type strains. Under these conditions the severity of the recessive eye phenotype in sunrise, caused by a pax6b mutation, was increased, while in dreumes, caused by a sufu mutation, it was decreased. In another strain, a previously unobserved spectrum of severe structural eye malformations, reminiscent of anophthalmia, microphthalmia, and nanophthalmia complex in humans, was uncovered by this limited inhibition of Hsp90 function. Inbreeding of offspring from selected unaffected carrier parents led to significantly elevated malformation frequencies and revealed the oligogenic nature of this phenotype. Unlike in Drosophila, Hsp90 inhibition can decrease developmental stability in zebrafish, as indicated by increased asymmetric presentation of anophthalmia, microphthalmia, and nanophthalmia and sunrise phenotypes. Analysis of the sunrise pax6b mutation suggests a molecular mechanism for the buffering of mutations by Hsp90. The zebrafish studies imply that mild perturbation of Hsp90 function at critical developmental stages may underpin the variable penetrance and expressivity of many developmental anomalies where the interaction between genotype and environment plays a major role.

Genetic variation is not always expressed as a single consistent phenotype even in familial diseases. Unilateral malformations in paired organs, such as the failure of an eye to develop on one side only, also remind us that gene function is often modified by environmental factors. Following observations by others in fruit flies, we explored the underlying mechanisms for such phenotypic fluctuation, using zebrafish as a vertebrate model. Earlier work suggested involvement of chaperone proteins like Hsp90, which assist with normal protein folding during development and also work overtime to keep proteins functional in response to environmental stress. Using specific drugs at defined times in early development for the limited reduction of Hsp90 activity, we showed that different cryptic genetic variants could be revealed consistently in genetically distinct fish strains. Once uncovered, the frequency of these variants was increased by inbreeding, confirming the role of underlying genetic factors. Similarly, we could modify the phenotypic severity of some—but not all—known gene variants, worsening some and improving others. It emerged that the most susceptible variants were those carrying amino acid alterations, in which assisted protein folding may either restore near normal function or facilitate malfunction, thus worsening phenotype. This insight may allow us to prevent recurrent malformations by minimizing or perhaps even counteracting the effects of exposure to environmental stress during development.

Thermally induced and developmentally regulated expression of a small heat shock protein in Trichinella spiralis

A cDNA encoding a small heat shock protein of Trichinella spiralis, Ts-sHsp, was cloned and expressed and is herein characterized. This cDNA encoded a predicted protein of 165 amino acids, which had a high sequence identity in alpha crystallin domain with various small heat shock proteins of other organisms. A Western blot analysis indicated that anti-Ts-sHsp recombinant antibody recognized the protein of adults and larvae migrating at about 19 kDa. An in situ localization study showed the protein to be abundantly present in the body wall muscle cells, hypodermis, stichocytes, and esophagus of muscle larvae. The Ts-sHsp recombinant protein possessed chaperone activity to suppress the thermally-induced aggregation of citrate synthase. This sHsp was expressed at various developmental stages of T. spiralis, but at different levels. A high level was observed in mature muscle larvae (infective larvae), which was much higher than the levels seen in adults, newborn larvae, or immature muscle larvae. The expression of the sHsp gene was thermal inducible, thus responding to both cold (0 degrees C) and heat shock (43 degrees C) stress; however, at different patterns. The expression of Ts-sHsp increased gradually from 3 to 72 h after cold stress, while the expression was elevated to its highest after 3 h heat stress and then decreased. These results suggest that this small heat shock protein likely plays a role in the tolerance to both chemical and physical stresses, thereby enhancing the survival ability of Trichinella muscle larvae.

Biological robustness in complex host-pathogen systems

Infectious diseases are still the number one killer of human beings. Even in developed countries, infectious diseases continue to be a major health threat. This article explores a conceptual framework for understanding infectious diseases in the context of the complex dynamics between microbe and host, and explores theoretical strategies for anti-infectives. The central pillar of this conceptual framework is that biological robustness is a fundamental property of systems that is closely interlinked with the evolution of symbiotic host-pathogen systems. There are specific architectural features of such robust yet evolvable systems and interpretable trade-offs between robustness, fragility, resource demands, and performance. This concept applies equally to both microbes and host. Pathogens have evolved to exploit the host using various strategies as well as effective escape mechanisms. Modular pathogenicity islands (PAI) derived from horizontal gene transfer, highly variable surface molecules, and a range of other countermeasures enhance the robustness of a pathogen against attacks from the host immune system. The host has likewise evolved complex defensive mechanisms to protect itself against pathogenic threats, but the host immune system includes several trade-offs that can be exploited by pathogens and induces undesirable inflammatory reactions. Due to the complexity of the dynamics emerging from the interactions of multiple microbes and a host, effective counter-measures require an in-depth understanding of system dynamics as well as detailed molecular mechanisms of the processes that are involved.

Seasonal variation in heat shock proteins Hsp70 and Hsp90 expression in an exposed and a shaded habitat of Iris pumila

Seasonal variation in heat shock proteins Hsp70 and Hsp90 expression was studied in the leaves of two naturally growing Iris pumila populations, one inhabiting an open dune site, and the other the understorey of a Pinus silvestris stand. The Hsps were quantified by an immunoblotting procedure. The level of the Hsps was found to vary significantly both across seasons and between habitats. The mean Hsp70 concentration was significantly greater at the open area than in the woodland understorey, reaching its maximum in the summer, especially in plants experiencing full sunlight. Two Hsp90 isoforms, referred to as Hsp90a (86 kDa) and Hsp90b (84 kDa), were detected. At both habitats, the level of Hsp90a was highest in autumn, that of Hsp90b in spring, whereas both of them reached a nadir in summer. Throughout the growing season, the relative abundance of Hsp90b was higher in plants growing under vegetation canopy in comparison to those inhabiting the open dune site. An inverse relationship between the phenotypic variation in specific leaf area and the level of Hsp90b over seasons at both habitats was observed, suggesting the role of this protein in buffering phenotypic variation in the wild.

Control of canalization and evolvability by Hsp90

Partial reduction of Hsp90 increases expression of morphological novelty in qualitative traits of Drosophila and Arabidopsis, but the extent to which the Hsp90 chaperone also controls smaller and more likely adaptive changes in natural quantitative traits has been unclear. To determine the effect of Hsp90 on quantitative trait variability we deconstructed genetic, stochastic and environmental components of variation in Drosophila wing and bristle traits of genetically matched flies, differing only by Hsp90 loss-of-function or wild-type alleles. Unexpectedly, Hsp90 buffering was remarkably specific to certain normally invariant and highly discrete quantitative traits. Like the qualitative trait phenotypes controlled by Hsp90, highly discrete quantitative traits such as scutellor and thoracic bristle number are threshold traits. When tested across genotypes sampled from a wild population or in laboratory strains, the sensitivity of these traits to many types of variation was coordinately controlled, while continuously variable bristle types and wing size, and critically invariant left-right wing asymmetry, remained relatively unaffected. Although increased environmental variation and developmental noise would impede many types of selection response, in replicate populations in which Hsp90 was specifically impaired, heritability and ‘extrinsic evolvability’, the expected response to selection, were also markedly increased. However, despite the overall buffering effect of Hsp90 on variation in populations, for any particular individual or genotype in which Hsp90 was impaired, the size and direction of its effects were unpredictable. The trait and genetic-background dependence of Hsp90 effects and its remarkable bias toward invariant or canalized traits support the idea that traits evolve independent and trait-specific mechanisms of canalization and evolvability through their evolution of non-linearity and thresholds. Highly non-linear responses would buffer variation in Hsp90-dependent signaling over a wide range, while over a narrow range of signaling near trait thresholds become more variable with increasing probability of triggering all-or-none developmental responses.

Modularity and intrinsic evolvability of Hsp90-buffered change

Hsp90 controls dramatic phenotypic transitions in a wide array of morphological features of many organisms. The genetic-background dependence of specific abnormalities and their response to laboratory selection suggested Hsp90 could be an ‘evolutionary capacitor’, allowing developmental variation to accumulate as neutral alleles under normal conditions and manifest selectable morphological differences during environmental stress. The relevance of Hsp90-buffered variation for evolution has been most often challenged by the idea that large morphological changes controlled by Hsp90 are unconditionally deleterious. To address this issue, we tested an Hsp90-buffered abnormality in Drosophila for unselected pleiotropic effects and correlated fitness costs. Up to 120-fold differences in penetrance among six highly related selection lines, started from an initially small number of flies and rapidly selected for and against a deformed eye trait (dfe), did not translate into measurable differences in any of several tests of viability, lifespan or competitive fitness. Nor were 17 dfe Quantitative Trait Loci (QTL) associated with fitness effects in over 1,400 recombinant lines. Our ability to detect measurable effects of inbreeding, media environment and the white mutation in the selection line backgrounds independent of dfe penetrance suggests that, within the limitations of laboratory tests of fitness, this large morphological change controlled by Hsp90 was selectable independent of strong, correlated and unconditionally deleterious effects—abundant, polygenic variation hidden by Hsp90 allows potentially deleterious alleles to be readily replaced during selection by less deleterious alleles with similar phenotypic effects. Hsp90 links environmental stress with the expression of developmental variation controlling unprecedented morphological plasticity. As outlined here and in the companion paper of this issue, the complex genetic architecture of Hsp90-buffered variation supports a remarkable modularity of Hsp90 effects on quantitative and qualitative phenotypes, consistent with the ‘Hsp90 capacitor hypothesis’ and standard quantitative genetic models of threshold traits.

Heat-shock proteins: new keys to the development of cytoprotective therapies

As molecular chaperones, heat-shock proteins (HSPs) function to limit protein aggregation, facilitate protein refolding and chaperone other proteins. Under conditions of cellular stress, intracellular HSP levels increase in order to provide cellular protection and maintain homeostasis. Evidence exists that the HSP family may be secreted into the circulation via lipid raft-mediated, granule-mediated or exosome-mediated exocytosis in haematopoietic and tumour cells. Extracellular HSPs exert immunomodulatory activities and play an important role in innate immune activation against pathogen infection. Membrane-bound Hsp70 in tumour cells or released chaperone-tumour associated antigen complex represent a target structure for the cytolytic attack by natural killer cells or T lymphocytes. Cellular stresses induce stress granule formation to evade detrimental cellular effects, mediating preconditioning phenotype. Therefore, induction of cellular stress tolerance by preconditioning (e.g., heat shock) might be potential therapeutic targets.

Chaperone and anti-chaperone: Two-faced synuclein as stimulator of synaptic evolution

Previous studies have shown that beta-synuclein (beta-syn), the homologue of alpha-syn, inhibited alpha-syn aggregation and stabilized Akt cell survival signaling molecule, suggesting that beta-syn was protective against alpha-syn-related neurodegenerative disorders, such as Parkinson's disease and diffuse Lewy body disease. However, emerging evidence argues that the situation may be not so simple. Two missense mutations of beta-syn were identified in familial and sporadic diffuse Lewy body disease, and wild type beta-syn was induced to form fibril structures in vitro, while, alpha-syn was shown to be protective against neurodegeneration caused by deletion of cysteine-string protein-alpha, the presynaptic cochaperone to Hsc70 in mice. Collectively, alpha- and beta-syn are both, but in varying degrees, featured with two opposite properties, namely normal chaperone and anti-chaperone. By reviewing recent progress in syn biology with a particular focus on beta-syn, this manuscript refers to the intriguing possibility that the dual syn proteins might have acquired a driving force for synaptic evolution. Hypothetically, the anti-chaperone syn may provoke stress-induced diverse responses, whereas, the chaperone syn may provide buffering for them, allowing accumulation of nonlethal phenotypic variations in synapses. Consequently, dual syn proteins may cope with forthcoming stresses in the brain by stimulating adaptive evolution. In this context, failure to regulate this process due to various causes, such as gene mutations and environmental risk factors, may result in imperfect adaptability against stresses, leading to neurodegenerative disorders.

Why molecular chaperones buffer mutational damage: a case study with a yeast Hsp40/70 system

The malfunctioning of molecular chaperones may result in uncovering genetic variation. The molecular basis of this phenomenon remains largely unknown. Chaperones rescue proteins unfolded by environmental stresses and therefore they might also help to stabilize mutated proteins and thus mask damages. To test this hypothesis, we carried out a genomewide mutagenesis followed by a screen for mutations that were synthetically harmful when the RAC-Ssb1/2 cytosolic chaperones were inactive. Mutants with such a phenotype were found and mapped to single nucleotide substitutions. However, neither the genes identified nor the nature of genetic lesions implied that folding of the mutated proteins was being supported by the chaperones. In a second screen, we identified temperature-sensitive (ts) mutants, a phenotype indicative of structural instability of proteins. We tested these for an association with sensitivity to loss of chaperone activity but found no such correlation as might have been expected if the chaperones assisted the folding of mutant proteins. Thus, molecular chaperones can mask the negative effects of mutations but the mechanism of such buffering need not be direct. A plausible role of chaperones is to stabilize genetic networks, thus making them more tolerant to malfunctioning of their constituents.

Heat-shock promoters: targets for evolution by P transposable elements in Drosophila

Transposable elements are potent agents of genomic change during evolution, but require access to chromatin for insertion—and not all genes provide equivalent access. To test whether the regulatory features of heat-shock genes render their proximal promoters especially susceptible to the insertion of transposable elements in nature, we conducted an unbiased screen of the proximal promoters of 18 heat-shock genes in 48 natural populations of Drosophila. More than 200 distinctive transposable elements had inserted into these promoters; greater than 96% are P elements. By contrast, few or no P element insertions segregate in natural populations in a “negative control” set of proximal promoters lacking the distinctive regulatory features of heat-shock genes. P element transpositions into these same genes during laboratory mutagenesis recapitulate these findings. The natural P element insertions cluster in specific sites in the promoters, with up to eight populations exhibiting P element insertions at the same position; laboratory insertions are into similar sites. By contrast, a “positive control” set of promoters resembling heat-shock promoters in regulatory features harbors few P element insertions in nature, but many insertions after experimental transposition in the laboratory. We conclude that the distinctive regulatory features that typify heat-shock genes (in Drosophila) are especially prone to mutagenesis via P elements in nature. Thus in nature, P elements create significant and distinctive variation in heat-shock genes, upon which evolutionary processes may act.

Transposable elements can be a major source of evolutionary change. Their insertion can directly affect the genes into, or next to, which they insert. To insert, however, they must first gain access to the host gene. The authors reasoned that, because the DNA in the promoters (i.e., regulatory regions) of heat-shock genes is unusually accessible, these genes might harbor many transposable elements. With a technique that can detect any insertion into a gene, they discovered more than 200 distinctive transposable elements in the promoter regions of heat-shock genes in fruit flies from the wild—but few or none in the promoter regions of more typical genes. Surprisingly, out of the one hundred kinds of transposable elements in fruit flies, almost all were P elements. P elements are remarkable because they invaded the fruit fly genome only during the last century. These findings imply that the combination of accessible DNA and the recent invasion of P elements have left a distinctive imprint on the promoters of heat-shock genes.

Heat-shock protein 90 inhibitors in cancer therapy: 17AAG and beyond

Heat-shock protein 90 (HSP90) has diverse functions in mammalian cells. It acts as molecular chaperone, together with several co-chaperone molecules (such as Hop, Hip, p23, cdc37, Aha, and immunophilins). HSP90 binds to its client proteins (such as steroid receptors, AKT, Bcr-Abl, Apaf-1, survivin, cyclin dependent kinases which are involved in signal transduction that regulate cell cycle, survival, and death, and promote their proper protein folding, assembly, and transportation across different cellular compartments. Failure of Hsp90 chaperone activity leads to misfolding of client proteins, which leads to ubiquitination and proteasome degradation, and this deregulating cellular homeostasis. Since tumor cells frequently overexpress the active form of HSP90, which is more susceptible to inhibition by small molecules such as geldanamycin and its analogs, HSP90 became an attractive target for cancer therapy. This paper will review the recent advances in HSP90-biology and will discuss the emerging role of the HSP90 inhibitors such as 17-allylamino-17 demethoxy-geldanamycin and other HSP-90-directed small molecules in cancer therapy.

Fold designability, distribution, and disease

Fold designability has been estimated by the number of families contained in that fold. Here, we show that among orthologous proteins, sequence divergence is higher for folds with greater numbers of families. Folds with greater numbers of families also tend to have families that appear more often in the proteome and greater promiscuity (the number of unique “partner” folds that the fold is found with within the same protein). We also find that many disease-related proteins have folds with relatively few families. In particular, a number of these proteins are associated with diseases occurring at high frequency. These results suggest that family counts reflect how certain structures are distributed in nature and is an important characteristic associated with many human diseases.

Most proteins are composed of structural domains that can be classified into “folds.” Domains with the same fold type share overall structural similarity. The number of amino acid sequences that encode a fold is termed the “designability” of the fold. Folds that have higher designability are thought to be more robust to stresses and mutations. Such features may also allow the fold to appear in a greater variety of contexts. Here, the authors show that proteins with folds estimated to be of higher designability are more widespread amongst proteins in human, mouse, and yeast, consistent with this hypothesis. The authors also find that many hereditary disease-associated proteins have folds estimated to be of low designability. A number of these diseases occur at a relatively high frequency. These results suggest that the estimate of designability employed reflects how certain structures are distributed in nature and is an important characteristic associated with many human diseases.

Age Effect on HSP70: Decreased Resistance to Ischemic and Oxidative Stress in HDF

BACKGROUND

Heat pre-conditioning results in induction of heat shock proteins including HSP70 that gives a cytoprotective effect against further stress. However, HSP70 induction is attenuated in aged cells. The lower HSP70-levels may contribute to the impaired stress response seen in the aged, and to the higher rates of chronic wounds in aged, which arise from repeated ischemia-reperfusion injury. The aim of this study was to investigate a possible connection by comparing the viability of heat pre-conditioned aged versus young human dermal fibroblasts (HDF) after exposure to stress.

MATERIALS AND METHODS

Young (15-28) and aged (61-77) HDF were heat pre-conditioned (42 degrees C, 1 h) and after recovery (1, 2, or 20 h) treated with carbonyl-cyanide-m-chlorophenylhydrazone (hypoxic stress) or with hydrogen peroxide (oxidative stress) for 1 h. HSP70 levels were determined by Western blot. Cell damage was assessed by quantifying lactic dehydrogenase (LDH) in conditioned media. Aged HDF were transfected with HSP70-plasmid, consecutively heat pre-conditioned and exposed to oxidative stress.

RESULTS

HSP70 increased in heat pre-conditioned young HDF by 96, 189, and 237% after 1, 2, and 20-h recovery, respectively, and in aged HDF by 27, 61, and 26%. LDH-release was only decreased in young HDF 20-h after heat-treatment compared with non-heat treated cells (P < 0.001). HSP70-transfection of aged HDF with plasmid reduced LDH-release by 29%.

CONCLUSIONS

Heat pre-conditioning fails to protect aged HDF to oxidative or hypoxic stress due in part to impaired HSP70 induction compared to young.

Ecological–genetic feedback in DNA repair in wild barley, Hordeum spontaneum

Regulation of genetic variation in natural populations is a problem of primary importance to evolutionary biology. In the reported study, the repair efficiency of double strand DNA breaks was compared in six wild barley accessions from Israeli natural populations of H. spontaneum: three from mesic populations (one from Maalot and two from Mount Meron, Upper Galilee) and three from xeric populations (one from Wadi Quilt in the Judean Desert and two from Sede Boqer, in the northern Negev Desert). Pulsed field gel electrophoresis was used to score double-strand breaks of DNA (DSBs) caused by methyl methanesulphonate (MMS) treatment. All six accessions were also tested for heat tolerance: four of these, three xeric and one mesic (from Maalot population), were scored as heat tolerant whereas both accessions from Mount Meron population displayed heat sensitivity. MMS caused a significant increase in the level of DSBs relative to the control in all accessions. The major questions were whether and how the efficiency of DNA repair after mutagenic treatment is affected by the environmental conditions and accession's adaptation to these conditions. Differences were found among the accessions in the repair pattern. Plants of two out of the four heat tolerant accessions did not manage to repair DNA neither at 25 degrees Celsius nor at 37 degrees Celsius. The remaining two heat tolerant accessions significantly repaired the breaks at 37 degrees Celsius, but not at 25 degrees Celsius. By contrast, plants of the two heat susceptible accessions significantly lowered the level of DSBs at 25 degrees Celsius but not at 37 degrees Celsius. Therefore, the accessions that proved capable to repair the induced damages in DNA at one of the two temperatures displayed a pattern that may imply the existence of a negative feedback mechanism in regulation of genetic variation. Such a dependence of DNA integrity on environment and genotype may serve an important factor for maintaining relatively high level of mutability without increasing the genetic load.

Inbreeding by environmental interactions affect gene expression in Drosophila melanogaster

Genomewide gene expression patterns were investigated in inbred and noninbred Drosophila melanogaster lines under benign and stressful (high temperature) environmental conditions in a highly replicated experiment using Affymetrix gene chips. We found that both heat-shock protein and metabolism genes are strongly affected by temperature stress and that genes involved in metabolism are differentially expressed in inbred compared with noninbred lines, and that this effect is accentuated after heat stress exposure. Furthermore we show that inbreeding and temperature stress cause increased between-line variance in gene expression patterns. We conclude that inbreeding and environmental stress both independently and synergistically affect gene expression patterns. Interactions between inbreeding and the environment are often observed at the phenotypic level and our results reveal some of the genes that are involved at the individual gene level. Our observation of several metabolism genes being differentially expressed in inbred lines and more so after exposure to temperature stress, together with lower fitness in the investigated inbred lines, supports the hypothesis that superiority of heterozygous individuals partly derives from increased metabolic efficiency.

Sudden origins: a general mechanism of evolution based on stress protein concentration and rapid environmental change

A major theme in Darwinian evolutionary theory is that novelty arises through a process in which organisms and their features are gradually transformed. Morgan provided Darwinism and the evolutionary synthesis with the idea that minor mutations produce the minuscule morphological variations on which natural selection then acts, and that, although mutation is random, once a process of gradual genetic modification begins, it becomes directional and leads to morphological, and consequently organismal, transformation. In contrast, studies on the role of cell membrane physical states in regulating the expression of stress proteins in response to environmental shifts indicate the existence of a downstream mechanism that prevents or corrects genetic change (i.e., maintains "DNA homeostasis"). However, episodic spikes in various kinds of environmental stress that exceed an organism's cells' thresholds for expression of proper amounts of stress proteins responsible for protein folding (including stochastically occurring DNA repair) may increase mutation rate and genetic change, which in turn will alter the pattern of gene expression during development. If severe stress disrupts DNA homeostasis during meiosis (gametogenesis), this could allow for the appearance of significant mutational events that would otherwise be corrected or suppressed. In evolutionary terms, extreme spikes in environmental stress make possible the emergence of new genetic and consequent developmental and epigenetic networks, and thus also the emergence of potentially new morphological traits, without invoking geographic or other isolating mechanisms.

Hsp90: a chaperone for protein folding and gene regulation

Molecular chaperones are essential components of a quality control machinery present in the cell. They can either aid in the folding and maintenance of newly translated proteins, or they can lead to the degradation of misfolded and destabilized proteins. Hsp90 is a key member of this machinery. It is a ubiquitous molecular chaperone that is found in eubacteria and all branches of eukarya. It plays a central role in cellular signaling since it is essential for maintaining the activity of several signaling proteins, including steroid hormone receptors and protein kinases. Hsp90 is currently a novel anticancer drug target since it is overexpressed in some cancer cells. The chaperone typically functions as part of large complexes, which include other chaperones and essential cofactors that regulate its function. It is thought that different cofactors target Hsp90 to different sets of substrates. However, the mechanism of Hsp90 function remains poorly understood. As part of an effort to elucidate the Hsp90 chaperone network, we carried out a large-scale proteomics study to identify physical and genetic interactors of the chaperone. We identified 2 highly conserved novel Hsp90 cofactors, termed Tah1 and Pih1, that bind to the chaperone and that also associate physically and functionally with the essential DNA helicases Rvb1 and Rvb2. These helicases are key components of the chromatin remodeling complexes Ino80 and SWR-C. Tah1 and Pih1 seem to represent a novel class of Hsp90 cofactors that allow the chaperone to indirectly affect gene regulation in the cell in addition to its ability to directly promote protein folding. In this review, we provide an overview of Hsp90 structure and function, and we discuss the literature that links the chaperone activity to gene regulation.