It's not magic - Hsp90 and its effects on genetic and epigenetic variation

Mechanisms of adaptation and evolution in Toxoplasma gondii

Toxoplasma has high host flexibility, infecting all nucleated cells of mammals and birds. This implies that during its infective process the parasite must constantly adapt to different environmental situations, which in turn leads to modifications in its metabolism, regulation of gene transcription, translation of mRNAs and stage specific factors. There are conserved pathways that support these adaptations, which we aim to elucidate in this review. We begin by exploring the widespread epigenetic mechanisms and transcription regulators, continue with the supportive role of Heat Shock Proteins (Hsp), the translation regulation, stress granules, and finish with the emergence of contingency genes in highly variable genomic domains, such as subtelomeres. Within epigenetics, the discovery of a new histone variant of the H2B family (H2B.Z), contributing to T. gondii virulence and differentiation, but also gene expression regulation and its association with the metabolic state of the parasite, is highlighted. Associated with the regulation of gene expression are transcription factors (TFs). An overview of the main findings on TF and development is presented. We also emphasize the role of Hsp90 and Tgj1 in T. gondii metabolic fitness and the regulation of protein translation. Translation regulation is also highlighted as a mechanism for adaptation to conditions encountered by the parasite as well as stress granules containing mRNA and proteins generated in the extracellular tachyzoite. Another important aspect in evolution and adaptability are the subtelomeres because of their high variability and gene duplication rate. Toxoplasma possess multigene families of membrane proteins and contingency genes that are associated with different metabolic stresses. Among them parasite differentiation and environmental stresses stand out, including those that lead tachyzoite to bradyzoite conversion. Finally, we are interested in positioning protozoa as valuable evolution models, focusing on research related to the Extended Evolutionary Synthesis, based on models recently generated, such as extracellular adaptation and ex vivo cyst recrudescence.

Mutational robustness and the role of buffer genes in evolvability

Organisms rely on mutations to fuel adaptive evolution. However, many mutations impose a negative effect on fitness. Cells may have therefore evolved mechanisms that affect the phenotypic effects of mutations, thus conferring mutational robustness. Specifically, so-called buffer genes are hypothesized to interact directly or indirectly with genetic variation and reduce its effect on fitness. Environmental or genetic perturbations can change the interaction between buffer genes and genetic variation, thereby unmasking the genetic variation's phenotypic effects and thus providing a source of variation for natural selection to act on. This review provides an overview of our understanding of mutational robustness and buffer genes, with the chaperone gene HSP90 as a key example. It discusses whether buffer genes merely affect standing variation or also interact with de novo mutations, how mutational robustness could influence evolution, and whether mutational robustness might be an evolved trait or rather a mere side-effect of complex genetic interactions.

DRMY1 promotes robust morphogenesis by sustaining the translation of cytokinin signaling inhibitor proteins

Robustness is the invariant development of phenotype despite environmental changes and genetic perturbations. In the Arabidopsis flower bud, four sepals robustly initiate and grow to constant size to enclose and protect the inner floral organs. We previously characterized the mutant development related myb-like1 ( drmy1 ), where 3-5 sepals initiate variably and grow to different sizes, compromising their protective function. The molecular mechanism underlying this loss of robustness was unclear. Here, we show that drmy1 has reduced TARGET OF RAPAMYCIN (TOR) activity, ribosomal content, and translation. Translation reduction decreases the protein level of ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), two cytokinin signaling inhibitors that are normally rapidly produced before sepal initiation. The resultant upregulation of cytokinin signaling disrupts robust auxin patterning and sepal initiation. Our work shows that the homeostasis of translation, a ubiquitous cellular process, is crucial for the robust spatiotemporal patterning of organogenesis.

Tracing genetic diversity captures the molecular basis of misfolding disease

Genetic variation in human populations can result in the misfolding and aggregation of proteins, giving rise to systemic and neurodegenerative diseases that require management by proteostasis. Here, we define the role of GRP94, the endoplasmic reticulum Hsp90 chaperone paralog, in managing alpha-1-antitrypsin deficiency on a residue-by-residue basis using Gaussian process regression-based machine learning to profile the spatial covariance relationships that dictate protein folding arising from sequence variants in the population. Covariance analysis suggests a role for the ATPase activity of GRP94 in controlling the N- to C-terminal cooperative folding of alpha-1-antitrypsin responsible for the correction of liver aggregation and lung-disease phenotypes of alpha-1-antitrypsin deficiency. Gaussian process-based spatial covariance profiling provides a standard model built on covariant principles to evaluate the role of proteostasis components in guiding information flow from genome to proteome in response to genetic variation, potentially allowing us to intervene in the onset and progression of complex multi-system human diseases.

Heat shock protein 90: biological functions, diseases, and therapeutic targets

Heat shock protein 90 (Hsp90) is a predominant member among Heat shock proteins (HSPs), playing a central role in cellular protection and maintenance by aiding in the folding, stabilization, and modification of diverse protein substrates. It collaborates with various co-chaperones to manage ATPase-driven conformational changes in its dimer during client protein processing. Hsp90 is critical in cellular function, supporting the proper operation of numerous proteins, many of which are linked to diseases such as cancer, Alzheimer's, neurodegenerative conditions, and infectious diseases. Recognizing the significance of these client proteins across diverse diseases, there is a growing interest in targeting Hsp90 and its co-chaperones for potential therapeutic strategies. This review described biological background of HSPs and the structural characteristics of HSP90. Additionally, it discusses the regulatory role of heat shock factor-1 (HSF-1) in modulating HSP90 and sheds light on the dynamic chaperone cycle of HSP90. Furthermore, the review discusses the specific contributions of HSP90 in various disease contexts, especially in cancer. It also summarizes HSP90 inhibitors for cancer treatment, offering a thoughtful analysis of their strengths and limitations. These advancements in research expand our understanding of HSP90 and open up new avenues for considering HSP90 as a promising target for therapeutic intervention in a range of diseases.

LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana

Isogenic individuals can display seemingly stochastic phenotypic differences, limiting the accuracy of genotype-to-phenotype predictions. The extent of this phenotypic variation depends in part on genetic background, raising questions about the genes involved in controlling stochastic phenotypic variation. Focusing on early seedling traits in Arabidopsis thaliana, we found that hypomorphs of the cuticle-related gene LIPID TRANSFER PROTEIN 2 (LTP2) greatly increased variation in seedling phenotypes, including hypocotyl length, gravitropism and cuticle permeability. Many ltp2 hypocotyls were significantly shorter than wild-type hypocotyls while others resembled the wild-type. Differences in epidermal properties and gene expression between ltp2 seedlings with long and short hypocotyls suggest a loss of cuticle integrity as the primary determinant of the observed phenotypic variation. We identified environmental conditions that reveal or mask the increased variation in ltp2 hypomorphs and found that increased expression of its closest paralog LTP1 is necessary for ltp2 phenotypes. Our results illustrate how decreased expression of a single gene can generate starkly increased phenotypic variation in isogenic individuals in response to an environmental challenge.

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus

Takifugu fasciatus is an aquaculture species with high economic value. In recent years, problems such as environmental pollution and inbreeding have caused a serious decline in T. fasciatus germplasm resources. In this study, a high-density genetic linkage map was constructed by whole-genome resequencing. The map consists of 4891 bin markers distributed across 22 linkage groups (LGs), with a total genetic coverage of 2381.353 cM and a mean density of 0.535 cM. Quantitative trait locus (QTL) localization analysis showed that a total of 19 QTLs associated with growth traits of T. fasciatus in the genome-wide significance threshold range, distributed on 11 LGs. In addition, 11 QTLs associated with cold tolerance traits were identified, each scattered on a different LG. Furthermore, we used QTL localization analysis to screen out three candidate genes (IGF1, IGF2, ADGRB) related to growth in T. fasciatus. Meanwhile, we screened three candidate genes (HSP90, HSP70, and HMGB1) related to T. fasciatus cold tolerance. Our study can provide a theoretical basis for the selection and breeding of cold-tolerant or fast-growing T. fasciatus.

Early acquired resistance to EGFR-TKIs in lung adenocarcinomas before radiographic advanced identified by CT radiomic delta model based on two central studies

Early acquired resistance (EAR) to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in lung adenocarcinomas before radiographic advance cannot be perceived by the naked eye. This study aimed to discover and validate a CT radiomic model to precisely identify the EAR. Training cohort (n = 67) and internal test cohort (n = 29) were from the First Affiliated Hospital of Fujian Medical University, and external test cohort (n = 29) was from the Second Affiliated Hospital of Xiamen Medical College. Follow-up CT images at three different times of each patient were collected: (1) baseline images before EGFR-TKIs therapy; (2) first follow-up images after EGFR-TKIs therapy (FFT); (3) EAR images, which were the last follow-up images before radiographic advance. The features extracted from FFT and EAR were used to construct the classic radiomic model. The delta features which were calculated by subtracting the baseline from either FFT or EAR were used to construct the delta radiomic model. The classic radiomic model achieved AUC 0.682 and 0.641 in training and internal test cohorts, respectively. The delta radiomic model achieved AUC 0.730 and 0.704 in training and internal test cohorts, respectively. Over the external test cohort, the delta radiomic model achieved AUC 0.661. The decision curve analysis showed that when threshold of the probability of the EAR to the EGFR-TKIs was between 0.3 and 0.82, the proposed model was more benefit than treating all patients. Based on two central studies, the delta radiomic model derived from the follow-up non-enhanced CT images can help clinicians to identify the EAR to EGFR-TKIs in lung adenocarcinomas before radiographic advance and optimize clinical outcomes.

LTP2 hypomorphs show genotype-by-environment interaction in early seedling traits in Arabidopsis thaliana

Isogenic individuals can display seemingly stochastic phenotypic differences, limiting the accuracy of genotype-to-phenotype predictions. The extent of this phenotypic variation depends in part on genetic background, raising questions about the genes involved in controlling stochastic phenotypic variation. Focusing on early seedling traits in Arabidopsis thaliana, we found that hypomorphs of the cuticle-related gene LTP2 greatly increased variation in seedling phenotypes, including hypocotyl length, gravitropism and cuticle permeability. Many ltp2 hypocotyls were significantly shorter than wild-type hypocotyls while others resembled the wild type. Differences in epidermal properties and gene expression between ltp2 seedlings with long and short hypocotyls suggest a loss of cuticle integrity as the primary determinant of the observed phenotypic variation. We identified environmental conditions that reveal or mask the increased variation in ltp2 hypomorphs, and found that increased expression of its closest paralog LTP1 is necessary for ltp2 phenotypes. Our results illustrate how decreased expression of a single gene can generate starkly increased phenotypic variation in isogenic individuals in response to an environmental challenge.

Glucocorticoid receptor regulates protein chaperone, circadian clock and affective disorder genes in the zebrafish brain

Glucocorticoid resistance is commonly observed in depression, and has been linked to reduced expression and/or function of the glucocorticoid receptor (NR3C1 in human, hereafter referred to as GR). Previous studies have shown that GR-mutant zebrafish exhibit behavioural abnormalities that are indicative of an affective disorder, suggesting that GR plays a role in brain function. We compared the brain methylomes and brain transcriptomes of adult wild-type and GR-mutant zebrafish, and identified 249 differentially methylated regions (DMRs) that are regulated by GR. These include a cluster of CpG sites within the first intron of fkbp5, the gene encoding the glucocorticoid-inducible heat shock protein co-chaperone Fkbp5. RNA-sequencing analysis revealed that genes associated with chaperone-mediated protein folding, the regulation of circadian rhythm and the regulation of metabolism are particularly sensitive to loss of GR function. In addition, we identified subsets of genes exhibiting GR-regulated transcription that are known to regulate behaviour, and are linked to unipolar depression and anxiety. Taken together, our results identify key biological processes and novel molecular mechanisms through which the GR is likely to mediate responses to stress in the adult zebrafish brain, and they provide further support for the zebrafish GR mutant as a model for the study of affective disorders.

Role of genetic architecture in phenotypic plasticity

Phenotypic plasticity, the ability of an organism to display different phenotypes across environments, is widespread in nature. Plasticity aids survival in novel environments. Herein, we review studies from yeast that allow us to start uncovering the genetic architecture of phenotypic plasticity. Genetic variants and their interactions impact the phenotype in different environments, and distinct environments modulate the impact of genetic variants and their interactions on the phenotype. Because of this, certain hidden genetic variation is expressed in specific genetic and environmental backgrounds. A better understanding of the genetic mechanisms of phenotypic plasticity will help to determine short- and long-term responses to selection and how wide variation in disease manifestation occurs in human populations.

Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication

Protein folding promotes and constrains adaptive evolution. We uncover this surprising duality in the role the protein-folding chaperone Hsp90 plays in mediating the interplay between proteome and the genome which acts to maintain the integrity of yeast metabolism in the face of proteotoxic stressors in anthropic niches. Of great industrial relevance, ethanol concentrations generated by fermentation in the making of beer and bread disrupt critical Hsp90-dependent nodes of metabolism and exert strong selective pressure for increased copy number of key genes encoding components of these nodes, yielding the classical genetic signatures of beer and bread domestication. This work establishes a mechanism of adaptive canalization in an ecology of major economic significance and highlights Hsp90-contingent variation as an important source of phantom heritability in complex traits.

Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains

Enhanced phenotypic diversity increases a population's likelihood of surviving catastrophic conditions. Hsp90, an essential molecular chaperone and a central network hub in eukaryotes, has been observed to suppress or enhance the effects of genetic variation on phenotypic diversity in response to environmental cues. Because many Hsp90-interacting genes are involved in signaling transduction pathways and transcriptional regulation, we tested how common Hsp90-dependent differential gene expression is in natural populations. Many genes exhibited Hsp90-dependent strain-specific differential expression in five diverse yeast strains. We further identified transcription factors (TFs) potentially contributing to variable expression. We found that on Hsp90 inhibition or environmental stress, activities or abundances of Hsp90-dependent TFs varied among strains, resulting in differential strain-specific expression of their target genes, which consequently led to phenotypic diversity. We provide evidence that individual strains can readily display specific Hsp90-dependent gene expression, suggesting that the evolutionary impacts of Hsp90 are widespread in nature.

Nothing in evolution makes sense except in the light of code biology

This article highlights the potential contribution of biological codes to the course and dynamics of evolution. The concept of organic codes, developed by Marcello Barbieri, has fundamentally changed our view of how living systems function. The notion that molecular interactions built on adaptors that arbitrarily link molecules from different "worlds" in a conventional, i.e., rule-based way, departs significantly from the law-based constraints imposed on livening things by physical and chemical mechanisms. In other words, living and non-living things behave like rules and laws, respectively, but this important distinction is rarely considered in current evolutionary theory. The many known codes allow quantification of codes that relate to a cell, or comparisons between different biological systems and may pave the way to a quantitative and empirical research agenda in code biology. A starting point for such an endeavour is the introduction of a simple dichotomous classification of structural and regulatory codes. This classification can be used as a tool to analyse and quantify key organising principles of the living world, such as modularity, hierarchy, and robustness, based on organic codes. The implications for evolutionary research are related to the unique dynamics of codes, or ´Eigendynamics´ (self-momentum) and how they determine the behaviour of biological systems from within, whereas physical constraints are imposed mainly from without. A speculation on the drivers of macroevolution in light of codes is followed by the conclusion that a meaningful and comprehensive understanding of evolution depends including codes into the equation of life.

Standing genetic variation as a potential mechanism of novel cave phenotype evolution in the freshwater isopod, Asellus aquaticus

Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F₂ crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the orange eye phenotype and therefore the orange eye phenotype is hidden within the cave populations. Our goal was to investigate the origin of the orange eye alleles within the Slovenian cave populations by examining A. aquaticus individuals from Slovenian and Romanian surface populations and Asellus aquaticus infernus individuals from a Romanian cave population. We found orange eye individuals present in lab raised surface populations of A. aquaticus from both Slovenia and Romania. Using a mapping approach with crosses between individuals of two surface populations, we found that the region known to be responsible for the orange eye phenotype within the two previously examined Slovenian cave populations was also responsible within both the Slovenian and the Romanian surface populations. Complementation crosses between orange eye Slovenian and orange eye Romanian surface individuals suggest that the same gene is responsible for the orange eye phenotype in both surface populations. Additionally, we observed a low frequency phenotype of eye loss in crosses generated between the two surface populations and also in the Romanian surface population. Finally, in a cave population from Romania, A. aquaticus infernus, we found that the same region is also responsible for the orange eye phenotype as the Slovenian cave populations and the Slovenian and Romanian surface populations. Therefore, we present evidence that variation present in the cave populations could originate from standing variation present in the surface populations and/or transgressive hybridization of different surface phylogenetic lineages rather than de novo mutations.

AGO1 and HSP90 buffer different genetic variants in Arabidopsis thaliana

Argonaute 1 (AGO1), the principal protein component of microRNA-mediated regulation, plays a key role in plant growth and development. AGO1 physically interacts with the chaperone HSP90, which buffers cryptic genetic variation in plants and animals. We sought to determine whether genetic perturbation of AGO1 in Arabidopsis thaliana would also reveal cryptic genetic variation, and if so, whether AGO1-dependent loci overlap with those dependent on HSP90. To address these questions, we introgressed a hypomorphic mutant allele of AGO1 into a set of mapping lines derived from the commonly used Arabidopsis strains Col-0 and Ler. Although we identified several cases in which AGO1 buffered genetic variation, none of the AGO1-dependent loci overlapped with those buffered by HSP90 for the traits assayed. We focused on 1 buffered locus where AGO1 perturbation uncoupled the traits days to flowering and rosette leaf number, which are otherwise closely correlated. Using a bulk segregant approach, we identified a nonfunctional Ler hua2 mutant allele as the causal AGO1-buffered polymorphism. Introduction of a nonfunctional hua2 allele into a Col-0 ago1 mutant background recapitulated the Ler-dependent ago1 phenotype, implying that coupling of these traits involves different molecular players in these closely related strains. Taken together, our findings demonstrate that even though AGO1 and HSP90 buffer genetic variation in the same traits, these robustness regulators interact epistatically with different genetic loci, suggesting that higher-order epistasis is uncommon. Plain Language Summary Argonaute 1 (AGO1), a key player in plant development, interacts with the chaperone HSP90, which buffers environmental and genetic variation. We found that AGO1 buffers environmental and genetic variation in the same traits; however, AGO1-dependent and HSP90-dependent loci do not overlap. Detailed analysis of a buffered locus found that a nonfunctional HUA2 allele decouples days to flowering and rosette leaf number in an AGO1-dependent manner, suggesting that the AGO1-dependent buffering acts at the network level.

Hexavalent chromium-induced epigenetic instability and transposon activation lead to phenotypic variations and tumors in Drosophila

Developmental robustness represents the ability of an organism to resist phenotypic variations despite environmental insults and inherent genetic variations. Derailment of developmental robustness leads to phenotypic variations that can get fixed in a population for many generations. Environmental pollution is a significant worldwide problem with detrimental consequences of human development. Understanding the genetic basis for how pollutants affect human development is critical for developing interventional therapies. Here, we report that environmental stress induced by hexavalent chromium, Cr(VI), a potent industrial pollutant, compromises developmental robustness, leading to phenotypic variations in the progeny. These phenotypic variations arise due to epigenetic instability and transposon activation in the somatic tissues of the progeny rather than novel genetic mutations and can be reduced by increasing the dosage of Piwi - a Piwi-interacting RNA-binding protein, in the ovary of the exposed mother. Significantly, the derailment of developmental robustness by Cr(VI) exposure leads to tumors in the progeny, and the predisposition to develop tumors is fixed in the population for at least three generations. Thus, we show for the first time that environmental pollution can derail developmental robustness and predispose the progeny of the exposed population to develop phenotypic variations and tumors.

Adaptation of the yeast gene knockout collection is near-perfectly predicted by fitness and diminishing return epistasis

Adaptive evolution of clonally dividing cells and microbes is the ultimate cause of cancer and infectious diseases. The possibility of constraining the adaptation of cell populations, by inhibiting proteins enhancing the evolvability, has therefore attracted interest. However, our current understanding of how genes influence adaptation kinetics is limited, partly because accurately measuring adaptation for many cell populations is challenging. We used a high-throughput adaptive laboratory evolution platform to track the adaptation of >18,000 cell populations corresponding to single-gene deletion strains in the haploid yeast deletion collection. We report that the preadaptation fitness of gene knockouts near-perfectly (R2= 0.91) predicts their adaptation to arsenic, leaving at the most a marginal role for dedicated evolvability gene functions. We tracked the adaptation of another >23,000 gene knockout populations to a diverse range of selection pressures and generalized the almost perfect (R2=0.72-0.98) capacity of preadaptation fitness to predict adaptation. We also reconstructed mutations in FPS1, ASK10, and ARR3, which together account for almost all arsenic adaptation in wild-type cells, in gene deletions covering a broad fitness range and show that the predictability of arsenic adaptation can be understood as a by global epistasis, where excluding arsenic is more beneficial to arsenic unfit cells. The paucity of genes with a meaningful evolvability effect on adaptation diminishes the prospects of developing adjuvant drugs aiming to slow antimicrobial and chemotherapy resistance.

Thermal stress and mutation accumulation increase heat shock protein expression in Daphnia

Understanding the short- and long-term consequences of climate change is a major challenge in biology. For aquatic organisms, temperature changes and drought can lead to thermal stress and habitat loss, both of which can ultimately lead to higher mutation rates. Here, we examine the effect of high temperature and mutation accumulation on gene expression at two loci from the heat shock protein (HSP) gene family, HSP60 and HSP90. HSPs have been posited to serve as 'mutational capacitors' given their role as molecular chaperones involved in protein folding and degradation, thus buffering against a wide range of cellular stress and destabilization. We assayed changes in HSP expression across 5 genotypes of Daphnia magna, a sentinel species in ecology and environmental biology, with and without acute exposure to thermal stress and accumulated mutations. Across genotypes, HSP expression increased ~ 6× in response to heat and ~ 4× with mutation accumulation, individually. Both factors simultaneously (lineages with high mutation loads exposed to high heat) increased gene expression ~ 23×-much more than that predicted by an additive model. Our results corroborate suggestions that HSPs can buffer against not only the effects of heat, but also mutations-a combination of factors both likely to increase in a warming world.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10682-022-10209-1.

Hsp90: From Cellular to Organismal Proteostasis

Assuring a healthy proteome is indispensable for survival and organismal health. Proteome disbalance and the loss of the proteostasis buffer are hallmarks of various diseases. The essential molecular chaperone Hsp90 is a regulator of the heat shock response via HSF1 and a stabilizer of a plethora of signaling proteins. In this review, we summarize the role of Hsp90 in the cellular and organismal regulation of proteome maintenance.

Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host

Although generalist insect herbivores can migrate and rapidly adapt to a broad range of host plants, they can face significant difficulties when accidentally migrating to novel and marginally-suitable hosts. What happens, both in performance and gene expression regulation, if these marginally-suitable hosts must be used for multiple generations before migration to a suitable host can take place, largely remains unknown. In this study, we established multigenerational colonies of the whitefly Bemisia tabaci, a generalist phloem-feeding species, adapted to a marginally-suitable host (habanero pepper) or an optimal host (cotton). We used reciprocal host tests to estimate the differences in performance of the populations on both hosts under optimal (30 oC) and mild-stressful (24 oC) temperature conditions, and documented the associated transcriptomic changes. The habanero pepper-adapted population greatly improved its performance on habanero pepper but did not reach its performance level on cotton, the original host. It also showed reduced performance on cotton, relative to the non-adapted population, and an antagonistic effect of the lower-temperature stressor. The transcriptomic data revealed that most of the expression changes, associated with long-term adaptation to habanero pepper, can be categorized as "evolved" with no initial plastic response. Three molecular functions dominated: enhanced formation of cuticle structural constituents, enhanced activity of oxidation-reduction processes involved in neutralization of phytotoxins and reduced production of proteins from the cathepsin B family. Taken together, these findings indicate that generalist insects can adapt to novel host plants by modifying the expression of a relatively small set of specific molecular functions.

The sculpting of somatic mutational landscapes by evolutionary forces and their impacts on aging-related disease

Aging represents the major risk factor for the development of cancer and many other diseases. Recent findings show that normal tissues become riddled with expanded clones that are frequently driven by cancer‐associated mutations in an aging‐dependent fashion. Additional studies show how aged tissue microenvironments promote the initiation and progression of malignancies, while young healthy tissues actively suppress the outgrowth of malignant clones. Here, we discuss conserved mechanisms that eliminate poorly functioning or potentially malignant cells from our tissues to maintain organismal health and fitness. Natural selection acts to preserve tissue function and prevent disease to maximize reproductive success but these mechanisms wane as reproduction becomes less likely. The ensuing age‐dependent tissue decline can impact the shape and direction of clonal somatic evolution, with lifestyle and exposures influencing its pace and intensity. We also consider how aging‐ and exposure‐dependent clonal expansions of “oncogenic” mutations might both increase cancer risk late in life and contribute to tissue decline and non‐malignant disease. Still, we can marvel at the ability of our bodies to avoid cancers and other diseases despite the accumulation of billions of cells with cancer‐associated mutations.

Gene expression studies of plastic and evolutionary responses to global warming

Phenotypic plasticity can be a rapid response for coping with global warming, yet may be insufficient to protect species from extinction. Evolutionary adaptation may reinforce adaptive or oppose maladaptive plastic responses. With advances in technology whole transcriptomes can provide us with an unprecedented overview of genes and functional processes underlying the interplay between plasticity and evolution. We advocate that insects provide ideal opportunities to study plasticity in non-adapted and thermally adapted populations to infer reaction norms across the whole transcriptome ('reactionomes'). This can advance our understanding of how the interplay between plasticity and evolution shapes responses to warming. So far, a limited number of studies suggest predominantly maladaptive plastic responses to novel environments that are reduced with time, but much more research is needed to infer general patterns.

Co-option of stress mechanisms in the origin of evolutionary novelties

It is widely accepted that stressful conditions can facilitate evolutionary change. The mechanisms elucidated thus far accomplish this with a generic increase in heritable variation that facilitates more rapid adaptive evolution, often via plastic modifications of existing characters. Through scrutiny of different meanings of stress in biological research, and an explicit recognition that stressors must be characterized relative to their effect on capacities for maintaining functional integrity, we distinguish between: (1) previously identified stress‐responsive mechanisms that facilitate evolution by maintaining an adaptive fit with the environment, and (2) the co‐option of stress‐responsive mechanisms that are specific to stressors leading to the origin of novelties via compensation. Unlike standard accounts of gene co‐option that identify component sources of evolutionary change, our model documents the cost‐benefit trade‐offs and thereby explains how one mechanism—an immediate response to acute stress—is transformed evolutionarily into another—routine protection from recurring stressors. We illustrate our argument with examples from cell type origination as well as processes and structures at higher levels of organization. These examples suggest a general principle of evolutionary origination based on the capacity to switch between regulatory states related to reproduction and proliferation versus survival and differentiation.

The nature of coxofemoral joint pathology across family Canidae

We evaluated coxofemoral joints from museum specimens of: Vulpes lagopus; Vulpes vulpes; Vulpes velox; Nyctereutes procyonoides; Urocyon cinereoargenteus; Aenocyon [Canis] dirus; Canis latrans; Canis lupus lupus; Canis lupus familiaris; C. l. familiaris × latrans; and Canis dingo. Acetabular components included: fossa; articular surface; medial and lateral articular margins; and periarticular surfaces. Acetabular components variably revealed: osteophyte-like features; varying appearance of articular margin rims (especially contour changes); rough bone surfaces (especially fossa and articular surface); and surface wear. Proximal femoral components included: articular surface; articular margin; periarticular surfaces; and joint capsule attachment. Femoral components variably revealed: rough bone surface; bone loss; articular margin osteophyte-like features; caudal post-developmental mineralized prominence; and enthesophytes along the joint capsule attachment. Non-metric multidimensional scaling was used to analyze right-left asymmetric relationships between observed traits, across taxa. Significantly different acetabular trait asymmetry involved only C. latrans-C. l. familiaris; V. vulpes-N. procyonoides, and U. cinereoargenteus-N. procyonoides. There were no significant lateralized differences in proximal femoral traits involving modern canids, ancient and modern C. l. familiaris, or modern vulpines. Thus, the observations were strongly bilateral. We hypothesized high similarity of traits across taxa. The data confirm the hypothesis and strongly suggest broad and deep morphological and mechanistic conservation that almost certainly pre-existed (at least) all modern canids. Further zoological studies are needed to evaluate phylogenic implications in greater detail.

Expression Patterns of the Heat Shock Protein 90 (Hsp90) Gene Suggest Its Possible Involvement in Maintaining the Dormancy of Dinoflagellate Resting Cysts

Heat shock protein 90 (Hsp90) is a highly conserved molecular chaperone functioning in cellular structural folding and conformational integrity maintenance and thus plays vital roles in a variety of biological processes. However, many aspects of these functions and processes remain to be fully elucidated, particularly for non-model organisms. Dinoflagellates are a group of eukaryotes that are exceedingly important in primary production and are responsible for the most harmful algal blooms (HABs) in aquatic ecosystems. The success of dinoflagellates in dominating the plankton community is undoubtedly pertinent to their remarkable adaptive strategies, characteristic of resting cyst production and broad tolerance to stresses of temperature and others. Therefore, this study was conducted to examine the putative roles of Hsp90 in the acclimation to temperature stress and life stage alterations of dinoflagellates. Firstly, we isolated the full-length cDNA of an Hsp90 gene (StHsp90) via RACE from the cosmopolitan HAB species Scrippsiella trochoidea and tracked its transcriptions in response to varied scenarios via real-time qPCR. The results indicated that StHsp90 displayed significant mRNA augment patterns, escalating during 180-min treatments, when the cells were exposed to elevated and lowered temperatures. Secondly, we observed prominently elevated StHsp90 transcriptions in the cysts that were stored at the cold and dark conditions compared to those in newly formed resting cysts and vegetative cells. Finally, and perhaps most importantly, we identified 29 entries of Hsp90-encoding genes with complete coding regions from a dinoflagellate-specific environmental cDNA library generated from marine sediment assemblages. The observed active transcription of these genes in sediment-buried resting cysts was fully supported by the qPCR results for the cold-stored resting cysts of S. trochoidea. Hsp90s expressions in both laboratory-raised and field-collected cysts collectively highlighted the possible involvement and engagement of Hsp90 chaperones in the resting stage persistence of dinoflagellates.

Plasticity of rosette size in response to nitrogen availability is controlled by an RCC1-family protein

Nitrogen (N) is fundamental to plant growth, development and yield. Genes underlying N utilization and assimilation are well-characterized, but mechanisms underpinning plasticity of different phenotypes in response to N remain elusive. Here, using Arabidopsis thaliana accessions, we dissected the genetic architecture of plasticity in early and late rosette diameter, flowering time and yield, in response to three levels of N in the soil. Furthermore, we found that the plasticity in levels of primary metabolites were related with the plasticities of the studied traits. Genome-wide association analysis identified three significant associations for phenotypic plasticity, one for early rosette diameter and two for flowering time. We confirmed that the gene At1g19880, hereafter named as PLASTICITY OF ROSETTE TO NITROGEN 1 (PROTON1), encoding for a regulator of chromatin condensation 1 (RCC1) family protein, conferred plasticity of rosette diameter in response to N. Treatment of PROTON1 T-DNA line with salt implied that the reduced plasticity of early rosette diameter was not a general growth response to stress. We further showed that plasticities of growth and flowering-related traits differed between environmental cues, indicating decoupled genetic programs regulating these traits. Our findings provide a prospective to identify genes that stabilize performance under fluctuating environments.

Genotype-Phenotype Relationships in the Context of Transcriptional Adaptation and Genetic Robustness

Genetic manipulations with a robust and predictable outcome are critical to investigate gene function, as well as for therapeutic genome engineering. For many years, knockdown approaches and reagents including RNA interference and antisense oligonucleotides dominated functional studies; however, with the advent of precise genome editing technologies, CRISPR-based knockout systems have become the state-of-the-art tools for such studies. These technologies have helped decipher the role of thousands of genes in development and disease. Their use has also revealed how limited our understanding of genotype-phenotype relationships is. The recent discovery that certain mutations can trigger the transcriptional modulation of other genes, a phenomenon called transcriptional adaptation, has provided an additional explanation for the contradicting phenotypes observed in knockdown versus knockout models and increased awareness about the use of each of these approaches. In this review, we first cover the strengths and limitations of different gene perturbation strategies. Then we highlight the diverse ways in which the genotype-phenotype relationship can be discordant between these different strategies. Finally, we review the genetic robustness mechanisms that can lead to such discrepancies, paying special attention to the recently discovered phenomenon of transcriptional adaptation. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The QSAR Paradigm in Fragment-Based Drug Discovery: From the Virtual Generation of Target Inhibitors to Multi-Scale Modeling

Fragment-Based Drug Design (FBDD) has established itself as a promising approach in modern drug discovery, accelerating and improving lead optimization, while playing a crucial role in diminishing the high attrition rates at all stages in the drug development process. On the other hand, FBDD has benefited from the application of computational methodologies, where the models derived from the Quantitative Structure-Activity Relationships (QSAR) have become consolidated tools. This mini-review focuses on the evolution and main applications of the QSAR paradigm in the context of FBDD in the last five years. This report places particular emphasis on the QSAR models derived from fragment-based topological approaches to extract physicochemical and/or structural information, allowing to design potentially novel mono- or multi-target inhibitors from relatively large and heterogeneous databases. Here, we also discuss the need to apply multi-scale modeling, to exemplify how different datasets based on target inhibition can be simultaneously integrated and predicted together with other relevant endpoints such as the biological activity against non-biomolecular targets, as well as in vitro and in vivo toxicity and pharmacokinetic properties. In this context, seminal papers are briefly analyzed. As huge amounts of data continue to accumulate in the domains of the chemical, biological and biomedical sciences, it has become clear that drug discovery must be viewed as a multi-scale optimization process. An ideal multi-scale approach should integrate diverse chemical and biological data and also serve as a knowledge generator, enabling the design of potentially optimal chemicals that may become therapeutic agents.

Heat Shock Proteins: Potential Modulators and Candidate Biomarkers of Peripartum Cardiomyopathy

Peripartum cardiomyopathy (PPCM) is a potentially life-threatening condition in which heart failure and systolic dysfunction occur late in pregnancy or within months following delivery. To date, no reliable biomarkers or therapeutic interventions for the condition exist, thus necessitating an urgent need for identification of novel PPCM drug targets and candidate biomarkers. Leads for novel treatments and biomarkers are therefore being investigated worldwide. Pregnancy is generally accompanied by dramatic hemodynamic changes, including a reduced afterload and a 50% increase in cardiac output. These increased cardiac stresses during pregnancy potentially impair protein folding processes within the cardiac tissue. The accumulation of misfolded proteins results in increased toxicity and cardiac insults that trigger heart failure. Under stress conditions, molecular chaperones such as heat shock proteins (Hsps) play crucial roles in maintaining cellular proteostasis. Here, we critically assess the potential role of Hsps in PPCM. We further predict specific associations between the Hsp types Hsp70, Hsp90 and small Hsps with several proteins implicated in PPCM pathophysiology. Furthermore, we explore the possibility of select Hsps as novel candidate PPCM biomarkers and drug targets. A better understanding of how these Hsps modulate PPCM pathogenesis holds promise in improving treatment, prognosis and management of the condition, and possibly other forms of acute heart failure.

Connexin 43 contributes to phenotypic robustness of the mouse skull

BACKGROUND

We compared skull shape and variation among genetically modified mice that exhibit different levels of connexin43 (Cx43) channel function, to determine whether Cx43 contributes to craniofacial phenotypic robustness. Specifically, we used two heterozygous mutant mouse models (G60S/+ and I130T/+) that, when compared to their wildtype counterparts, have an ~80% and ~50% reduction in Cx43 function, respectively.

RESULTS

Both mutant strains showed significant differences in skull shape compared to wildtype littermates and while these differences were more severe in the G60S/+ mouse, shape differences were localized to similar regions of the skull in both mutants. However, increased skull shape variation was observed in G60S/+ mutants only. Additionally, covariation of skull structures was disrupted in the G60S/+ mutants only, indicating that while a 50% reduction in Cx43 function is sufficient to cause a shift in mean skull shape, the threshold for Cx43 function for disrupting craniofacial phenotypic robustness is lower.

CONCLUSIONS

Collectively, our results indicate Cx43 can contribute to phenotypic robustness of the skull through a nonlinear relationship between Cx43 gap junctional function and phenotypic outcomes.

Linking hsp90's role as an evolutionary capacitator to the development of cancer

This paper links Heat Shock Protein Hsp90 as an evolutionary capacitator with the development of cancer. Hsp90 stabilises proteins associated with cancer in a number of ways. Canalisation allows for the accumulation of malignant mutations in the genome, and selection of beneficial phenotypes when cancer cells are stressed, allowing oncogenic development and progression. Hsp90 may allow for mutational 'big bangs' that can trigger primary malignant transformation. Hsp90 buffers catastrophic mutations in the oncogenome to prevent protein degradation and cellular apoptosis. Hsp90 was found to prevent the degradation of mutated p53, encouraging uncontrolled proliferation of cancer cells. Hsp90 buffering of mutations in response to cytotoxic therapy can lead to expression of beneficial phenotypes when Hsp90 is supressed and development of drug resistance. Trials with Hsp90 inhibitors have shown some success as an adjunctive therapy in preventing cancer progression, development of drug resistance, and even re-sensitisation to therapy after chemoresistance has developed.

Overexpression of SlHSP90.2 leads to altered root biomass and architecture in tomato (Solanum lycopersicum)

The Heat shock proteins 90 family plays pivotal roles in root growth and plant development. Its isoforms have been identified in several plant species with transcripts presents in almost all stages of plant growth. However, its functional relevance has not been completely established. Therefore, in this study, we provide evidence about the role of SlHSP90.2 in tomato (Solanum lycopersicum) root development. Using tomato cultivars with differing root phenotypes, we have shown that SlHSP90.2 transcripts are in accordance with root architecture, i.e. high rooting cultivars had more expression of SlHSP90.2 as compared to low rooting cultivars. Moreover, overexpression of SlHSP90.2 gene in transgenic tomato plants showed significant increase in root biomass and architecture, as evident from the analysis of fresh and dry weights of root and shoot samples, primary root length and length and number of lateral roots. The transgenic lines are also more tolerant to salinity and drought stresses. The results of the present study suggest that genetic manipulation of HSP90.2 homologs in other crops can offer promising leads to develop plant with better root biomass and architecture and improved agronomics traits, like better water and mineral absorption, salinity and drought tolerance potential.

Genomic Variation, Evolvability, and the Paradox of Mental Illness

Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.

Inhibition of Embryonic HSP 90 Function Promotes Variation of Cold Tolerance in Zebrafish

Accumulating evidence indicates that heat shock protein 90 (HSP90) plays essential roles in modulation of phenotypic plasticity in vertebrate development, however, the roles of HSP90 in modulation of cold tolerance capacity in fish are still unclear. In the present study, we showed that transient inhibition of embryonic HSP90 function by a chemical inhibitor or low conductivity stress promoted variation of cold tolerance capacity in adult zebrafish. Further work showed that embryonic HSP90 inhibition enhanced cold tolerance in adult zebrafish could be transmitted to their offspring. RNA-seq data showed that embryonic HSP90 inhibition enhanced cold tolerance involves variation of gene expression related to proteasome, lysosome, autophagy, and ribosome. Experiments with zebrafish ZF4 cells showed that two differentially expressed genes atg9b and psmd12 were up-regulated by radicicol treatment and provided protective roles for cells under cold stress, indicating that up-regulation of autophagy and proteasome function contributes to enhanced cold tolerance. The present work sheds a light on the roles of HSP90 in regulation of phenotypic plasticity associated with thermal adaptation in fish.

Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe

Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants Solidago canadensis and S. gigantea, we tested whether such differentiation might have occurred through heritable epigenetic changes in cytosine methylation. In a 2-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in S. canadensis, but three genetic clusters in S. gigantea. Solidago canadensis showed latitudinal clines in flowering phenology and growth. In S. gigantea, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, probably through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.

The Boggarts of biology: how non-genetic changes influence the genotype

The notion that there is a one-one mapping from genotype to phenotype was overturned a long time ago. Along with genotype and environment, 'non-genetic changes' orchestrated by altered RNA and protein molecules also guide the development of phenotype. The idea that there is a route through which changes in phenotype can lead to changes in genotype impinges on several phenomena of molecular, developmental, evolutionary and applied interest. Phenotypic changes that do not alter the underlying DNA sequence have been studied across model systems (eg: DNA and histone modifications, RNA editing, prion formation) and are known to play an important role in short-term adaptation. However, because of their transient nature and unstable inheritance, the role of such changes in long-term evolution has remained controversial. I classify and review three ways in which non-genetic changes can influence genotype and impact cellular fitness across generations, with an emphasis on the enticing idea that they may act as stepping stones for genetic adaptation. I focus on work from microbial systems and attempt to highlight recent experiments and models that bear on this idea. Overall, I review evidence which suggests that non-genetic changes can impact phenotype via their influence on the genotype, and thus play a role in evolutionary change.

Molecular Chaperones: Molecular Assembly Line Brings Metabolism and Immunity in Shape

Molecular chaperones are a set of conserved proteins that have evolved to assist the folding of many newly synthesized proteins by preventing their misfolding under conditions such as elevated temperatures, hypoxia, acidosis and nutrient deprivation. Molecular chaperones belong to the heat shock protein (HSP) family. They have been identified as important participants in immune functions including antigen presentation, immunostimulation and immunomodulation, and play crucial roles in metabolic rewiring and epigenetic circuits. Growing evidence has accumulated to indicate that metabolic pathways and their metabolites influence the function of immune cells and can alter transcriptional activity through epigenetic modification of (de)methylation and (de)acetylation. However, whether molecular chaperones can regulate metabolic programs to influence immune activity is still largely unclear. In this review, we discuss the available data on the biological function of molecular chaperones to immune responses during inflammation, with a specific focus on the interplay between molecular chaperones and metabolic pathways that drive immune cell fate and function.

What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit?

The complexity of heredity has been appreciated for decades: Many traits are controlled not by a single genetic locus but instead by polymorphisms throughout the genome. The importance of complex traits in biology and medicine has motivated diverse approaches to understanding their detailed genetic bases. Here, we focus on recent systematic studies, many in budding yeast, which have revealed that large numbers of all kinds of molecular variation, from noncoding to synonymous variants, can make significant contributions to phenotype. Variants can affect different traits in opposing directions, and their contributions can be modified by both the environment and the epigenetic state of the cell. The integration of prospective (synthesizing and analyzing variants) and retrospective (examining standing variation) approaches promises to reveal how natural selection shapes quantitative traits. Only by comprehensively understanding nature's genetic tool kit can we predict how phenotypes arise from the complex ensembles of genetic variants in living organisms.

Schizophrenia: Developmental Variability Interacts with Risk Factors to Cause the Disorder: Nonspecific Variability-Enhancing Factors Combine with Specific Risk Factors to Cause Schizophrenia

A new etiological model is proposed for schizophrenia that combines variability-enhancing nonspecific factors acting during development with more specific risk factors. This model is better suited than the current etiological models of schizophrenia, based on the risk factors paradigm, for predicting and/or explaining several important findings about schizophrenia: high co-morbidity rates, low specificity of many risk factors, and persistence in the population of the associated genetic polymorphisms. Compared with similar models, e.g., de-canalization, common psychopathology factor, sexual-selection, or differential sensitivity to the environment, this proposal is more general and integrative. Recently developed research methods have proven the existence of genetic and environmental factors that enhance developmental variability. Applying such methods to newly collected or already available data can allow for testing the hypotheses upon which this model is built. If validated, this model may change the understanding of the etiology of schizophrenia, the research models, and preventionbrk paradigms.

Persistent Activation of mRNA Translation by Transient Hsp90 Inhibition

The heat shock protein 90 (Hsp90) chaperone functions as a protein-folding buffer and plays a role promoting the evolution of new heritable traits. To better understand how Hsp90 can affect mRNA translation, we screen more than 1,600 factors involved in mRNA regulation for physical interactions with Hsp90 in human cells. The mRNA binding protein CPEB2 strongly binds Hsp90 via its prion domain. In a yeast model, transient inhibition of Hsp90 results in persistent activation of a CPEB translation reporter even in the absence of exogenous CPEB that persists for 30 generations after the inhibitor is removed. Ribosomal profiling reveals that some endogenous yeast mRNAs, including HAC1, show a persistent change in translation efficiency following transient Hsp90 inhibition. Thus, transient loss of Hsp90 function can promote a nongenetic inheritance of a translational state affecting specific mRNAs, introducing a mechanism by which Hsp90 can promote phenotypic variation.

Peer pressure: evolutionary responses to biotic pressures in wine yeasts

In the macroscopic world, ecological interactions between multiple species of fauna and flora are recognised as major role-players in the evolution of any particular species. By comparison, research on ecological interactions as a driver of evolutionary adaptation in microbial ecosystems has been neglected. The evolutionary history of the budding yeast Saccharomyces cerevisiae has been extensively researched, providing an unmatched foundation for exploring adaptive evolution of microorganisms. However, in most studies, the habitat is only defined by physical and chemical parameters, and little attention is paid to the impact of cohabiting species. Such ecological interactions arguably provide a more relevant evolutionary framework. Within the genomic phylogenetic tree of S. cerevisiae strains, wine associated isolates form a distinct clade, also matched by phenotypic evidence. This domestication signature in genomes and phenomes suggests that the wine fermentation environment is of significant evolutionary relevance. Data also show that the microbiological composition of wine fermentation ecosystems is dominated by the same species globally, suggesting that these species have co-evolved within this ecosystem. This system therefore presents an excellent model for investigating the origins and mechanisms of interspecific yeast interactions. This review explores the role of biotic stress in the adaptive evolution of wine yeast.

Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis

Metabolic changes alter the cellular milieu; can this also change intracellular protein folding? Since proteostasis can modulate mutational buffering, if change in metabolism has the ability to change protein folding, arguably, it should also alter mutational buffering. Here we find that altered cellular metabolic states in E. coli buffer distinct mutations on model proteins. Buffered-mutants have folding problems in vivo and are differently chaperoned in different metabolic states. Notably, this assistance is dependent upon the metabolites and not on the increase in canonical chaperone machineries. Being able to reconstitute the folding assistance afforded by metabolites in vitro, we propose that changes in metabolite concentrations have the potential to alter protein folding capacity. Collectively, we unravel that the metabolite pools are bona fide members of proteostasis and aid in mutational buffering. Given the plasticity in cellular metabolism, we posit that metabolic alterations may play an important role in cellular proteostasis.

Changes in osmotic homeostasis alter metabolites and therefore chemical milieu of the cells. Here, the authors show that altering metabolites in E. coli also change the cellular capacity for buffering mutations that impair protein folding and influences proteostasis irrespective of molecular chaperones

The role of HSP90 molecular chaperones in hepatocellular carcinoma

Misfolded proteins have enhanced formation of toxic oligomers and nonfunctional protein copies lead to recruiting wild-type protein types. Heat shock protein 90 (HSP90) is a molecular chaperone generated by cells that are involved in many cellular functions through regulation of folding and/or localization of large multi-protein complexes as well as client proteins. HSP90 can regulate a number of different cellular processes including cell proliferation, motility, angiogenesis, signal transduction, and adaptation to stress. HSP90 makes the mutated oncoproteins able to avoid misfolding and degradation and permits the malignant transformation. As a result, HSP90 is an important factor in several signaling pathways associated with tumorigenicity, therapy resistance, and inhibiting apoptosis. Clinically, the upregulation of HSP90 expression in hepatocellular carcinoma (HCC) is linked with advanced stages and inappropriate survival in cases suffering from this kind of cancer. The present review comprehensively assesses HSP90 functions and its possible usefulness as a potential diagnostic biomarker and therapeutic option for HCC.

Molecular Chaperones Accelerate the Evolution of Their Protein Clients in Yeast

Protein stability is a major constraint on protein evolution. Molecular chaperones, also known as heat-shock proteins, can relax this constraint and promote protein evolution by diminishing the deleterious effect of mutations on protein stability and folding. This effect, however, has only been stablished for a few chaperones. Here, we use a comprehensive chaperone–protein interaction network to study the effect of all yeast chaperones on the evolution of their protein substrates, that is, their clients. In particular, we analyze how yeast chaperones affect the evolutionary rates of their clients at two very different evolutionary time scales. We first study the effect of chaperone-mediated folding on protein evolution over the evolutionary divergence of Saccharomyces cerevisiae and S. paradoxus. We then test whether yeast chaperones have left a similar signature on the patterns of standing genetic variation found in modern wild and domesticated strains of S. cerevisiae. We find that genes encoding chaperone clients have diverged faster than genes encoding non-client proteins when controlling for their number of protein–protein interactions. We also find that genes encoding client proteins have accumulated more intraspecific genetic diversity than those encoding non-client proteins. In a number of multivariate analyses, controlling by other well-known factors that affect protein evolution, we find that chaperone dependence explains the largest fraction of the observed variance in the rate of evolution at both evolutionary time scales. Chaperones affecting rates of protein evolution mostly belong to two major chaperone families: Hsp70s and Hsp90s. Our analyses show that protein chaperones, by virtue of their ability to buffer destabilizing mutations and their role in modulating protein genotype–phenotype maps, have a considerable accelerating effect on protein evolution.

Hsp90 and complex birth defects: A plausible mechanism for the interaction of genes and environment

How genes and environment interact to cause birth defects is not well understood, but key to developing new strategies to modify risk. The threshold model has been proposed to represent this complex interaction. This model stipulates that while environmental exposure or genetic mutation alone may not result in a defect, factors in combination increase phenotypic variability resulting in more individuals crossing the disease threshold where birth defects manifest. Many environmental factors that contribute to birth defects induce widespread cellular stress and misfolding of proteins. Yet, the impact of the stress response on the threshold model is not typically considered in discephering the etiology of birth defects. This mini-review will explore a potential mechanism for gene-environment interactions co-opted from studies of evolution. This model stipulates that heat shock proteins that mediate the stress response induced by environmental factors can influence the number of individuals that cross disease thresholds resulting in increased incidence of birth defects. Studies in the field of evolutionary biology have demonstrated that heat shock proteins and Hsp90 in particular provide a link between environmental stress, genotype and phenotype. Hsp90 is a highly expressed molecular chaperone that assists a wide variety of protein clients with folding and conformational changes needed for proper function. Hsp90 also chaperones client proteins with potentially deleterious amino acid changes to suppress variation caused by genetic mutations. However, upon exposure to stress, Hsp90 abandons its normal physiological clients and is diverted to assist with the misfolded protein response. This can impact the activity of signaling pathways that involve Hsp90 clients as well as unmask suppressed protein variation, essentially creating complex traits in a single step. In this capacity Hsp90 acts as an evolutionary capacitor allowing stored variation to accumulate and then become expressed in times of stress. This mechanism provides a substrate which natural selection can act upon at the population level allowing survival of the species with selective pressure. However, at the level of the individual, this mechanism can result in simultaneous expression of deleterious variants as well as reduced activity of a variety of Hsp90 chaperoned pathways, potentially shifting phenotypic variability over the disease threshold resulting in birth defects.