Pore-forming protein structure analysis in membranes using multiple independent fluorescence techniques

A large number of transmembrane proteins form aqueous pores or channels in the phospholipid bilayer, but the structural bases of pore formation and assembly have been determined experimentally for only a few of the proteins and protein complexes. The polypeptide segments that form the transmembrane pore and the secondary structure that creates the aqueous-lipid interface can be identified using multiple independent fluorescence techniques (MIFT). The information obtained from several different, but complementary, fluorescence analyses, including measurements of emission intensity, fluorescence lifetime, accessibility to aqueous and to lipophilic quenching agents, and fluorescence resonance energy transfer (FRET) can be combined to characterize the nature of the protein-membrane interaction directly and unambiguously. The assembly pathway can also be determined by measuring the kinetics of the spectral changes that occur upon pore formation. The MIFT approach therefore allows one to obtain structural information that cannot be obtained easily using alternative techniques such as crystallography. This review briefly outlines how MIFT can reveal the identity, location, conformation, and topography of the polypeptide sequences that interact with the membrane.     

Maternal effects provide phenotypic adaptation to local environmental conditions

In outcrossing plants, seed dispersal distance is often less than pollen movement. If the scale of environmental heterogeneity within a population is greater than typical seed dispersal distances but less than pollen movement, an individual's environment will be similar to that of its mother but not necessarily its father. Under these conditions, environmental maternal effects may evolve as a source of adaptive plasticity between generations, enhancing offspring fitness in the environment that they are likely to experience. This idea is illustrated using Campanula americana, an herb that grows in understory and light-gap habitats. Estimates of seed dispersal suggest that offspring typically experience the same light environment as their mother. In a field experiment testing the effect of open vs understory maternal light environments, maternal light directly influenced offspring germination rate and season, and indirectly affected germination season by altering maternal flowering time. Results to date indicate that these maternal effects are adaptive; further experimental tests are ongoing. Evaluating maternal environmental effects in an ecological context demonstrates that they may provide phenotypic adaptation to local environmental conditions.     

Small heat shock proteins and adaptation of various Drosophila species to hyperthermia

The dynamics and the level of accumulation of small heat shock proteins (sHSP group 21–27) after a heat exposure were studied in three Drosophila species differing in thermotolerance. The southern species Drosophila virilis, having the highest thermotolerance, surpassed thermosensitive D. lummei and D. melanogaster in the level of sHSPs throughout the temperature range tested. The results suggest an important role of sHSPs in the molecular mechanisms of adaptation to adverse environmental conditions, particularly to hyperthermia.     

The pore-forming action of polyenes: From model membranes to living organisms

The incidence of resistant fungal pathogens has been increasing, especially in immuno-compromised people. As such, considerable research has been focused on discovering anti-fungal agents with new mechanisms of action and on optimizing the use of existing agents. In this context, interest in the polyene group of anti-fungals has recently been renewed, since they are known to be effective against a broad spectrum of fungal pathogens that only rarely develop a resistance to them. In the past 10?years considerable efforts have been made to improve their efficacy and, simultaneously, to reduce their toxicity. Knowledge about the basic mechanisms of their action will be of crucial importance to further optimizing their use. The mechanisms of polyene action at the membrane level are reviewed here, focusing primarily on their pore-forming activity and on the resulting osmotic responses of artificial lipid vesicles and different eukaryotic cells.     

细胞程序性死亡在植物适应逆境中的意义

细胞程序性死亡是近年来生命科学的研究热点之一,它不仅在植物生长发育中起重要作用,而且与植物适应逆境也密切相关。本文就细胞程序性死亡在植物适应逆境中的重要作用进行了综述,以期对细胞程序性死亡的研究进一步深入和对植物适应逆境的潜力有新的认识。     

Epigenetic variation contributes to environmental adaptation of Arabidopsis thaliana

Epigenetic variation is frequently observed in plants and direct relationships between differences in DNA methylation and phenotypic responses to changing environments have often been described. The identification of contributing genetic loci, however, was until recently hampered by the lack of suitable genome wide mapping resources that specifically segregate for epigenetic marks. The development of epi-RIL populations in the model species Arabidopsis thaliana has alleviated this obstacle, enabling the accurate genetic analysis of epigenetic variation. Comprehensive morphological phenotyping of a ddm1 derived epi-RIL population in different environments and subsequent epi-QTL mapping revealed a high number of epi-QTLs and pleiotropic effects of several DMRs on numerous traits. For a number of these epi-QTLs epistatic interactions could be observed, further adding to the complexity of epigenetic regulation. Moreover, linkage to epigenetic marks indicated a specific role for DNA-methylation variation, rather than TE transposition, in plastic responses to changing environments. These findings provide supportive evidence for a role of epigenetic regulation in evolutionary and adaptive processes.     

Extracellular factors of bacterial adaptation to unfavorable environmental conditions

Data on extracellular compounds of bacteria involved in their adaptation to unfavorable environmental conditions are reviewed, including high or low temperatures, growth-inhibiting or bactericidal concentrations of toxic substances (oxidants, phenols, and heavy metals) and antibiotics, deviation of pH values from optimum levels, and salinity of the medium. Chemically, the compounds identified belong to diverse types (proteins, hydrocarbons, organic acids, nucleotides, amino acids, lipopeptides, volatile substances, etc.). Most of them remain unidentified, and their properties are studied using biological testing. It is proposed to view extracellular adaptation factors (EAFs) as a new group of biologically active substances. EAFs may be divided into several subgroups by the mechanism of action. These subgroups include protectors (stabilizers), signaling molecules inducing defense responses, regulators (e.g., adhesion regulators) not acting as inducers, and antidotes (neutralizers). The fields of EAF study include screening (search for new compounds, using biological tests), identification, and research into mechanisms of action. EAFs may find utility in biotechnology, medicine, agriculture, and environmental protection.     

Sequence and structural parameters enhancing adaptation of proteins to low temperatures

A systematic analysis compared sequence and structural parameters distributions between 13 pairs of psychrophilic and mesophilic proteins for elucidating the cold adaptation parameters. The results of statistical test (t-test) revealed that helical content, tight turn content, disulfide bonds and hydrogen bonds do not show significant difference between psychrophilic and mesophilic proteins. However, it was demonstrated in this study that a larger proportion of open beta-turn in psychrophilic proteins is an effective parameter in specific activity at low temperature. In addition, substitution of amino acids of charged and aliphatic groups with amino acids of tiny and small groups in protein chains, tight turns and alpha-helices in the direction from mesophilic to psychrophilic proteins is one of the mechanisms of low temperature adaptation. Such sequence and structural parameter differences would help to develop a strategy for designing cold-adapted proteins.     

Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses

In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.     

X-ray and Cryo-electron Microscopy Structures of Monalysin Pore-forming Toxin Reveal Multimerization of the Pro-form

β-Barrel pore-forming toxins (β-PFT), a large family of bacterial toxins, are generally secreted as water-soluble monomers and can form oligomeric pores in membranes following proteolytic cleavage and interaction with cell surface receptors. Monalysin has been recently identified as a β-PFT that contributes to the virulence of Pseudomonas entomophila against Drosophila. It is secreted as a pro-protein that becomes active upon cleavage. Here we report the crystal and cryo-electron microscopy structure of the pro-form of Monalysin as well as the crystal structures of the cleaved form and of an inactive mutant lacking the membrane-spanning region. The overall structure of Monalysin displays an elongated shape, which resembles those of β-pore-forming toxins, such as Aerolysin, but is devoid of a receptor-binding domain. X-ray crystallography, cryo-electron microscopy, and light-scattering studies show that pro-Monalysin forms a stable doughnut-like 18-mer complex composed of two disk-shaped nonamers held together by N-terminal swapping of the pro-peptides. This observation is in contrast with the monomeric pro-form of the other β-PFTs that are receptor-dependent for membrane interaction. The membrane-spanning region of pro-Monalysin is fully buried in the center of the doughnut, suggesting that upon cleavage of pro-peptides, the two disk-shaped nonamers can, and have to, dissociate to leave the transmembrane segments free to deploy and lead to pore formation. In contrast with other toxins, the delivery of 18 subunits at once, nearby the cell surface, may be used to bypass the requirement of receptor-dependent concentration to reach the threshold for oligomerization into the pore-forming complex.     

Evolutionary responses to environmental change: trophic interactions affect adaptation and persistence

According to recent reviews, the question of how trophic interactions may affect evolutionary responses to climate change remains unanswered. In this modelling study, we explore the evolutionary dynamics of thermal and plant–herbivore interaction traits in a warming environment. We find the herbivore usually reduces adaptation speed and persistence time of the plant by reducing biomass. However, if the plant interaction trait and thermal trait are correlated, herbivores can create different coevolutionary attractors. One attractor has a warmer plant thermal optimum, and the other a colder one compared with the environment. A warmer plant thermal strategy is given a head start under warming, the only case where herbivores can increase plant persistence under warming. Persistence time of the plant under warming is maximal at small or large thermal niche width. This study shows that considering trophic interactions is necessary and feasible for understanding how ecosystems respond to climate change.     

Inhibitor of apoptosis proteins and apoptosis

Apoptosis is a physiological cell death process that plays a critical role in development, homeostasis, and immune defense of multicellular animals. Inhibitor of apoptosis proteins (IAPs) constitute a family of proteins that possess between one and three baculovirus IAP repeats. Some of them also have a really interesting new gene finger domain, and can prevent cell death by binding and inhibiting active caspases, but are regulated by IAP antagonists. Some evidence also indicates that IAP can modulate the cell cycle and signal transduction. The three main factors, IAPs, IAP antagonists, and caspases, are involved in regulating the progress of apoptosis in many species. Many studies and assumptions have been focused on the anfractuous interactions between these three main factors to explore their real functional model in order to develop potential anticancer drugs. In this review, we describe the classification, molecular structures, and properties of IAPs and discuss the mechanisms of apoptosis. We also discuss the promising significance of clinical applications of IAPs in the diagnosis and treatment of malignancy.     

Responses of Symbiodinium microadriaticum clade B to different environmental conditions

The effects of various environmental parameters on zooxanthellae isolated from the sea anemone Condylactis gigantea were studied under controlled conditions in the laboratory. We determined that the zooxanthellae, identified as Symbiodinium microadriaticum, (by Trench. B.) belong to clade B. These algae were exposed to a range of temperatures (17, 21.7, 26 °C), light intensities (25, 30, 45, 85 μmol q m⁻² s⁻¹) and nutrient regimes. While growth rate was relatively independent of treatment, respiration increased significantly with temperature. Both light and temperature did have a significant effect on photosynthetic parameters.The cultured zooxanthellae responded to the environment in ways similar to those of freshly isolated ones, and survived under a wide range of temperatures (17, 21.7, 26 °C).In general, clade B seems to be flexible and well adapted to the temperature range encountered in seawater throughout its wide global distribution.     

Oxygen stress and adaptation of a semi-aquatic plant: rice ( Oryza sativa)

One of the major abiotic stresses that affects plant growth and development is anoxia or hypoxia. Rice is a semi-aquatic plant bestowed with the capability of overcoming oxygen limitation for a considerable period of time. For instance, it can withstand submergence stress either by inherent metabolic adaptations (resistant type), or by keeping its leaves above the water surface by continuously elongating the stem (avoiding type). In the former case, an interplay of several metabolic pathways engaged in anaerobic fermentation keeps the submerged plant alive for a certain period of time. In the latter type, also known as deepwater rice, continuous stem elongation brought about by a series of reactions in planta enables the shoot to remain above the water surface and thus maintain respiration and photosynthesis. However, the earliest event, i.e., sensing the oxygen level that brings about all the changes, has not been clearly understood. This paper intends to evaluate the metabolic adaptations of rice plants to oxygen constraints. Electronic Publication     

Involvement of phospholipids in resistance and adaptation of Escherichia coli to acid conditions and to long-term survival

In Escherichia coli membranes, three major phospholipids are formed: phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and cardiolipin (CL). We report here the survival of mutants lacking either PE or both PG and CL at an acid pHo and during long-term survival experiments. Stationary phase cultures of E. coli lacking PE are much more sensitive to acid shock (pHo 3) than the wild-type strain. Moreover, in the strain lacking PE, long-term survival in stationary phase is impaired and after 5 days no viable cells are recovered. The survival of an exponential phase culture to acid shock is known to be increased if the culture is exposed to moderately acid conditions (pHo 5) prior to a shift to pHo 3. If either PE or both PG and CL are missing, the exposure to pHo 5 does not increase the survival at pHo 3.     

The rate of environmental change drives adaptation to an antibiotic sink

Recent accelerated trends of human-induced global changes are providing many examples of adaptation to novel environments. Although the rate of environmental change can vary dramatically, its effect on evolving populations is unknown. A crucial feature explaining the adaptation to harsh environments is the supply of beneficial mutations via immigration from a 'source' population. In this study, we tested the effect of immigration on adaptation to increasing concentrations of antibiotics. Using experimental population of Pseudomonas aeruginosa, a pathogenic bacterium, we show that higher immigration rates and a slow increase in antibiotic concentration result in a more rapid evolution of resistance; however, a high immigration rate combined with rapid increases in concentration resulted in higher maximal levels of resistance. These findings, which support recent theoretical work, have important implications for the control of antibiotic resistance because they show that rapid rates of change can produce variants with the ability to resist future treatments.     

Alkaline adaptation induces cross-protection against some environmental stresses and morphological change in Vibrio parahaemolyticus

The relationship between alkaline adaptation and the resistance against environmental stresses was examined in Vibrio parahaemolyticus. Alkali-adapted cells were found to have increased resistance against various stresses, including heat, crystal violet, deoxycholic acid, and hydrogen peroxide. However, alkali-adapted cells showed no increased resistance against acid stress and heat-adapted cells did not show increased resistance against alkaline stress. Furthermore, alkaline treatment induced cell elongation with heterogenous size of the bacterium.