Evolutionary Distant Organisms Research Articles

Glutathione metabolism is conserved in response to excessive copper exposure between mice liver and Aurelia coerulea polyps

BackgroundCopper (Cu) is a trace element that is engaged in various routine physiological processes. Excessive copper exposure can cause damage to organisms; however, it is unknown if the mechanisms underlying the response to Cu2+ among different species are conserved. MethodsAurelia coerulea polyps and mice models were exposed to Cu2+ to assess its effects on survival status and organ damage. Transcriptomic sequencing, BLAST, structural analysis, and real-time quantitative PCR were carried out to analyze the similarities and differences in the molecular composition and response mechanisms between two species when exposed to Cu2+. ResultsExcessive Cu2+ exposure led to toxic effects on both A. coerulea polyps and mice. The polyps were injured at a Cu2+ concentration of 3.0 mg L−1. In the mice, increasing Cu2+ concentrations were correlated with, the degree of liver damage, which manifested as hepatocyte apoptosis. In the 300 mg L−1 Cu2+ group of mice, livers cell death was primarily triggered by the phagosome and Toll-like signaling pathways. We found the glutathione metabolism was significantly altered in response to copper stress in both A. coerulea polyps and mice. Moreover, the similarity of gene sequences enriched at the two same sites in this pathway was as high as 41.05 %–49.82 % and 43.61 %–45.99 % respectively. Among them, there was a conservative region in the structure of A. coerulea polyps GSTK1 and mice Gsta2, but the overall difference is large. ConclusionGlutathione metabolism is a conserved copper response mechanism in evolutionary distant organisms such as A. coerulea polyps and mice, although mammals have a more complex regulatory network when it comes to copper-induced cell death.

Immunological Examination of Echinococcus granulosus as a Candidate for Cancer Treatment and Vaccine Development: A Review Study

Echinococcus granulosus, is a cestode parasite that causes cystic echinococcosis. The vaccination procedure with tumor-associated antigens, coming from evolutionary distant organisms such as parasites, can be beneficial to override tolerance problems encountered with human tumor-associated antigens-based cancer therapeutic approaches. In this article, different databases of PubMed, Google Scholar, IranDoc and SID were examined from 2001 to 2021 and related articles were investigated. The review of related studies concerning human beings' treatment revealed the possibility of inhibition of cancer development via HCF antigens and mucin peptides extracted from this cestode. Besides, HCF treatment in animal models mostly showed that anti-cancer immune responses were activated. Of note, an influential issue in the design process of an anti-cancer vaccine is triggering efficacious anti-tumor responses by using idyllic antigens for immunization against cancer. In this realm, many antigens have been studied for this purpose and showed different ranges of effectiveness. Based on the cross-reactivity among parasitic and tumor antigens, detection of parasitic antigens that are highly homologous with cancer antigens is an ideal objective for immunization against cancer cells. As the toxicity of HCF was reported in some studies, further research are required to shed light on finding an innovative anti-cancer vaccine derived from parasites. This review article is useful for health managers and researchers working on the anti-cancer vaccine development.

Feasibility of using melatonin content in pepper (Capsicum annuum) seeds as a physiological marker of chilling stress tolerance.

The presence of melatonin, a known animal hormone, has been confirmed in many evolutionary distant organisms, including higher plants. It is known that melatonin increases tolerance to stress factors as a wide spectrum antioxidant. Tolerant genotypes have generally higher melatonin content than sensitive ones, and exposure to stressful conditions is known to increase endogenous melatonin levels. However, endogenous melatonin levels in seeds have never been used to select genotypes tolerant to abiotic stresses. Thus, in this study, the existence of possible relationship between seed melatonin levels of 28 pepper (Capsicum annuum L.) genotypes and their germination and emergence performance under chilling conditions (15°C) was investigated. The results indicated that these parameters were much better for pepper genotypes with higher seed melatonin contents while those having less than 2ngg-1 additionally exhibited elevated levels of MDA and H2 O2 but lower antioxidant enzyme activities. Thus, a positive relationship between seed melatonin content and chilling stress tolerance has been shown, suggesting a possible use of endogenous melatonin levels as a criterion in selecting chilling stress tolerant varieties. To save considerable time, money and labour, it is recommended that genotypes with lower melatonin contents are excluded from breeding programmes that aim to develop new stress tolerant genotypes.

Regulation of the Actin Cytoskeleton via Rho GTPase Signalling in Dictyostelium and Mammalian Cells: A Parallel Slalom.

Both Dictyostelium amoebae and mammalian cells are endowed with an elaborate actin cytoskeleton that enables them to perform a multitude of tasks essential for survival. Although these organisms diverged more than a billion years ago, their cells share the capability of chemotactic migration, large-scale endocytosis, binary division effected by actomyosin contraction, and various types of adhesions to other cells and to the extracellular environment. The composition and dynamics of the transient actin-based structures that are engaged in these processes are also astonishingly similar in these evolutionary distant organisms. The question arises whether this remarkable resemblance in the cellular motility hardware is accompanied by a similar correspondence in matching software, the signalling networks that govern the assembly of the actin cytoskeleton. Small GTPases from the Rho family play pivotal roles in the control of the actin cytoskeleton dynamics. Indicatively, Dictyostelium matches mammals in the number of these proteins. We give an overview of the Rho signalling pathways that regulate the actin dynamics in Dictyostelium and compare them with similar signalling networks in mammals. We also provide a phylogeny of Rho GTPases in Amoebozoa, which shows a variability of the Rho inventories across different clades found also in Metazoa.

Assessment of Isoprene as a Possible Biosignature Gas in Exoplanets with Anoxic Atmospheres.

The search for possible biosignature gases in habitable exoplanet atmospheres is accelerating, although actual observations are likely years away. This work adds isoprene, C5H8, to the roster of biosignature gases. We found that isoprene geochemical formation is highly thermodynamically disfavored and has no known abiotic false positives. The isoprene production rate on Earth rivals that of methane (CH4; ∼500 Tg/year). Unlike methane, on Earth isoprene is rapidly destroyed by oxygen-containing radicals. Although isoprene is predominantly produced by deciduous trees, isoprene production is ubiquitous to a diverse array of evolutionary distant organisms, from bacteria to plants and animals-few, if any, volatile secondary metabolites have a larger evolutionary reach. Although non-photochemical sinks of isoprene may exist, such as degradation of isoprene by life or other high deposition rates, destruction of isoprene in an anoxic atmosphere is mainly driven by photochemistry. Motivated by the concept that isoprene might accumulate in anoxic environments, we model the photochemistry and spectroscopic detection of isoprene in habitable temperature, rocky exoplanet anoxic atmospheres with a variety of atmosphere compositions under different host star ultraviolet fluxes. Limited by an assumed 10 ppm instrument noise floor, habitable atmosphere characterization when using James Webb Space Telescope (JWST) is only achievable with a transit signal similar or larger than that for a super-Earth-sized exoplanet transiting an M dwarf star with an H2-dominated atmosphere. Unfortunately, isoprene cannot accumulate to detectable abundance without entering a run-away phase, which occurs at a very high production rate, ∼100 times the Earth's production rate. In this run-away scenario, isoprene will accumulate to >100 ppm, and its spectral features are detectable with ∼20 JWST transits. One caveat is that some isoprene spectral features are hard to distinguish from those of methane and also from other hydrocarbons containing the isoprene substructure. Despite these challenges, isoprene is worth adding to the menu of potential biosignature gases.

Programmed Cell Senescence in the Mouse Developing Spinal Cord and Notochord.

Programmed cell senescence is a cellular process that seems to contribute to embryo development, in addition to cell proliferation, migration, differentiation and programmed cell death, and has been observed in evolutionary distant organisms such as mammals, amphibians, birds and fish. Programmed cell senescence is a phenotype similar to stress-induced cellular senescence, characterized by the expression of the cell cycle inhibitors p21CIP1/WAF and p16INK4A, increased activity of a lysosomal enzyme with beta-galactosidase activity (coined senescence-associated beta-galactosidase) and secretion of growth factors, interleukins, chemokines, metalloproteases, etc., collectively known as a senescent-associated secretory phenotype that instructs surrounding tissue. How wide is the distribution of programmed cell senescence during mouse development and its specific mechanisms to shape the embryo are still poorly understood. Here, we investigated whether markers of programmed cell senescence are found in the developing mouse spinal cord and notochord. We found discrete areas and developmental windows with high senescence-associated beta galactosidase in both spinal cord and notochord, which was reduced in mice embryos developed ex-utero in the presence of the senolytic ABT-263. Expression of p21CIP1/WAF was documented in epithelial cells of the spinal cord and the notochord, while p16INK4A was observed in motoneurons. Treatment with the senolytic ABT-263 decreased the number of motoneurons, supporting their senescent phenotype. Our data suggest that a subpopulation of motoneurons in the developing spinal cord, as well as some notochord cells undergo programmed cell senescence.

Phytomelatonin: An overview of the importance and mediating functions of melatonin against environmental stresses

Recently, melatonin has gained significant importance in plant research. The presence of melatonin in the plant kingdom has been known since 1995. It is a molecule that is conserved in a wide array of evolutionary distant organisms. Its functions and characteristics have been found to be similar in both plants and animals. The review focuses on the role of melatonin pertaining to physiological functions in higher plants. Melatonin regulates physiological functions regarding auxin activity, root, shoot, and explant growth, activates germination of seeds, promotes rhizogenesis (growth of adventitious and lateral roots), and holds up impelled leaf senescence. Melatonin is a natural bio-stimulant that creates resistance in field crops against various abiotic stress, including heat, chemical pollutants, cold, drought, salinity, and harmful ultra-violet radiation. The full potential of melatonin in regulating physiological functions in higher plants still needs to be explored by further research.

Open gaps in the evolution of the eukaryotic nucleotide excision repair

Nucleotide excision repair (NER) is the most versatile DNA repair pathway as it removes different kinds of bulky lesions. Due to its essential role for genome integrity, it has appeared early in the evolution of species. However, most published studies are focused on humans, mice, yeast or bacteria. Considering the large amount of information on genome databases, it is currently possible to retrieve sequences from NER components in many organisms. Therefore, we have characterized the potential orthologs of 10 critical components of the human NER pathway in 12 eukaryotic species by using similarity and structural criteria through the use of bioinformatics tools. This approach has allowed us to characterize gene and protein structures comparatively, taking a glance at some evolutionary aspects of the NER pathway. We have obtained significant search results for the majority of the proteins in most of the organisms studied, mainly for factors that play a pivotal role in the pathway. However, we have revisited significant differences and found new aspects that may imply a distinct functioning of this pathway in different organisms. Through the demonstration of the heterogeneity of the gene structures and a variety in the protein architecture of the NER components evaluated, our results show important differences between human NER and evolutionarily distant eukaryotes. We highlight the lack of a canonical XPD in chicken, the divergence of XPA in plants and protozoans and the absence of XPE in the invertebrate species analyzed. In spite of this, it is remarkable the presence of this excision repair mechanism in a high number of evolutionary distant organisms, being present since the origin of eukaryotes.

Common Functions of Disordered Proteins across Evolutionary Distant Organisms.

Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence–structure–function relationship. Hence, classic sequence- or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism.

Iron redox pathway revealed in ferritin via electron transfer analysis

Ferritin protein is involved in biological tissues in the storage and management of iron - an essential micro-nutrient in the majority of living systems. While there are extensive studies on iron-loaded ferritin, its functionality in iron delivery is not completely clear. Here, for the first time, differential pulse voltammetry (DPV) has been successfully adapted to address the challenge of resolving a cascade of fast and co-occurring redox steps in enzymatic systems such as ferritin. Using DPV, comparative analysis of ferritins from two evolutionary-distant organisms has allowed us to propose a stepwise resolution for the complex mix of concurrent redox steps that is inherent to ferritins and to fine-tune the structure-function relationship of each redox step. Indeed, the cyclic conversion between Fe3+ and Fe2+ as well as the different oxidative steps of the various ferroxidase centers already known in ferritins were successfully discriminated, bringing new evidence that both the 3-fold and 4-fold channels can be functional in ferritin.

The development of cell senescence.

Cellular senescence was traditionally considered a stress response that protected the organism by limiting the proliferation of damaged and unwanted cells. However, the recent identification of developmentally-programmed cellular senescence during embryo development has changed our view of the process. There are now a number of examples of developmental senescence in evolutionary distant organisms ranging from mammals to fish, showing senescence at various sites during specific time windows of development. Developmental senescence shares many features with stress-induced senescence but also present some specific characteristics. The different examples of developmental senescence provide evidence of the diverse functions contributed by senescence and represent an opportunity to learn more about this process. Also, the existence of senescence during embryogenesis opens the possibility of identifying human developmental syndromes caused by alterations in this response. Studying in more detail this process will expand our understanding of cellular senescence and could offer new insights into the cause of human pathologies.

Structural insights into SUMO E1-E2 interactions in Arabidopsis uncovers a distinctive platform for securing SUMO conjugation specificity across evolution.

SUMOylation of proteins involves the concerted action of the E1-activating enzyme, E2-conjugating enzyme and E3-ligases. An essential discrimination step in the SUMOylation pathway corresponds to the initial interaction between E1 ubiquitin-fold domain (UFD) and E2 enzymes. Although E2 orthologs possess high sequence identity, the E2 binding region of the UFD domains has diverged across evolution. Moreover, in reciprocal in vitro conjugation reactions Arabidopsis E1 and E2 SCE1 fail to interact efficiently with cognate human E2 Ubc9 and E1 partners, respectively. To gain more insights into the properties of this interface in evolutionary distant organisms, we solved the crystal structure of SUMO E2 SCE1 and its complex with E1 UFD in Arabidopsis. In addition to a few common structural determinants, the interface between the E1 UFD and E2 in Arabidopsis is distinct compared with human and yeast, in particular by the presence of a longer α-helix in the Arabidopsis UFD domain. Despite the variability of E1 UFD domains in these surfaces, they establish specific interactions with highly conserved surfaces of their cognate E2 enzymes. Functional analysis of the different E2 interface residues between human and Arabidopsis revealed Val37 (Met36 in human), as a determinant that provides specificity in the E1-E2 recognition in plants.

POWIĄZANIA POMIĘDZY GRZYBAMI PODZIEMNYMI A MAŁYMI SSAKAMI

Grzyby podziemne charakteryzuje proces tworzenia i dojrzewania zarodników przebiegający w obrębie gasteroidalnych (zamkniętych) owocników pod powierzchnią ziemi. Cecha ta powstała niezależnie u przedstawicieli gromad Ascomycota, Basidiomycota i Mucoromycota. Zarodniki grzybów podziemnych rozprzestrzeniane są przez organizmy wektorowe, np. gryzonie. Owocniki stanowią często dla zwierząt ważne uzupełnienie diety lub jej główny element, dostarczając zwierzętom substancje takie jak woda, białka, tłuszcze, witaminy czy związki o charakterze prozdrowotnym. Grzyby podziemne w większości tworzą związki ektomikoryzowe, głównie z drzewami. Ich relacje ze zwierzętami mają więc wpływ na rozpropagowanie inokulum mikoryzowego tych grzybów nie tylko w środowisku leśnym ale również na terenach bezleśnych. W zależności te włączone są również drapieżniki, które, żywiąc się mykofagicznymi ssakami, biorą udział w dalekim transporcie zarodników. Istnienie ścisłych relacji pomiędzy grzybami podziemnymi a konsumującymi je gryzoniami a także drapieżnikami oraz drzewami ektomikoryzowymi, tworzy sieć zależności ekologicznych pomiędzy ewolucyjnie odległymi od siebie organizmami.

Recurrence-based information processing in gene regulatory networks.

Cellular information processing is generally attributed to the complex networks of genes and proteins that regulate cell behavior. It is still unclear, however, what are the main features of those networks that allow a cell to encode and interpret its ever changing environment. Here, we address this question by studying the computational capabilities of the transcriptional regulatory networks of five evolutionary distant organisms. We identify in all cases a cyclic recurrent structure, formed by a small core of genes, that is essential for dynamical encoding and information integration. The recent history of the cell is projected nonlinearly into this recurrent reservoir of nodes, where it is encoded by its transient dynamics, while the rest of the network forms a readout layer devoted to decode and interpret the high-dimensional dynamical state of the recurrent core. In that way, gene regulatory networks act as echo-state networks that perform optimally in standard memory-demanding tasks, with most of their memory residing in the recurrent reservoir. The biological significance of these results is analyzed in the particular case of the bacterium Escherichia coli. Our work thus suggests that recurrent nonlinear dynamics is a key element for the processing of complex time-dependent information by cells.

Production of a Human Cell Line with a Plant Chromosome.

It is a major challenge in biology to know whether chromosome functions of replication, segregation, gene expression, inheritance, etc. are conserved among evolutionary distant organisms where common structural features are maintained. Establishment of hybrid cell lines between evolutionary distant organisms, such as humans and plants, would be one of the promising synthetic approaches to study the evolutionary conservation of chromosome functions. In this chapter, we describe the protocol for successful establishment of human cell lines with a functional plant chromosome. Systematic analyses of hybrid cells will facilitate the evolutionary study of organisms with respect to chromosome functions. It will also provide a basic platform for genome writing and construction of chromosomal shuttle vectors .

Plant-Derived Transcription Factors for Orthologous Regulation of Gene Expression in the Yeast Saccharomyces cerevisiae.

Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects for which a tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harboring cognate cis-regulatory motifs driving a yEGFP reporter. Transcriptional output of the different driver/reporter combinations varied over a wide spectrum, with EDLL being a considerably stronger transcription activation domain in yeast than the GAL4 activation domain, in particular when fused to Arabidopsis NAC TFs. Notably, the strength of several NAC-EDLL fusions exceeded that of the strong yeast TDH3 promoter by 6- to 10-fold. We furthermore show that plant TFs can be used to build regulatory systems encoded by centromeric or episomal plasmids. Our library of TF-DNA binding site combinations offers an excellent tool for diverse synthetic biology applications in yeast.

Melatonin restricts Pb-induced PCD by enhancing BI-1 expression in tobacco suspension cells.

Melatonin is a conserved substance, which was discovered in the evolutionary distant organisms like bacteria, plants, invertebrates and vertebrates. Recent studies have shown that melatonin despite its possible role in photoperiod processes, has been found to be a direct free radical scavenger and an indirect antioxidant. In this report the impact of exogenous melatonin on the Bax inhibitor-1 (BI-1) expression level in Nicotiana tabacum L. line Bright Yellow 2 (BY-2) suspension cells exposed to lead was examined. BI-1 is a well-conserved protein in plants and animals that serves as the inhibitor of mammalian proapoptotic proteins as well as plant ROS-induced cell death. Our results showed that pretreatment with 200 nm melatonin, expressing BI-1 and fortified tobacco suspension cells against damages induced by lead. The obtained results revealed, that melatonin significantly increases BY-2 cells proliferation and protects BY-2 cells against death. Moreover, the conducted analyses showed for the first time that the protective effect of melatonin may be connected not only with its antioxidant properties but also with its direct impact on elevating BI-1 expression and lead-induced programmed cell death (PCD) restriction.

Enhanced amino acid utilization sustains growth of cells lacking Snf1/AMPK

The metabolism of proliferating cells shows common features even in evolutionary distant organisms such as mammals and yeasts, for example the requirement for anabolic processes under tight control of signaling pathways. Analysis of the rewiring of metabolism, which occurs following the dysregulation of signaling pathways, provides new knowledge about the mechanisms underlying cell proliferation.The key energy regulator in yeast Snf1 and its mammalian ortholog AMPK have earlier been shown to have similar functions at glucose limited conditions and here we show that they also have analogies when grown with glucose excess. We show that loss of Snf1 in cells growing in 2% glucose induces an extensive transcriptional reprogramming, enhances glycolytic activity, fatty acid accumulation and reliance on amino acid utilization for growth. Strikingly, we demonstrate that Snf1/AMPK-deficient cells remodel their metabolism fueling mitochondria and show glucose and amino acids addiction, a typical hallmark of cancer cells.

Role of Lipids in Folding, Misfolding and Function of Integral Membrane Proteins.

The lipid bilayer that constitutes cell membranes imposes environmental constraints on the structure, folding and function of integral membrane proteins. The cell membrane is an enormously heterogeneous and dynamic system in its chemical composition and associated physical forces. The lipid compositions of cell membranes not only vary over the tree of life but also differ by subcellular compartments within the same organism. Even in the same subcellular compartment, the membrane composition shows strong temporal and spatial dependence on the environmental or biological cues. Hence, one may expect that the membrane protein conformations and their equilibria strongly depend on the physicochemical variables of the lipid bilayer. Contrary to this expectation, the structures of homologous membrane proteins belonging to the same family but from evolutionary distant organisms exhibit a striking similarity. Furthermore, the atomic structures of the same protein in different lipid environments are also very similar. This suggests that certain stable folds optimized for a specific function have been selected by evolution. On the other hand, there is growing evidence that, despite the overall stability of the protein folds, functions of certain membrane proteins require a particular lipid composition in the bulk bilayer or binding of specific lipid species. Here I discuss the specific and nonspecific modulation of folding, misfolding and function of membrane proteins by lipids and introduce several diseases that are caused by misfolding of membrane proteins.

Glutathione levels modulation as a strategy in host-parasite interactions-insights for biology of cancer.

OPINION article Front. Pharmacol., 05 August 2014Sec. Experimental Pharmacology and Drug Discovery Volume 5 - 2014 | https://doi.org/10.3389/fphar.2014.00180