Unicellular Eukaryotic Organisms Research Articles

Precambrian paleontology and acrochrons of the biosphere evolution: On the theory of the expanding biosphere

What is pre-life? We have no idea, since it is hidden in chemical molecules that conceal its future genetic potential. From the biological standpoint, a prokaryotic cyanobacteria cell represents a culmination of biochemical evolution. Its appearance on the Earth marked the starting point of the formation of the first biogeocoenosis on the planet, i.e., the onset of its biosphere. After having started, approximately 4.0–3.7 Ga ago, biosphere evolution has continued uninterrupted on the Earth. Its whole course is reflected in the geochronological record of the stratisphere, the stratified shell of the Earth. In the stratigraphic sense, this record comprises the Archean, Proterozoic (i.e., Karelian and Riphean), and Phanerozoic (i.e., Paleozoic, Mesozoic, and Cenozoic). They correspond to acrochrons, i.e., the main stages in biosphere evolution. According to the Precambrian paleontology, the first three acrochrons represent a pre-Vendian stage in the evolution of unicellular prokaryotic and eukaryotic organisms that terminated in the Riphean with the appearance of their colonial communities. The true metacellular structure of tissue Metaphyta and Metazoa started forming only in the Late Neoproterozoic (Late Riphean). The Vendian Period was marked by a radiation of macrotaxonomic diversity with the appearance of the main multicellular types of the Phanerozoic organization level. Therefore, the last acrochron (lasting from approximately 650 Ma ago) should be considered as corresponding to the Vendian-Phanerozoic period. The Cambrian explosion corresponds to the mass expansion of skeletal Metazoa.

Systems biology of yeast cell death

Programmed cell death (PCD) (including apoptosis) is an essential process, and many human diseases of high prevalence such as neurodegenerative diseases and cancer are associated with deregulations in the cell death pathways. Yeast Saccharomyces cerevisiae, a unicellular eukaryotic organism, shares with multicellular organisms (including humans) key components and regulators of the PCD machinery. In this article, we review the current state of knowledge about cell death networks, including the modeling approaches and experimental strategies commonly used to study yeast cell death. We argue that the systems biology approach will bring valuable contributions to our understanding of regulations and mechanisms of the complex cell death pathways.

The spatiotemporal dynamics of longevity-defining cellular processes and its modulation by genetic, dietary, and pharmacological anti-aging interventions

The spatiotemporal dynamics of longevity-defining cellular processes and its modulation by genetic, dietary, and pharmacological anti-aging interventions

Boolean Model of Yeast Apoptosis as a Tool to Study Yeast and Human Apoptotic Regulations

Programmed cell death (PCD) is an essential cellular mechanism that is evolutionary conserved, mediated through various pathways and acts by integrating different stimuli. Many diseases such as neurodegenerative diseases and cancers are found to be caused by, or associated with, regulations in the cell death pathways. Yeast Saccharomyces cerevisiae, is a unicellular eukaryotic organism that shares with human cells components and pathways of the PCD and is therefore used as a model organism. Boolean modeling is becoming promising approach to capture qualitative behavior and describe essential properties of such complex networks. Here we present large literature-based and to our knowledge first Boolean model that combines pathways leading to apoptosis (a type of PCD) in yeast. Analysis of the yeast model confirmed experimental findings of anti-apoptotic role of Bir1p and pro-apoptotic role of Stm1p and revealed activation of the stress protein kinase Hog proposing the maximal level of activation upon heat stress. In addition we extended the yeast model and created an in silico humanized yeast in which human pro- and anti-apoptotic regulators Bcl-2 family and Valosin-contain protein (VCP) are included in the model. We showed that accumulation of Bax in silico humanized yeast shows apoptotic markers and that VCP is essential target of Akt Signaling. The presented Boolean model provides comprehensive description of yeast apoptosis network behavior. Extended model of humanized yeast gives new insights of how complex human disease like neurodegeneration can initially be tested.

Apple Can Act as Anti-Aging on Yeast Cells

In recent years, epidemiological and biochemical studies have shown that eating apples is associated with reduction of occurrence of cancer, degenerative, and cardiovascular diseases. This association is often attributed to the presence of antioxidants such as ascorbic acid (vitamin C) and polyphenols. The substances that hinder the presence of free radicals are also able to protect cells from aging. In our laboratory we used yeast, a unicellular eukaryotic organism, to determine in vivo efficacy of entire apples and their components, such as flesh, skin and polyphenolic fraction, to influence aging and oxidative stress. Our results indicate that all the apple components increase lifespan, with the best result given by the whole fruit, indicating a cooperative role of all apple components.

Conservation of the Human Integrin-Type Beta-Propeller Domain in Bacteria

Integrins are heterodimeric cell-surface receptors with key functions in cell-cell and cell-matrix adhesion. Integrin α and β subunits are present throughout the metazoans, but it is unclear whether the subunits predate the origin of multicellular organisms. Several component domains have been detected in bacteria, one of which, a specific 7-bladed β-propeller domain, is a unique feature of the integrin α subunits. Here, we describe a structure-derived motif, which incorporates key features of each blade from the X-ray structures of human αIIbβ3 and αVβ3, includes elements of the FG-GAP/Cage and Ca2+-binding motifs, and is specific only for the metazoan integrin domains. Separately, we searched for the metazoan integrin type β-propeller domains among all available sequences from bacteria and unicellular eukaryotic organisms, which must incorporate seven repeats, corresponding to the seven blades of the β-propeller domain, and so that the newly found structure-derived motif would exist in every repeat. As the result, among 47 available genomes of unicellular eukaryotes we could not find a single instance of seven repeats with the motif. Several sequences contained three repeats, a predicted transmembrane segment, and a short cytoplasmic motif associated with some integrins, but otherwise differ from the metazoan integrin α subunits. Among the available bacterial sequences, we found five examples containing seven sequential metazoan integrin-specific motifs within the seven repeats. The motifs differ in having one Ca2+-binding site per repeat, whereas metazoan integrins have three or four sites. The bacterial sequences are more conserved in terms of motif conservation and loop length, suggesting that the structure is more regular and compact than those example structures from human integrins. Although the bacterial examples are not full-length integrins, the full-length metazoan-type 7-bladed β-propeller domains are present, and sometimes two tandem copies are found.

Substrate Preferences and Catalytic Parameters Determined by Structural Characteristics of Sterol 14α-Demethylase (CYP51) from Leishmania infantum

Leishmaniasis is a major health problem that affects populations of ∼90 countries worldwide, with no vaccine and only a few moderately effective drugs. Here we report the structure/function characterization of sterol 14α-demethylase (CYP51) from Leishmania infantum. The enzyme catalyzes removal of the 14α-methyl group from sterol precursors. The reaction is essential for membrane biogenesis and therefore has great potential to become a target for antileishmanial chemotherapy. Although L. infantum CYP51 prefers C4-monomethylated sterol substrates such as C4-norlanosterol and obtusifoliol (V(max) of ∼10 and 8 min(-1), respectively), it is also found to 14α-demethylate C4-dimethylated lanosterol (V(max) = 0.9 min(-1)) and C4-desmethylated 14α-methylzymosterol (V(max) = 1.9 min(-1)). Binding parameters with six sterols were tested, with K(d) values ranging from 0.25 to 1.4 μM. Thus, L. infantum CYP51 is the first example of a plant-like sterol 14α-demethylase, where requirements toward the composition of the C4 atom substituents are not strict, indicative of possible branching in the postsqualene portion of sterol biosynthesis in the parasite. Comparative analysis of three CYP51 substrate binding cavities (Trypanosoma brucei, Trypanosoma cruzi, and L. infantum) suggests that substrate preferences of plant- and fungal-like protozoan CYP51s largely depend on the differences in the enzyme active site topology. These minor structural differences are also likely to underlie CYP51 catalytic rates and drug susceptibility and can be used to design potent and specific inhibitors.

Splintrons in Giardia intestinalis: Spliceosomal introns in a split form.

The divergent eukaryotic unicellular organism Giardia intestinalis is an intestinal parasite in humans and various animals. An analysis of a draft genome sequence suggested that G. intestinalis has a much simpler genome organization and gene repertoire than those of other model eukaryotic organisms (e.g., Arabidopsis and human). This general picture of the G. intestinalis genome seemingly agrees with the fact that only four spliceosomal (cis-spliced) introns have been identified in this organism to date. We have recently shown that G. intestinalis possesses a unique gene expression system incorporating spliceosome-mediated trans-splicing. Some protein-coding genes in G. intestinalis are split into multiple pieces in the genome and each gene fragment is independently transcribed. Two particular pre-mRNAs directly interact with each other by forming an intermolecular-stem structure and are then trans-spliced into a mature mRNA by spliceosomes. We believe that this trans-splicing secondarily arose from the system that excises canonical (cis-splicing) introns. Based on these findings, we suspect that similar phenomena-split genes and post-transcriptional assemblage of their transcripts via trans-splicing-may be prevalent in more distinct eukaryotic lineages than previously known, particularly in organisms possessing "intron-poor" genomes.

Splintrons in Giardia intestinalis

The divergent eukaryotic unicellular organism Giardia intestinalis is an intestinal parasite in humans and various animals. An analysis of a draft genome sequence suggested that G. intestinalis has a much simpler genome organization and gene repertoire than those of other model eukaryotic organisms (e.g., Arabidopsis and human). This general picture of the G. intestinalis genome seemingly agrees with the fact that only four spliceosomal (cis-spliced) introns have been identified in this organism to date. We have recently shown that G. intestinalis possesses a unique gene expression system incorporating spliceosome-mediated trans-splicing. Some protein-coding genes in G. intestinalis are split into multiple pieces in the genome and each gene fragment is independently transcribed. Two particular pre-mRNAs directly interact with each other by forming an intermolecular-stem structure and are then trans-spliced into a mature mRNA by spliceosomes. We believe that this trans-splicing secondarily arose from the system that excises canonical (cis-splicing) introns. Based on these findings, we suspect that similar phenomena—split genes and post-transcriptional assemblage of their transcripts via trans-splicing—may be prevalent in more distinct eukaryotic lineages than previously known, particularly in organisms possessing ‘intron-poor’ genomes.

Vesicular traffic in cell navigation

Cell navigation is the process whereby cells or cytoplasmic extensions are guided from one point to another in multicellular organisms or, in the case of unicellular eukaryotic organisms, in the environment. Recent work has demonstrated that membrane trafficking plays an important role in this process. Here, we review the role of soluble N-ethylmaleimide-sensitive fusion attachment protein (SNAP) receptors (SNAREs), which constitute the core machinery for membrane fusion and are essential for intracellular vesicular trafficking. We discuss the important functions of several vesicular- and target-SNAREs, in particular vesicular-associated membrane proteins 1, 2, 3, 4 and 7; vti1a/b; SNAP23 and SNAP25; and syntaxins 1, 3, 6 and 13. We conclude that endosomal SNAREs are important for cell navigation, a concept that opens avenues for fundamental research. There are also possible therapeutic applications because some of these SNAREs are the targets of clostridial neurotoxins.

Optimal feeding and swimming gaits of biflagellated organisms

Locomotion is widely observed in life at micrometric scales and is exhibited by many eukaryotic unicellular organisms. Motility of such organisms can be achieved through periodic deformations of a tail-like projection called the eukaryotic flagellum. Although the mechanism allowing the flagellum to deform is largely understood, questions related to the functional significance of the observed beating patterns remain unresolved. Here, we focus our attention on the stroke patterns of biflagellated phytoplanktons resembling the green alga Chlamydomonas. Such organisms have been widely observed to beat their flagella in two different ways--a breaststroke and an undulatory stroke--both of which are prototypical of general beating patterns observed in eukaryotes. We develop a general optimization procedure to determine the existence of optimal swimming gaits and investigate their functional significance with respect to locomotion and nutrient uptake. Both the undulatory and the breaststroke represent local optima for efficient swimming. With respect to the generation of feeding currents, we found the breaststroke to be optimal and to enhance nutrient uptake significantly, particularly when the organism is immersed in a gradient of nutrients.

Horizontal and vertical growth of S. cerevisiae metabolic network

BackgroundThe growth and development of a biological organism is reflected by its metabolic network, the evolution of which relies on the essential gene duplication mechanism. There are two current views about the evolution of metabolic networks. The retrograde model hypothesizes that a pathway evolves by recruiting novel enzymes in a direction opposite to the metabolic flow. The patchwork model is instead based on the assumption that the evolution is based on the exploitation of broad-specificity enzymes capable of catalysing a variety of metabolic reactions.ResultsWe analysed a well-studied unicellular eukaryotic organism, S. cerevisiae, and studied the effect of the removal of paralogous gene products on its metabolic network. Our results, obtained using different paralog and network definitions, show that, after an initial period when gene duplication was indeed instrumental in expanding the metabolic space, the latter reached an equilibrium and subsequent gene duplications were used as a source of more specialized enzymes rather than as a source of novel reactions. We also show that the switch between the two evolutionary strategies in S. cerevisiae can be dated to about 350 million years ago.ConclusionsOur data, obtained through a novel analysis methodology, strongly supports the hypothesis that the patchwork model better explains the more recent evolution of the S. cerevisiae metabolic network. Interestingly, the effects of a patchwork strategy acting before the Euascomycete-Hemiascomycete divergence are still detectable today.

Telomere maintenance in liquid crystalline chromosomes of dinoflagellates

The organisation of dinoflagellate chromosomes is exceptional among eukaryotes. Their genomes are the largest in the Eukarya domain, chromosomes lack histones and may exist in liquid crystalline state. Therefore, the study of the structural and functional properties of dinoflagellate chromosomes is of high interest. In this work, we have analysed the telomeres and telomerase in two Dinoflagellata species, Karenia papilionacea and Crypthecodinium cohnii. Active telomerase, synthesising exclusively Arabidopsis-type telomere sequences, was detected in cell extracts. The terminal position of TTTAGGG repeats was determined by in situ hybridisation and BAL31 digestion methods and provides evidence for the linear characteristic of dinoflagellate chromosomes. The length of telomeric tracts, 25-80kb, is the largest among unicellular eukaryotic organisms to date. Both the presence of long arrays of perfect telomeric repeats at the ends of dinoflagellate chromosomes and the existence of active telomerase as the primary tool for their high-fidelity maintenance demonstrate the general importance of these structures throughout eukaryotes. We conclude that whilst chromosomes of dinoflagellates are unique in many aspects of their structure and composition, their telomere maintenance follows the most common scenario.

MAPK signaling in inflammation-associated cancer development

Mitogen-activated protein (MAP) kinases comprise a family of protein-serine/threonine kinases, which are highly conserved in protein structures from unicellular eukaryotic organisms to multicellular organisms, including mammals. These kinases, including ERKs, JNKs and p38s, are regulated by a phosphorelay cascade, with a prototype of three protein kinases that sequentially phosphorylate one another. MAPKs transduce extracellular signals into a variety of cellular processes, such as cell proliferation, survival, death, and differentiation. Consistent with their essential cellular functions, MAPKs have been shown to play critical roles in embryonic development, adult tissue homeostasis and various pathologies. In this review, we discuss recent findings that reveal the profound impact of these pathways on chronic inflammation and, particularly, inflammation-associated cancer development.

Protein splicing and its evolution in eukaryotes

Inteins, or protein introns, are parts of protein sequences that are post-translationally excised, their flanking regions (exteins) being spliced together. This process was called protein splicing. Originally inteins were found in prokaryotic or unicellular eukaryotic organisms. But the general principles of post-translation protein rearrangement are evolving yielding different post-translation modification of proteins in multicellular organisms. For clarity, these non-intein mediated events call either protein rearrangements or protein editing. The most intriguing example of protein editing is proteasome-mediated splicing of antigens in vertebrates that may play important role in antigen presentation. Other examples of protein rearrangements are maturation of Hg-proteins (critical receptors in embryogenesis) as well as maturation of several metabolic enzymes. Despite a lack of experimental data we try to analyze some intriguing examples of protein splicing evolution.

Amoebae and algae can prolong the survival of Campylobacter species in co-culture

Several species of free-living amoebae can cause disease in humans. However, in addition to the direct pathogenicity of e.g. Acanthamoebae and Naegleria species , they are recognized as environmental hosts, indirectly involved in the epidemiology of many pathogenic bacteria. Although several studies have demonstrated intracellular survival of many different bacteria in these species, the extent of such interactions as well as the implications for the epidemiology of the bacterial species involved, are largely unknown and probably underestimated. In this study, we evaluated eight different unicellular eukaryotic organisms, for their potential to serve as environmental hosts for Campylobacter species. These organisms include four amoebozoas ( Acanthamoeba polyphaga, Acanthamoeba castellanii, Acanthamoeba rhysodes and Hartmanella vermiformis), one alveolate ( Tetrahymena pyriformis), one stramenopile ( Dinobryon sertularia), one eugoenozoa ( Euglena gracilis) and one heterolobosea ( Naegleria americana). Campylobacter spp. including Campylobacter jejuni, Campylobacter coli and Campylobacter lari are the most common cause of gastroenteritis in the western world. Survival and replication of these three species as well as Campylobacter hyointestinalis were assessed in co-cultures with the eukaryotic organisms. Campylobacter spp. generally survived longer in co-cultures, compared to when incubated in the corresponding growth media. The eukaryotic species that best promoted bacterial survival was the golden algae D. sertularia. Three species of amoebozoas, of the genus Acanthamoeba promoted both prolonged survival and replication of Campylobacter spp. The high abundance in lakes, ponds and water distribution networks of these organisms indicate that they might have a role in the epidemiology of campylobacteriosis, possibly contributing to survival and dissemination of these intestinal pathogens to humans and other animals. The results suggest that not only C. jejuni, but a variety of Campylobacter spp. can interact with different eukaryotic unicellular organisms.

The small ubiquitin-like modifier (SUMO) is essential in cell cycle regulation in Trypanosoma brucei

SUMO, a reversible post-translational protein modifier, plays important roles in many processes of higher eukaryotic cell life. Although SUMO has been identified in many eukaryotes, SUMO and SUMO system are still unknown in some eukaryotic unicellular organisms, such as Trypanosoma brucei ( T. brucei). In this study, only one SUMO homologue (TbSUMO) was identified in T. brucei. Expression of TbSUMO was knocked down by using RNA interference technique in procyclic-form T. brucei. The growth of TbSUMO-deficient cells was significantly inhibited. TbSUMO-deficient cells were arrested in G 2/M phase accompanied with an obvious increase of 0N1K cells (zoids), and failed in chromosome segregation. These results indicate that TbSUMO is essential in cell cycle regulation, with one important role in mitosis. Meanwhile, the enrichment of zoids suggests the inhibition of mitosis does not prevent the cell division in procyclic-form T. brucei. HA-tagged TbSUMO was overexpressed in T. brucei and was shown to be localized to the nucleus through the whole cell cycle, further revealing its distinguished functions in nucleus. All these accumulated data imply that a SUMO system essential for regulating cell cycle progression might exist in the procyclic-form T. brucei.

Sponges (Porifera) and eukaryotic, unicellular plankton: A case study on Aplysina aerophoba, Nardo 1886 in the Northern Adriatic

Sponges (Porifera), in general, are pumping water through their bodies. This water contains planktonic eukaryotic and procaryotic organisms as well as particulate and dissolved organic matter as potential food source. We analyzed the eukaryotic unicellular plankton fraction from water surrounding sponges of the species Aplysina aerophoba, Nardo 1886, from sponge tissue, as well as from water expelled from those sponges. We found sponges without any remnants of plankton in their tissue, as well as specimens which incorporated high numbers of remnants of organisms after planktonic “blooms”. In laboratory experiments, sponges were not showing any uptake of plankton from their surrounding water. Sponges are generally considered as inner filter feeders. However, our results indicate that eukaryotic unicellular plankton organisms are not the main food resource of the common sponge A. aerophoba. This raises the question if filter feeding is actually the main characteristic of the poriferan lifestyle.

Toxicity of nanoparticles of ZnO, CuO and TiO 2 to yeast Saccharomyces cerevisiae

The aim of this study was to evaluate the toxic effect of nanosized ZnO, CuO and TiO 2 to Saccharomyces cerevisiae – a widely used unicellular eukaryotic model organisms in molecular and cell biology . The effect of metal oxide nanoparticles, their bulk forms and respective ionic forms were compared. The bioavailable Zn 2+ and Cu 2+ ions in the growth medium were quantified by recombinant microbial sensors. Nano and bulk TiO 2 were not toxic even at 20000 mg/l. Both, nano and bulk ZnO were of comparable toxicity (8-h EC 50 121–134 mg ZnO/l and 24-h EC 50 131–158 mg/l). The toxicity was explained by soluble Zn-ions as proved by the microbial sensor. However, nano CuO was about 60-fold more toxic than bulk CuO: 8-h EC 50 were 20.7 and 1297 mg CuO/l and 24-h EC 50 were 13.4 and 873 mg/l, respectively. The increase in toxicity of both CuO formulations at 24th hour of growth was due to the increased dissolution of copper ions from CuO over time. Comparison of EC 50 values of nano CuO, bulk CuO and Cu 2+ with bioavailable copper concentrations in the growth medium showed that the solubilized Cu-ions explained only about 50% of the toxicity of both, nano and bulk CuO. To our knowledge, this is the first study that evaluates the toxicity of ZnO, CuO and TiO 2 nanoparticles to S. cerevisiae.

Initial Study on the Toxicity of Silver Nanoparticles (NPs) against Paramecium caudatum

In this initial study, the toxicity effect of silver NPs against a model unicellular eukaryotic organism of Paramecium caudatum was studied. For the purpose of this study, a dialysis-based method was adapted, which allowed the preparation of stable aqueous dispersions of silver NPs in various silver concentrations that were necessary for the evaluation of toxicity limits of these particles. The obtained results demonstrate that the silver NPs do not exhibit any toxicity action against the tested unicellular eukaryotic organism below the concentration of 25 mg·L−1 whereas ionic silver retains its toxicity even at a concentration of 0.4 mg·L−1. Such a considerable difference in the toxicity effect of these two forms of silver has not been observed in the previously published study concerning bacteria (Panáček, A.; Kvítek, L.; Prucek, R.; Kolář, M.; Večeřová, R.; Pizúrová, N.; Sharma, V. K.; Nevěčná, T.; Zbořil, R. J. Phys. Chem. B 2006, 110, 16248−16253). Additionally, it was proven that the surfactant/polymer modification can increase the toxicity of the silver NPs against the tested organism.