Sulfur assimilation and glutathione metabolism under cadmium stress in yeast, protists and plants

Glutathione (gamma-glu-cys-gly; GSH) is usually present at high concentrations in most living cells, being the major reservoir of non-protein reduced sulfur. Because of its unique redox and nucleophilic properties, GSH serves in bio-reductive reactions as an important line of defense against reactive oxygen species, xenobiotics and heavy metals. GSH is synthesized from its constituent amino acids by two ATP-dependent reactions catalyzed by gamma-glutamylcysteine synthetase and glutathione synthetase. In yeast, these enzymes are found in the cytosol, whereas in plants they are located in the cytosol and chloroplast. In protists, their location is not well established. In turn, the sulfur assimilation pathway, which leads to cysteine biosynthesis, involves high and low affinity sulfate transporters, and the enzymes ATP sulfurylase, APS kinase, PAPS reductase or APS reductase, sulfite reductase, serine acetyl transferase, O-acetylserine/O-acetylhomoserine sulfhydrylase and, in some organisms, also cystathionine beta-synthase and cystathionine gamma-lyase. The biochemical and genetic regulation of these pathways is affected by oxidative stress, sulfur deficiency and heavy metal exposure. Cells cope with heavy metal stress using different mechanisms, such as complexation and compartmentation. One of these mechanisms in some yeast, plants and protists is the enhanced synthesis of the heavy metal-chelating molecules GSH and phytochelatins, which are formed from GSH by phytochelatin synthase (PCS) in a heavy metal-dependent reaction; Cd(2+) is the most potent activator of PCS. In this work, we review the biochemical and genetic mechanisms involved in the regulation of sulfate assimilation-reduction and GSH metabolism when yeast, plants and protists are challenged by Cd(2+).     

Not in your usual Top 10: protists that infect plants and algae

Fungi, nematodes and oomycetes belong to the most prominent eukaryotic plant pathogenic organisms. Unicellular organisms from other eukaryotic lineages, commonly addressed as protists, also infect plants. This review provides an introduction to plant pathogenic protists, including algae infecting oomycetes, and their current state of research.     

Molecular evolution of calmodulin-like domain protein kinases (CDPKs) in plants and protists

Many genes for calmodulin-like domain protein kinases (CDPKs) have been identified in plants and Alveolate protists. To study the molecular evolution of the CDPK gene family, we performed a phylogenetic analysis of CDPK genomic sequences. Analysis of introns supports the phylogenetic analysis; CDPK genes with similar intron/exon structure are grouped together on the phylogenetic tree. Conserved introns support a monophyletic origin for plant CDPKs, CDPK-related kinases, and phosphoenolpyruvate carboxylase kinases. Plant CDPKs divide into two major branches. Plant CDPK genes on one branch share common intron positions with protist CDPK genes. The introns shared between protist and plant CDPKs presumably originated before the divergence of plants from Alveolates. Additionally, the calmodulin-like domains of protist CDPKs have intron positions in common with animal and fungal calmodulin genes. These results, together with the presence of a highly conserved phase zero intron located precisely at the beginning of the calmodulin-like domain, suggest that the ancestral CDPK gene could have originated from the fusion of protein kinase and calmodulin genes facilitated by recombination of ancient introns. Received: 11 July 2000 / Accepted: 18 April 2001     

Autophagy in protists

Autophagy is the degradative process by which eukaryotic cells digest their own components using acid hydrolases within the lysosome. Originally thought to function almost exclusively in providing starving cells with nutrients taken from their own cellular constituents, autophagy is in fact involved in numerous cellular events including differentiation, turnover of macromolecules and organelles, and defense against parasitic invaders. During the last 10-20 years, molecular components of the autophagic machinery have been discovered, revealing a complex interactome of proteins and lipids, which, in a concerted way, induce membrane formation to engulf cellular material and target it for lysosomal degradation. Here, our emphasis is autophagy in protists. We discuss experimental and genomic data indicating that the canonical autophagy machinery characterized in animals and fungi appeared prior to the radiation of major eukaryotic lineages. Moreover, we describe how comparative bioinformatics revealed that this canonical machinery has been subject to moderation, outright loss or elaboration on multiple occasions in protist lineages, most probably as a consequence of diverse lifestyle adaptations. We also review experimental studies illustrating how several pathogenic protists either utilize autophagy mechanisms or manipulate host-cell autophagy in order to establish or maintain infection within a host. The essentiality of autophagy for the pathogenicity of many parasites, and the unique features of some of the autophagy-related proteins involved, suggest possible new targets for drug discovery. Further studies of the molecular details of autophagy in protists will undoubtedly enhance our understanding of the diversity and complexity of this cellular phenomenon and the opportunities it offers as a drug target.     

The tubulins of animals,plants, fungi and protists implications for metazoan evolution

Summary -Tubulin subunits from trout (S. gairdneri) sperm tails, sea urchin (S. purpuratus) cilia, protistan alga (C. elongatum) flagella and rose (Paul's Scarlet) cytoplasm have been characterized by limited proteolytic cleavage with the enzymeStaphylococcus aureus protease and electrophoresis of the digestion products on SDS-PAGE. The resulting patterns corresponded to either of two major types representative of animal and non-animal -tubulins, respectively. A total of 28 -tubulins have now been characterized by this method. They are classified in this paper according to the type of cleavage pattern generated by the enzymeS. aureus protease. The implications of these results for metazoan evolution are discussed.     

Protein kinases in protists

Summary The vast preponderance of our understanding of protein kinases comes from studies of mammalian or of other higher eukaryotic systems. A survey of the Wilson reference databank yielded 3,807 citations for protein kinases; only nine of these were reports of protein kinases in protists. It is apparent, nonetheless, that this understudied group offers unique opportunities for resolving the mechanisms by which protein kinases mediate a variety of cellular processes. Moreover, generalities about cofactor requirements (e.g., Ca²⁺ alone activates many protist protein kinases), substrate specificity, and the nature of the enzymes themselves (monomeric versus dimeric cyclic-nucleotide dependent protein kinases) will certainly need to be modified.     

Programmed cell death in protists

Programmed cell death in protists does not seem to make sense at first sight. However, apoptotic markers in unicellular organisms have been observed in all but one of the six/eight major groups of eukaryotes suggesting an ancient evolutionary origin of this regulated process. This review summarizes the available data on apoptotic markers in non-opisthokonts and elucidates potential functions and evolution of programmed cell death. A newly discovered family of caspase-like proteases, the metacaspases, is considered to exert the function of caspases in unicellular organisms. Important results on metacaspases, however, showed that they cannot be always correlated to the measured proteolytic activity during protist cell death. Thus, a major challenge for apoptosis research in a variety of protists remains the identification of the molecular cell death machinery.     

Calcified structures and calcification in protists

Summary The diversity of calcified structures found in protists, the mechanisms utilized to form these structures, and the role these structures play in the taxonomy and systematics of the protists are presented. The two most frequently studied orders of protists which produce calcified structures, the coccolithophorids and foraminifera, are featured. However, consideration is given to the less known and least studied organisms.     

Endosymbiotic associations within protists

The establishment of an endosymbiotic relationship typically seems to be driven through complementation of the host''s limited metabolic capabilities by the biochemical versatility of the endosymbiont. The most significant examples of endosymbiosis are represented by the endosymbiotic acquisition of plastids and mitochondria, introducing photosynthesis and respiration to eukaryotes. However, there are numerous other endosymbioses that evolved more recently and repeatedly across the tree of life. Recent advances in genome sequencing technology have led to a better understanding of the physiological basis of many endosymbiotic associations. This review focuses on endosymbionts in protists (unicellular eukaryotes). Selected examples illustrate the incorporation of various new biochemical functions, such as photosynthesis, nitrogen fixation and recycling, and methanogenesis, into protist hosts by prokaryotic endosymbionts. Furthermore, photosynthetic eukaryotic endosymbionts display a great diversity of modes of integration into different protist hosts.In conclusion, endosymbiosis seems to represent a general evolutionary strategy of protists to acquire novel biochemical functions and is thus an important source of genetic innovation.     

Siliceous structures and silicification in flagellated protists

Summary Flagellated protists produce a diverse range of siliceous structures, such as internal and external skeletons, scales, spines, bristles, cell walls, cyst walls, and loricae. The different groups of silica-depositing flagellates, i.e., chrysophytes/synurophytes, choanoflagellates, dinoflagellates, ebriids, silicoflagellates, thaumatomastigids, and the genusPetasaria are reviewed. Brief mention is also given to those algal groups in which silicification is uncommon and rare (i.e., chlorophytes, euglenophytes, haptophytes/prymnesiophytes, xanthophytes/tribophytes), but in which silicified structures nevertheless occur in few flagellate genera. Special attention is given to aspects of morphology and development of the different siliceous structures as well as on aspects of systematics and taxonomy.     

RNAi pathways in parasitic protists and worms

Tropical diseases caused by parasitic worms and protists are of major public health concern affecting millions of people worldwide. New therapeutic and diagnostic tools would be of great help in dealing with the public health and economic impact of these diseases. RNA interference (RNAi) pathways utilize small non-coding RNAs to regulate gene expression in a sequence-specific manner. In recent years, a wealth of data about the mechanisms and biological functions of RNAi pathways in distinct groups of eukaryotes has been described. Often, RNAi pathways have unique features that are restricted to groups of eukaryotes. The focus of this review will be on RNAi pathways in specific groups of parasitic eukaryotes that include Trypanosoma cruzi, Plasmodium and Schistosoma mansoni. These parasites are the causative agents of Chagas disease, Malaria, and Schistosomiasis, respectively, all of which are tropical diseases that would greatly benefit from the development of new diagnostic and therapeutic tools. In this context, we will describe specific features of RNAi pathways in each of these parasitic eukaryotic groups and discuss how they could be exploited for the treatment of tropical diseases.     

Arginyl-tRNA-protein transferase in eucaryotic protists

Soluble extracts of $\text{Saccharomyces cerevisiae}$ and $\text{Blastocladiella emersonii}$ were found to catalyze the specific transfer of arginine from a mixture of [¹⁴C] aminoacyl-tRNAs into protein. Arginine transfer was stimulated by bovine serum albumin. Glu-Ala, Asp-Ala and cystinyl-$\text{bis}$-Ala inhibited incorporation into protein, whereas dipeptides with other NH₂-terminal residues linked to alanine did not. These results indicate the presence of an enzyme in eucaryotic protists with the same donor and acceptor specificity as mammalian arginyl-tRNA-protein transferase.     

The Golgi apparatus in parasitic protists

This review summarizes the current reports on the Golgi apparatus of parasitic protists. Numerous recent publications have demonstrated that studies on intracellular traffic in parasites essentially advanced our knowledge on the Golgi structure and function, which has been traditionally based on research on yeast and mammalian cultured cells. It has been reported that the parasitic lifestyle determines the functional and structural peculiarities of the secretory systems in unrelated groups of unicellular parasites that make them different from those in mammalian and yeast cells. This review covers the best-studied protists, predominantly those of high medical importance, belonging to the following taxa: Parabasalia (Trichomonas), Diplomonada (Giardia), Entamoebidae (Entamoeba), parasitic Alveolata of the phyllum Apicomplexa (Toxoplasma, Plasmodium), and Kinetoplastida (Trypanosoma, Leishmania). The morphology of the Golgi organelle in eukaryotes from various taxonomic groups has been compared. Within three of the six highest taxa of Eukaryota (Adl et al., 2005) a minimum of eight groups are represented by species lacking Golgi dictiosomes. However, biochemical and/or molecular (genomic) evidence indicate that an organelle with the functions of the Golgi was present in every lineage of eukaryotes studied thus far. Loss of the Golgi organelle is a secondary event as proven by identification of Golgi genes in the genomes of Golgi-lacking lineages. The loss might have occurred independently several times in evolution. Neither the number of stacks, nor the size of the organelle correlates with the intensity of secretion or the position of the species on the evolutionary tree (in terms of presumably early/lately diverged lineages).     

Occurrence of articulins and epiplasmins in protists

The cortex of ciliates. dinoflagellates, and euglenoids comprises a unique structure called the epiplasm, implicated in pattern-forming processes of the cell cortex and in maintaining cell shape. Articulins, a novel class of cytoskeletal proteins, are major constituents of the epiplasm in the flagellate Euglena gracilis and the ciliate Pseudomicrothorax dubius. The hallmark of articulins is a core domain of repetitive motifs of alternating valine and proline residues, the VPV-motif. The VPV-motif repeats are 12 residues long. Positively and negatively charged residues segregate in register with valine and proline positions. The VPV-motif is unique to articulins. The terminal domains flanking the core are generally hydrophobic and contain a series of hexa- or heptapeptide repeats rich in glycine and hydrophobic residues. Using molecular and immunological tools we show that articulins are also present in the dinoflagellate Amphidinium carterae and the ciliates Paramecium tetraurelia and Paramecium caudatum, Tetrahymena pyriformis, and Euplotes aediculatus. Our analysis further shows that epiplasmins, a group of epiplasmic proteins first characterized in Paramecium, are also present in all these species. Moreover, we present evidence that epiplasmins and articulins represent two distinct classes of cytoskeletal proteins.     

Alternative nutritional strategies in protists: symposium introduction and a review of freshwater protists that combine photosynthesis and heterotrophy

The alternative nutritional strategies in protists that were addressed during the symposium by that name at the 2010 annual meeting of the International Society of Protistologists and here in contributed papers, include a range of mechanisms that combine photosynthesis with heterotrophy in a single organism. Often called mixotrophy, these multiple trophic level combinations occur across a broad range of organisms and environments. Consequently, there is great variability in the physiological abilities and relative importance of phototrophy vs. phagotrophy and/or osmotrophy in mixotrophic protists. Recently, research papers addressing ecological questions about mixotrophy in marine systems have been more numerous than those that deal with freshwater systems, a trend that is probably partly due to a realization that many harmful algal blooms in coastal marine systems involve mixotrophic protists. After an introduction to the symposium presentations, recent studies of mixotrophy in freshwater systems are reviewed to encourage continuing research on their importance to inland waters.     

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists

MOTIVATION: Prediction of the coding potential for stretches of DNA is crucial in gene calling and genome annotation, where it is used to identify potential exons and to position their boundaries in conjunction with functional sites, such as splice sites and translation initiation sites. The ability to discriminate between coding and non-coding sequences relates to the structure of coding sequences, which are organized in codons, and by their biased usage. For statistical reasons, the longer the sequences, the easier it is to detect this codon bias. However, in many eukaryotic genomes, where genes harbour many introns, both introns and exons might be small and hard to distinguish based on coding potential. RESULTS: Here, we present novel approaches that specifically aim at a better detection of coding potential in short sequences. The methods use complementary sequence features, combined with identification of which features are relevant in discriminating between coding and non-coding sequences. These newly developed methods are evaluated on different species, representative of four major eukaryotic kingdoms, and extensively compared to state-of-the-art Markov models, which are often used for predicting coding potential. The main conclusions drawn from our analyses are that (1) combining complementary sequence features clearly outperforms current Markov models for coding potential prediction in short sequence fragments, (2) coding potential prediction benefits from length-specific models, and these models are not necessarily the same for different sequence lengths and (3) comparing the results across several species indicates that, although our combined method consistently performs extremely well, there are important differences across genomes. SUPPLEMENTARY DATA: http://bioinformatics.psb.ugent.be/.     

The mitochondrial genome of protists

The data on the structure and functions of the mitochondrial genomes of protists (Protozoa and unicellular red and green algae) are reviewed. It is emphasized that mitochondrial gene structure and composition, as well as organization of mitochondrial genomes in protists are more diverse than in multicellular eukaryotes. The gene content of mitochondrial genomes of protists are closer to those of plants than animals or fungi. In the protist mitochondrial DNA, both the universal (as in higher plants) and modified (as in animals and fungi) genetic codes are used. In the overwhelming majority of cases, protist mitochondrial genomes code for the major and minor rRNA components, some tRNAs, and about 30 proteins of the respiratory chain and ribosomes. Based on comparison of the mitochondrial genomes of various protists, the origin and evolution of mitochondria are briefly discussed.