Evidence for an active rare biosphere within freshwater protists community

Studies on the active rare biosphere at the RNA level are mainly focused on Bacteria and Archaea and fail to include the protists, which are involved in the main biogeochemical cycles of the earth. In this study, the richness, composition and activity of the rare protistan biosphere were determined from a temporal survey of two lakes by pyrosequencing. In these ecosystems, the always rare OTUs represented 77.2% of the total OTUs and 76.6% of the phylogenetic diversity. From the various phylogenetic indices computed, the phylogenetic units (PUs) constituted exclusively by always rare OTUs were discriminated from the other PUs. Therefore, the rare biosphere included mainly taxa that are distant from the reference databases compared to the dominant ones. In addition, the rarest OTUs represented 59.8% of the active biosphere depicted by rRNA and the activity (rRNA:rDNA ratio) increased with the rarity. The high rRNA:rDNA ratio determined in the rare fraction highlights that some protists were active at low abundances and contribute to ecosystem functioning. Interestingly, the always rare and active OTUs were characterized by seasonal changes in relation with the main environmental parameters measured. In conclusion, the rare eukaryotes represent an active, dynamic and overlooked fraction in the lacustrine ecosystems.     

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.     

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.     

Metazoan Maelstrom is an RNA-binding protein that has evolved from an ancient nuclease active in protists

Piwi-interacting RNAs (piRNAs) guide Piwi argonautes to their transposon targets for silencing. The highly conserved protein Maelstrom is linked to both piRNA biogenesis and effector roles in this pathway. One defining feature of Maelstrom is the predicted MAEL domain of unknown molecular function. Here, we present the first crystal structure of the MAEL domain from Bombyx Maelstrom, which reveals a nuclease fold. The overall architecture resembles that found in Mg²⁺- or Mn²⁺-dependent DEDD nucleases, but a clear distinguishing feature is the presence of a structural Zn²⁺ ion coordinated by the conserved ECHC residues. Strikingly, metazoan Maelstrom orthologs across the animal kingdom lack the catalytic DEDD residues, and as we show for Bombyx Maelstrom are inactive as nucleases. However, a MAEL domain-containing protein from amoeba having both sequence motifs (DEDD and ECHC) is robustly active as an exoribonuclease. Finally, we show that the MAEL domain of Bombyx Maelstrom displays a strong affinity for single-stranded RNAs. Our studies suggest that the ancient MAEL nuclease domain evolved to function as an RNA-binding module in metazoan Maelstrom.     

Cadmium detoxification in protists

Studies on cadmium (Cd) detoxification mechanisms mostly concern multicellular organisms, while information on eukaryotic unicellular organisms such as protists is very scanty. This study focuses on these organisms, and deals with the response of some species of ciliates to a non-essential metal like Cd. The effect of accumulation and tolerance are reported for Tetrahymena pyriformis T. pigmentosa and T. thermophila, and for three species of Hypotrichida. Cd is bound to both particulate and soluble fractions. These two compartments, which play an important role in intracellular metal homeostasis, are different in the species considered. In Hypotrichida, the particulate compartment binds Cd very promptly, while it is still present often three days of treatment in the soluble fraction of Tetrahymena. Two Cd-Zn binding isothioneins were isolated from the soluble fraction of T. pyriformis and T. pigmentosa. The primary structure revealed that the equivalent proteins from the two species have identical sequences and that the two isoforms differ only in the presence or absence of a lysine residue at the N-terminus. These metallothioneins are unusually long and have a unique internal homology which suggests that the proteins originate by gene duplication. The chains contain 331 cysteine residues, 16 of which are arranged in unique repeating motifs. The similarities of protist metallothioneins with other eukaryotic metallothioneins are discussed.     

Cryptic diversity in intestinal protists

In the past few years our understanding of genetic variation within and between species of intestinal parasitic protists has changed significantly. New species names have been assigned and others have been dropped in response to new data. In this review, I summarise these findings and discuss their implications for future studies. In several cases the findings suggest that caution needs to be exercised to prevent premature conclusions being reached.     

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.     

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).     

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.     

The origins of parasitism in the protists

The origins of parasitism among the protists are, like the group itself, polyphyletic. Probably the majority of present-day parasitic forms evolved from free-living ancestors which were ingested as part of the food of their hosts, though origins from ectoparasitic forms and via a phase of facultative parasitism are possibilities, particularly among the ciliated protozoa and (for ectoparasitism) the Kinetoplasta. Sporozoan parasites most probably developed via a stage which was ingested and became adapted to life in the host's gut. Further developments in parasitism involved deeper penetration into the host's tissues and the adoption of more than one host in the life cycle, thus avoiding entirely the potentially hazardous phase of existence outside the host.