New tyrosinases with putative action against contaminants of emerging concern.

Tyrosinases (EC 1.14.18.1) are type-3 copper metalloenzymes with strong oxidative capacities and low allosteric selectivity to phenolic and non-phenolic aromatic compounds, which have been used as biosensors and biocatalysts to mitigate the impacts of environmental contaminants over aquatic ecosystems. However, the widespread use of these polyphenol oxidases is limited by elevated production costs and restricted knowledge on their spectrum of action. Here, six tyrosinase homologs were identified and characterized from the genomes of four widespread freshwater ciliates using bioinformatics. Next, we performed a virtual screening to calculate binding energies between 3D models of these homologs and ~ 1000 contaminants of emerging concern (CECs), as an indirect approach to identify likely and unlikely targets for tyrosinases. Many fine chemicals, pharmaceuticals, personal care products, illicit drugs, natural toxins, and pesticides exhibited strong binding energies to these new tyrosinases, suggesting the spectrum of targets of these enzymes might be considerably broader than previously thought. Many ciliates, including those carrying tyrosinase genes, are fast-growing unicellular microeukaryotes that can be efficiently cultured, at large scales, under in vitro conditions, suggesting these organisms should be regarded as potential low-cost sources of new environmental biotechnological molecules.

The Sanguicolous Apostome Metacollinia luciensis Jankowski 1980 (Colliniidae, Apostomatia, Ciliophora) Is Not Closely Related to Other Sanguicolous Apostomes.

The apostome family Colliniidae includes species that are adapted to the hemocoel/blood of various invertebrates, particularly crustaceans. To explore the phylogeny of these sanguicolous apostomes, Metacollinia luciensis was collected in August 2015 at Roscoff from the amphipod host, Orchestia gammarellus. Ciliates were Protargol stained and DNA was extracted. The small subunit rRNA (SSUrRNA) and cytochrome c oxidase subunit I (cox1) genes were amplified. Molecular phylogenetic analyses of the SSUrRNA genes unambiguously grouped M. luciensis with other apostomes with robust bootstrap support, but separated it distinctly from the pseudocolliniid clade. While there are only cox1 sequences for a subset of these apostomes, M. luciensis was also distant from the pseudocolliniids and separated from them by species of the exuviotrophic apostome Hyalophysa. These results confirm the distinctness of the families Colliniidae and Pseudocolliniidae.

Specific inhibitors of lysozyme and peptidases inhibit the growth of the rumen protozoan Entodinium caudatum without decreasing feed digestion or fermentation in vitro.

AIMS: Experiments were designed to determine the effects of different chemical inhibitors of lysozyme and peptidases on rumen protozoa and the associated prokaryotes, and in vitro fermentation using Entodinium caudatum as a model protozoan species. METHODS AND RESULTS: Imidazole (a lysozyme inhibitor), phenylmethylsulphonyl fluoride (PMSF, a serine peptidase inhibitor) and iodoacetamide (IOD, a cysteine peptidase inhibitor) were evaluated in vitro both individually and in two- and three-way combinations using E. caudatum monocultures with respect to their ability to inhibit the protozoan and their effect on feed digestion, fermentation and the microbiota. All the three inhibitors, both individually and in combination, decreased E. caudatum counts (P < 0·001), and IOD and its combinations with the other inhibitors significantly (P < 0·01) decreased ammonia concentration, with the two- and three-way combinations showing additive effective. Feed digestion was not affected, but fermentation and microbial diversity were affected mostly by PMSF, IOD and their combinatorial treatments potentially due to the overgrowth of Streptococcus luteciae accompanying with the disappearance of host ciliates. CONCLUSIONS: Entodinium caudatum depends on lysozyme and peptidase for digestion and utilization of the engulfed microbes and specific inhibition of these enzymes can inhibition E. caudatum without adversely affecting feed digestion or fermentation even though they changed the microbiota composition in the cultures. SIGNIFICANCE AND IMPACT OF THE STUDY: The peptidase inhibitors may have the potential to be used in controlling rumen protozoa to improve ruminal nitrogen utilization efficiency.

Short communication: Gelatinization and enzymatic hydrolysis characteristics relevant to digestion and analysis of glycogen granules isolated from ruminal protozoa.

Glycogen is an α-glucan produced by rumen microbes from various feed carbohydrates. It may be digested ruminally or intestinally to provide nutrients. The physicochemical and enzymatic hydrolysis characteristics of microbial glycogen have not been described in detail, but do influence its conversion to absorbable nutrients in vivo, its nutritional comparability with plant starch sources, and its accurate analysis in vitro. The objectives of this study were to determine presence or absence of a gelatinization response and to describe enzymatic digestion characteristics of glycogen granules isolated from ruminal protozoa obtained from lactating dairy cows. Protozoal glycogen granules were determined to be 98.3% α-glucan. Granules displayed gelatinization, the breaking of hydrogen bonds between molecules or branches, at 65°C compared with purified wheat and corn starches, which initiated gelatinization at 50 and 65°C, respectively. Digestion of ungelatinized samples with amyloglucosidase for 2 h at 39°C showed approximately 3-fold greater hydrolysis to glucose for protozoal glycogen (25.2% of dry matter; DM) than for wheat (9.9% of DM) or corn (8.2% of DM) starches. Based on enzymatic digestion results, protozoal glycogen may be more readily digested than intact corn or wheat starches and should be gelatinized or the hydrogen bonds otherwise disrupted to allow more complete recovery in enzymatic analysis.

A single amino acid residue regulates the substrate affinity and specificity of indoleamine 2,3-dioxygenase.

Indoleamine 2,3-dioxygenase (IDO) is a heme-containing enzyme that catalyses the oxidative cleavage of L-Trp. The ciliate Blepharisma stoltei has four IDO genes (IDO-I, -II, -III and -IV), which seem to have evolved via two sequential gene duplication events. Each IDO enzyme has a distinct enzymatic property, where IDO-III has a high affinity for L-Trp, whereas the affinity of the other three isoforms for L-Trp is low. IDO-I also exhibits a significant catalytic activity with another indole compound: 5-hydroxy-l-tryptophan (5-HTP). IDO-I is considered to be an enzyme that is involved in the biosynthesis of the 5-HTP-derived mating pheromone, gamone 2. By analysing a series of chimeric enzymes based on extant and predicted ancestral enzymes, we identified Asn131 in IDO-I and Glu132 in IDO-III as the key residues responsible for their high affinity for each specific substrate. These two residues were aligned in an identical position as the substrate-determining residue (SDR). Thus, the substrate affinity and specificity are regulated mostly by a single amino acid residue in the Blepharisma IDO-I and IDO-III enzymes.

Phylogenomic analysis of integral diiron membrane histidine motif-containing enzymes in ciliates provides insights into their function and evolutionary relationships.

The Integral Membrane Histidine Motif-containing Enzymes (IMHME) are a class of binuclear non-heme iron proteins widely distributed among prokaryotes and eukaryotes. They are characterized by a conserved tripartite motif consisting of eight to ten histidine residues. Their known function is the activation of the dioxygen moiety to serve as efficient catalysts for reactions of hydroxylation, desaturation or reduction. To date most studies on IMHME were carried out in metazoan, phototrophic or parasitic organisms, whereas genome-wide analysis in heterotrophic free living protozoa, such as the Ciliophora phylum, has not been undertaken. In the seven fully sequenced genomes available we retrieved 118 putative sequences of the IMHME type, albeit with large differences in number among the ciliates: 11 sequences in Euplotes octocarinatus, 7 in Ichthyophthirius multifiliis, 13 in Oxytricha trifallax, 18 in Stylonychia lemnae, 25 in Tetrahymena thermophila, 31 in Paramecium tetraurelia and 13 in Pseudocohnilembus persalinus. The pool of putative sequences was classified in 16 orthologous groups from which 11 were related to fatty acid desaturase (FAD) and 5 to the fatty acid hydroxylase (FAH) superfamilies. Noteworthy, a large diversity on the number and type of FAD / FAH proteins were found among the ciliates, a feature that, in principle, may be attributed to peculiarities of the evolutionary process, such as gene expansion and reduction, but also to horizontal gene transfer, as we demonstrate in this work. We identified twelve putative enzymatic activities, from which four were newly assigned activities: sphingolipid Δ4-desaturase, ω3/Δ15 fatty acid desaturase, a large group of alkane 1-monooxygenases, and acylamide-delta-3(E)-desaturase, although unequivocal allocation would require additional experiments. We also combined the phylogenetics analysis with lipids analysis, thereby allowing the detection of two enzymatic activities not previously reported: a C-5 sterol desaturase in P. tetraurelia and a delta-9 fatty acid desaturase in Cohnilembus reniformis. The analysis revealed a significant lower number of FAD's sequences in the spirotrichea ciliates than in the oligohymenophorea, emphasizing the importance of fatty acids trophic transfer among aquatic organisms as a source of variation in metabolic activity, individual and population growth rates, and reproduction.

Evolutionary history of the chitin synthases of eukaryotes.

Chitin synthases are widespread among eukaryotes and known to have a complex evolutionary history in some of the groups. We have reconstructed the chitin synthase phylogeny using the most taxonomically comprehensive dataset currently available and have shown the presence of independently formed paralogous groups in oomycetes, ciliates, fungi, and all diatoms except raphid pennates. There were also two cases of horizontal gene transfer (HGT): transfer from fungus to early diatoms gave rise to diatom paralogous group, while transfer from raphid pennate diatom to Acantamoeba ancestor is, to our knowledge, restricted to a single gene in amoeba. Early evolution of chitin synthases is heavily obscured by paralogy, and further sequencing effort is necessary.

Enzymes Involved in Pyrophosphate and Calcium Metabolism as Targets for Anti-scuticociliate Chemotherapy.

Inorganic pyrophosphate (PPi) is a key metabolite in cellular bioenergetics under chronic stress conditions in prokaryotes, protists and plants. Inorganic pyrophosphatases (PPases) are essential enzymes controlling the cellular concentration of PPi and mediating intracellular pH and Ca(2+) homeostasis. We report the effects of the antimalarial drugs chloroquine (CQ) and artemisinin (ART) on the in vitro growth of Philasterides dicentrarchi, a scuticociliate parasite of turbot; we also evaluated the action of these drugs on soluble (sPPases) and vacuolar H+-PPases (H+-PPases). CQ and ART inhibited the in vitro growth of ciliates with IC50 values of respectively 74 ± 9 µM and 80 ± 8 µM. CQ inhibits the H+ translocation (with an IC50 of 13.4 ± 0.2 µM), while ART increased translocation of H+ and acidification. However, both drugs caused a decrease in gene expression of H+-PPases. CQ significantly inhibited the enzymatic activity of sPPases, decreasing the consumption of intracellular PPi. ART inhibited intracellular accumulation of Ca(2+) induced by ATP, indicating an effect on the Ca(2+) -ATPase. The results suggest that CQ and ART deregulate enzymes associated with PPi and Ca(2+) metabolism, altering the intracellular pH homeostasis vital for parasite survival and providing a target for the development of new drugs against scuticociliatosis.

Biogenesis of telomerase ribonucleoproteins.

Telomerase adds simple-sequence repeats to the ends of linear chromosomes to counteract the loss of end sequence inherent in conventional DNA replication. Catalytic activity for repeat synthesis results from the cooperation of the telomerase reverse transcriptase protein (TERT) and the template-containing telomerase RNA (TER). TERs vary widely in sequence and structure but share a set of motifs required for TERT binding and catalytic activity. Species-specific TER motifs play essential roles in RNP biogenesis, stability, trafficking, and regulation. Remarkably, the biogenesis pathways that generate mature TER differ across eukaryotes. Furthermore, the cellular processes that direct the assembly of a biologically functional telomerase holoenzyme and its engagement with telomeres are evolutionarily varied and regulated. This review highlights the diversity of strategies for telomerase RNP biogenesis, RNP assembly, and telomere recruitment among ciliates, yeasts, and vertebrates and suggests common themes in these pathways and their regulation.

Natural strategies for the spatial optimization of metabolism in synthetic biology.

Metabolism is a highly interconnected web of chemical reactions that power life. Though the stoichiometry of metabolism is well understood, the multidimensional aspects of metabolic regulation in time and space remain difficult to define, model and engineer. Complex metabolic conversions can be performed by multiple species working cooperatively and exchanging metabolites via structured networks of organisms and resources. Within cells, metabolism is spatially regulated via sequestration in subcellular compartments and through the assembly of multienzyme complexes. Metabolic engineering and synthetic biology have had success in engineering metabolism in the first and second dimensions, designing linear metabolic pathways and channeling metabolic flux. More recently, engineering of the third dimension has improved output of engineered pathways through isolation and organization of multicell and multienzyme complexes. This review highlights natural and synthetic examples of three-dimensional metabolism both inter- and intracellularly, offering tools and perspectives for biological design.

Untangling the glutamate dehydrogenase allosteric nightmare.

Glutamate dehydrogenase (GDH) is found in all living organisms, but only animal GDH is regulated by a large repertoire of metabolites. More than 50 years of research to better understand the mechanism and role of this allosteric network has been frustrated by its sheer complexity. However, recent studies have begun to tease out how and why this complex behavior evolved. Much of GDH regulation probably occurs by controlling a complex ballet of motion necessary for catalytic turnover and has evolved concomitantly with a long antenna-like feature of the structure of the enzyme. Ciliates, the 'missing link' in GDH evolution, might have created the antenna to accommodate changing organelle functions and was refined in humans to, at least in part, link amino acid catabolism with insulin secretion.

EF-1α and mitochondrial ATP synthase ß chain: alteration of their expression in encystment-induced Colpoda cucullus.

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the total proteins contained in encystment-induced Colpoda cucullus showed that a 50-kDa protein (p50) disappeared, whereas the expression of a 49-kDa protein (p49) was enhanced in early phase of morphogenetic transformation into the resting cyst (i.e. 2-5 h after the onset of encystment induction). Puromycin or actinomycin D inhibited the alteration in the expression of p50 and p49 by the induction of encystment. These results suggest that the encystment-specific alteration in expression of these proteins is performed by a transcriptional regulation. Liquid chromatography tandem mass spectrometry analysis revealed that p50 is mitochondrial ATP synthase ß chains, and that p49 is elongation factor 1α.

[The study of molecular mechanisms of action of natural amino acids and serotonin on adenylyl and guanylyl cyclases of the ciliates].

It has been previously shown that some amino acids and their derivatives are capable of regulating the activity of adenylyl cyclase (AC) and guanylate cyclase (GC) in free-living ciliates Dileptus anser and Tetrahymena. The aim of this work was to study the molecular mechanisms of action of methionine, tyrosine, alanine and neurohormone serotonin on the activity of enzymes-cyclases and the identification of their specific receptors in D. anser and T. pyriformis. Methionine and serotonin significantly increased the basal AC activity in both ciliates, and the AC effect of serotonin in T. pyriformis was carried out with the participation of Ca2+-dependent form of AC and heterotrimetic G proteins. AC stimulating effect of tyrosine and alanine was expressed weakly and only detected in D. anser. Serotonin is both ciliates and alanine in D. anser stimulated GC activity, whereas methionine and tyrosine had no effect on GC. Methionine and serotonin bind to surface receptors of the ciliates with high affinity. K(D) for [methyl-3H] methionine binding to D. anser and T. pyriformis were 7.5 and 35.6 nM, and for [3H] serotonin binding were 2.7 and 4.7 nM, respectively. Alanine and tyrosine bind to the ciliates with low affinity. Thus, ciliates D. anser and T. pyriformis have chemosignaling systems regulated by amino acids and their derivatives and including the enzymes with cyclase activity. There is an assumption that these systems are similar to hormonal signaling systems of higher eukaryotes and are their predecessors.

[Effect of natural amino acids and sugars on cyclase activities in infusoria Tetrahymena pyriformis and Dileptus anser].

Natural amino acids and sugars in intracellular eukaryotes are known to regulate adenylyl cyclase (AC) and guanylyl cyclase (GC) systems that control the most important cell processes. The goal of the present work consisted in study of effects of natural amino acids and sugars and some of their derivatives on AC and GC activities of infusoria Tetrahymena pyriformis and Dileptus anser. Methionine, arginine, lysine, and tryptamine stimulated basic AC activity of T. pyriformis, whereas alanine, thyrosine, and cysteine decreased it. Methionine, glycine, alanine, thyrosine, arginine, and to the lesser degree tryptamine and histidine stimulated AC of D. anser. The GC activity of T. pyriformis are increased in the presence of tryptamine, tryptophane, histidine, arginine, and lysine, whereas glycine and aspartic acid, on the contrary, decreased it. Tryptamine, tryptophan, leucine, glutamic acid, serine, histidine, and alanine stimulated the GC activity of D. anser. Glucose, fructose, and sucrose stimulated the basal AC activity of both infusorians and GC of T. pyriformis, with glucose and sucrose increasing AC of T. pyriformis twice, while that of D. anser 4.5 times. Lactose stimulated AC and GC of T. pyriformis and was inefficient with respect to the D. anser cyclases, whereas mannose and galactose did not affect the enzyme activities in both infusorians. The study of the chemotactic response of infusorians to amino acids and sugars indicates that involved in realization of this response can be signaling pathways both dependent on and independent of cyclic nucleotides. Thus, it has been established for the first time that several amino acids and sugars affect functional activity of enzymes with cyclase activity of the infusorians T. pyriformis and D. anser. This confirms the hypothesis that at early stages of evolution the large spectrum of comparatively simple natural molecules has a hormone-like action.

[Regulation by cyclic adenosine monophosphate of functional activity of the adenylyl cyclase system of the infusorian Dileptus anser].

In some unicellular eukaryotes, cAMP performs functions not only of the second messenger, but also of hormone, the primary messenger. We have found that cAMP binds to surface receptors of the free-living infusorian Dileptus anser and stimulates activity of the adenylyl cyclase signaling system (AC-system) including heterotrimeric G-proteins and enzyme adenylyl cyclase (AC). The binding of cAMP to receptor is performed with a high affinity (K(D), 27 nM) and is highly specific, as cGMP and adenosine do not produce a marked effect on it. The infusorian cAMP-receptors have been shown to be coupled to G-proteins, which is indicated by a decrease of their affinity to the ligand in the presence of GTP, stimulation of the GTP-binding of G-proteins with the cyclic nucleotide, and block of the cAMP regulatory effects with suramin, an inhibitor of heterotrimeric G-proteins. cAMP stimulates dose-dependently the AC activity, its effect remaining virtually unchanged in the presence of cGMP, AMP, GMP, and adenosine. N6,O2-dibutyryl-cAMP, a non-hydrolyzed cAMP analog, only at comparatively high concentrations competes with cAMP for binding sites and decreases the cAMP stimulating effects on the AC activity and GTP binding. Thus, we have shown for the first time that the AC system of the infusorians D. anser is stimulated with the extracellular cAMP that in this case functions as the external signal regulates activity of extracellular cAMP-dependent effector systems.

Digestion and the distribution of acid phosphatase in Blepharisma.

Suspensions of Blepharisma intermedium were fed latex particles for 5 min and then were separated from the particles by filtration. Samples were fixed at intervals after separation and incubated to demonstrate acid phosphatase activity. They were subsequently embedded and sectioned for electron microscopy. During formation of the food vacuole, the vacuolar membrane is acid phosphatase-negative. Within 5 min, dumbbell-shaped acid phosphatase-positive bodies, possibly derived from the the acid phosphatase-positive Golgi apparatus, apparently fuse with the food vacuole and render it acid phosphatase-positive. A larger type of acid phosphatase-positive, vacuolated body may also fuse with the food vacuole at later stages. At about 20 min after formation, acid phosphatase-positive secondary pinocytotic vesicles pinch off from the food vacuoles and approach a separate system of membrane-bounded spaces. By 1 hr after formation, the food vacuole becomes acid phosphatase-negative, and the undigested latex particles are voided into the membrane-bounded spaces. The membrane-bounded spaces are closely associated with the food vacuole at all stages of digestion and are generally acid phosphatase-negative. Within the membrane-bounded spaces, dense, pleomorphic, granular bodies are found, in which are embedded mitochondria, paraglycogen granules, membrane-limited acid phosphatase-containing structures, and Golgi apparatuses. The granular bodies may serve as vehicles for the transport of organelles through the extensive, ramifying membrane-bounded spaces.

Functional evidence for an RNA template in telomerase.

The RNA moiety of the ribonucleoprotein enzyme telomerase from the ciliate Euplotes crassus was identified and its gene was sequenced. Functional analysis, in which oligonucleotides complementary to portions of the telomerase RNA were tested for their ability to prime telomerase in vitro, showed that the sequence 5' CAAAACCCCAAA 3' in this RNA is the template for synthesis of telomeric TTTTGGGG repeats by the Euplotes telomerase. The data provide a direct demonstration of a template function for a telomerase RNA and demarcate the outer boundaries of the telomeric template. Telomerase can now be defined as a specialized reverse transcriptase.

[Inhibition of the adenylyl cyclase signaling system by colchicine and vinblastine in ciliate Dileptus anser].

Cytoskeleton plays a key role in functioning of hormonal signaling systems in vertebrate animals. The data on the influence of cytoskeleton components, in particular the microtubules, on functional activity of chemosignaling systems of unicellular organisms are absent at the present time. The aim of this work was the study of influence of microtubule-disrupting agents, colchicine and vinblastine, on the adenylyl cyclase (AC) system of free-living ciliate Dileptus anser. The treatment of D. anser with colchicine and vinblastine (10(-5)-10(-6) M) weakly influenced basal activity of AC, but caused essential decrease or complete blocking of AC stimulation by non-hormonal (GppNHp, sodium fluoride) and hormonal (aldrenaline, serotonin, glucagon) agents. As a result of this treatment, a decrease of the basal level of GTP-binding of heterotrimeric G-proteins and inhibition of G-protein stumulation by the hormones were found. In the case of adrenaline it was that colchicine and vinblastine disturb the AC stimulation by the hormone, mediated with the G(s)-protein, but weakly influence its inhibitory AC effect, realized via the G(i)-protein. Thus, it was established for the first time that microtubules in unicellular organisms such as the ciliate D. anser are involved in regulation of functional activity of AC system, and their action is realized at the level of the G-proteins similar to the G(s)-proteins of the vertebrates.

The utilization and digestion of cellulose by the rumen ciliate Diploplastron affine.

Rumen protozoa are known to contribute to fibre digestion, but the fibrolytic enzymes of the majority of ciliate species have been poorly recognised to date. The aims of the study were, first, to determine the influence of crystalline cellulose on the survival and population density of the ciliate Diploplastron affine when cultured in vitro, and second to identify and characterise the protozoal enzymes catalysing the hydrolysis of cellulose. It was found that crystalline cellulose, when added to a culture medium, increased the number of protozoa maintained in vitro. We observed that the bacteria-free ciliates fermented microcrystalline cellulose and produced 43.3 nmol volatile fatty acids/protozoon/h. A cell extract prepared from the bacteria-free ciliates degraded crystalline cellulose in the rate of 11.5 nmol released glucose/mg protein/min, whereas the degradation rates of carboxymethyl-cellulose (CMC), avicel and cellobiose were 343, 6.8 and 145 nmol released glucose/mg protein/min respectively. Two distinct peaks in the activity of relevant enzymes were identified following ion exchange chromatography of the protozoal cell extract and the presence of two different CMC-ases were confirmed by zymographic studies. CMC was mainly degraded to mono- and disaccharides but that some other oligosaccharides were also present. Cellobiose was the only product of avicel digestion.

Relationship between two tandemly arranged and light-induced glutathione S-transferase genes from the ciliated protozoa Blepharisma japonicum.

Recently we reported a light-induced cDNA encoding glutathione S-transferase (GST) from the ciliated protozoa Blepharisma japonicum, which possessed photosensitive pigments. In this study, a novel cDNA encoding GST was further isolated, and the two GSTs (BjGST1 and BjGST2) showed high sequence identity of 86%. Phylogenetic trees indicated that the BjGSTs were distantly related to known classes of GSTs, and they could form a protozoa-specific class. The recombinant proteins also existed as homo- or heterodimers that exhibited different enzyme activities, appreciating the functional differentiation. Furthermore, the transcription levels of BjGST genes were coordinately regulated in response to light stimulation. In addition, the genomic structure analysis revealed that the two genes were tandemly arranged through an approximately 500-bp spacer region of unusual DNA structure containing cis-acting elements related to oxidative stress response. These results demonstrate that the two BjGSTs are expressed simultaneously and act cooperatively against photooxidative stress.