Kinetoplast DNA minicircles of trypanosomatids encode for a protein product

The major constituent of the trypanosomal kinetoplast DNA network are several thousand duplex DNA minicircles whose biological function is still unknown. The coding capacity and expression of these DNA minicircles, was studied in the trypanosomatid Crithidia fasciculata. Kinetoplast DNA minicircle fragments inserted into bacterial plasmid vectors were expressed in the bacterial cell. Sera elicited in rabbits, by immunization with the translational products of kinetoplast DNA minicircles in E. coli, reacted specifically with Crithidia fasciculata cellular antigens. It is inferred that kinetoplast DNA minicircles contain long open reading frames of nucleotides which are expressed in the trypanosomatid cell.     

Cytokinesis in trypanosomatids

The process of cytokinesis, where the cytoplasm of one cell is divided to produce two daughter cells, is intricate in trypanosomatids because of the requirement to replicate and segregate a number of single copy organelles, including the nucleus, kinetoplast, Golgi apparatus, and flagellum. Identifying regulators of the three stages of cytokinesis, initiation, furrow ingression, and abscission is complicated by the fact that cell division in trypanosomatids is easily perturbed and aberrant cells are readily produced during functional characterization of gene products. In this review, we discuss direct and indirect effects on cytokinesis, using Trypanosoma brucei as a model.     

Trypanothione: A unique bis-glutathionyl derivative in trypanosomatids

Background

Trypanosomatids are early-diverging eukaryotes devoid of the major disulfide reductases – glutathione reductase and thioredoxin reductase – that control thiol-redox homeostasis in most organisms. These protozoans have evolved a unique thiol-redox system centered on trypanothione, a bis-glutathionyl conjugate of spermidine. Notably, the trypanothione system is capable to sustain several cellular functions mediated by thiol-dependent (redox) processes.

Scope of review

This review provides a summary of some historical and evolutionary aspects related to the discovery and appearance of trypanothione in trypanosomatids. It also addresses trypanothione's biosynthesis, physicochemical properties and reactivity towards biologically-relevant oxidants as well as its participation as a cofactor for metal binding. In addition, the role of the second most abundant thiol of trypanosomatids, glutathione, is revisited in light of the putative glutathione-dependent activities identified in these organisms.

Major conclusions

Based on biochemical and genome data, the occurrence of a thiol-redox system that is strictly dependent on trypanothione appears to be a feature unique to the order Kinetoplastida. The properties of trypanothione, a dithiol, are the basis for its unique reactivity towards a wide diversity of oxidized and/or electrophilic moieties in proteins and low molecular weight compounds from endogenous or exogenous sources. Novel functions have emerged for trypanothione as a potential cofactor in iron metabolism.

General significance

The minimalist thiol-redox system, developed by trypanosomatids, is an example of metabolic fitness driven by the remarkable physicochemical properties of a glutathione derivative. From a pharmacological point of view, such specialization is the Achilles' heel of these ancient and deadly parasites. This article is part of a Special Issue entitled Cellular functions of glutathione.     

Polyamines in trypanosomatids.

Polyamines were determined by n-butanol extraction and thin-layer chromatography in four trypanosomatids: Trypanosoma brucei (rat infection) and cultures of Crithidia fasciculata, Leptomonas sp., and Trypanosoma mega. All had putrescine and spermidine but no detectable spermine. Putrescine and spermidine levels were quantitated for extracts of leptomonas during the normal growth cycle. Spermidine values peaked 18 h before peak cell populations. Spermidine-putrescine ratios for all organisms were related to the presumed phylogeny of the group.     

A theoretical study of acriflavin-DNA binding

A theoretical study of binding behaviour of acriflavin, a well-known mutagen, with DNA base pairs such as AT, GC, TA and CG has been performed using CNDO/2 method to compute net atomic charges and dipoles located at various centres in acriflavine as well as base pairs. Acriflavine-DNA base pair interactions have been evaluated using second order perturbation method with multicentered multipole approximation. Only minimum energy configurations have been reported. Results have been discussed with a view to obtain a comparative behaviour of other similar dyes like proflavine and acridine orange.     

A comparative study of the purine- and pyrimidine-metabolising enzymes of a range of trypanosomatids

A range of trypanosomatids (amastigotes and cultured promastigotes of Leishmania mexicana mexicana, cultured promastigotes of L. m. amazonensis, L. donovani and L. tarentolae, culture forms of Crithidia fasciculata, Herpetomonas muscarum muscarum and H. m. ingenoplastis and procyclic trypomastigotes of Trypanosoma brucei brucei) have been surveyed for the presence of purine- and pyrimidine-metabolising enzymes. Several common features were observed, including the presence of nucleosidases, catabolic phosphorylases, phosphoribosyltransferases, kinases and cytidine deaminase and the apparent absence of AMP deaminase, anabolic purine phosphorylase and cytosine deaminase. Significant differences between species were discovered, notably in adenine and adenosine metabolism. Nucleoside phosphotransferase active on inosine was detected in insect trypanosomatids but not in L. m. mexicana.     

Galactofuranose-containing glycoconjugates in trypanosomatids

Galactofuranose has been characterized in glycoinositolphospholipid(GIPL) anchor-like structures having a glycerolipid or a ceramide,as in lipopeptidophosphoglycan (LPPG) of Trypanosoma cruzi,in the oligosaccharide core of lipophosphoglycan (LPG) of Leishmaniaspecies, and also modifying high-mannose chains of trypanosomatidglycoproteins. Galactofuranose is usually present linked ß1     

A theoretical study of glucosamine synthase

Glucosamine synthase transfers the -amino group of glutamine to fructose, producing 1-glucosamine which is the key constituent of bacterial and fungal cell walls. In this study, model calculations were performed on substrate binding to the enzyme active site. Two models of the active site of glucosamine synthase were proposed, which assume two different sequences of aminoacids, Cys-Gly-Ile and Cys-Ala-Cys, the first one being the N-terminal sequence of the Escherichia coli enzyme. Several initial geometries were assumed for these tripeptides, the energy was then optimized by means of molecular mechanics. It has been found that the structure which is both energy optimal and satisfies the assumed cysteine sulphur arrangement consists of combinations of C ₇ ^eq and C ₇ ^ax conformations of single residues. Molecular mechanics calculations were then performed on glutamine and d-fructose-6-phosphate, which are the substrates of the enzymatic satalysis, and on their complex with the enzyme glutamine-binding site. The spatial configuration of the compounds under study, which is optimal as far as the reaction path is concerned, also turned out to be an energy minimum.     

A theoretical study of glucosamine synthase

Continuing our theoretical studies of glucosamine synthase catalysis, we have carried out MNDO and ab initio calculations of the first stage of the reaction, which involves the attack of a cysteine thiol group from the enzyme active site on the side chain carboxyamide group of glutamine, producing ammonia and thioester. The reactants were modelled by methyl mercaptate and acetamide, respectively. For two considered mechanisms of the reaction the energy surfaces were evaluated. Mechanism I, proposed by Chmara et al. (1985) involves the nucleophilic attack of a deprotonated thiol group on the carbonyl carbon atom. Mechanism II, postulated in our previous work (Tempczyk et al. 1989), assumes the concerted binding of the mercaptate sulphur to the carbonyl carbon and the sulfhydryl hydrogen to the amide nitrogen with simultaneous breaking of the S-H bond. The energy surface of mechanism I shows no minimum on the approach of the mercaptide anion towards the carbonyl carbon, which is also consistent with ab initio calculations in a 4-31 G basis set. Therefore, mechanism I seems to be unlikely. The same analysis of mechanism II shows that it leads to the desired products: methyl thioacetate and ammonia. The presence of a sulfhydryl hydrogen causes apparent pyramidicity of the amido nitrogen and lengthening of the C-N bond in the transition state, making conditions for the release of the ammonia molecule. The MNDO calculated energy barrier of the reaction is 50.1 kcal/mol and the approximate 4-31 G ab initio barrier (at the MNDO geometries of the substrate complex and the transition state) is 63 kcal/mol. The biggest energy contribution to the barrier comes from the breaking of the S-H bond, which also causes a large charge separation in the transition state. The latter affect may result in the stabilisation of the transition state in a real enzymatic environment when compared to the gas phase, e.g. by the interaction of the reacting center with a pair of oppositely charged amino acid side chains such as lysinium and glutamate (aspartate), which are present in the enzyme studied. To estimate the magnitude of this effect, molecular mechanics calculations were carried out on the reaction center at the transition state in our proposed model of the enzymatic active site. The site was supplemented by ammonium and acetate ion, which were to mimic the lysinium and glutamate/aspartate side chains. A transition state stabilization energy of 20 kcal/mol was obtained and this lowers the energy barrier to about 30 kcal/mol. This value is within the thermal energy range of an average protein and indicates that our mechanism is a possible route of glucosamine synthase catalysis. Offprint requests to: E. Borowski     

Replication of DNA minicircles in kinetoplasts isolated from Crithidia fasciculata: structure of nascent minicircles.

We have previously described an isolated kinetoplast system from Crithidia fasciculata capable of ATP-dependent replication of kinetoplast DNA minicircles (L. Birkenmeyer and D.S. Ray, J. Biol. Chem. 261: 2362-2368, 1986). We present here the identification of two new minicircle species observed in short pulse-labeling experiments in this system. The earliest labeled minicircle species (component A) contains both nascent H and L strands and is heterogeneous in sedimentation and electrophoretic migration. Component A has characteristics consistent with a Cairns-type structure in which the L strand is the leading strand and the H strand is the lagging strand. The other new species (component B) has a nascent 2.5-kilobase linear L strand with a single discontinuity that mapped to either of two alternative origins located 180 degrees apart on the minicircle map. Component B could be repaired to a covalently closed form by Escherichia coli polymerase I and T4 ligase but not by T4 polymerase and T4 ligase. Even though component B has a single gap in one strand, it had an electrophoretic mobility on an agarose gel (minus ethidium bromide) similar to that of a supercoiled circle with three supertwists. Treatment of component B with topoisomerase II converted it to a form that comigrated with a nicked open circular form (replicative form II). These results indicate that component B is a knotted topoisomer of a kinetoplast DNA minicircle with a single gap in the L strand.     

Concepts of species in trypanosomatids

This paper is a commentary on "Species concepts for trypanosomes: from morphological to molecular definitions?" by Wendy Gibson published in this journal [1]. Taxonomy has been traditionally based on expert opinion which is influenced among other factors by the philosophical and educational background of the expert concerned. This has resulted in widely different criteria for species among the trypanosomatids when compared to the actual genetic diversity involved. Gibson's paper presents an example of this within the trypanosome sub-genera. Although attempts have been made to put taxonomy on a more objective basis expert opinion still appears to dominate in the actual classifications in use.     

A theoretical study of polymorphism in VQIVYK fibrils

The VQIVYK fragment from the Tau protein, also known as PHF6, is essential for aggregation of Tau into neurofibrillary lesions associated with neurodegenerative diseases. VQIVYK itself forms amyloid fibrils composed of paired β-sheets. Therefore, the full Tau protein and VQIVYK fibrils have been intensively investigated. A central issue in these studies is polymorphism, the ability of a protein to fold into more than one structure. Using all-atom molecular simulations, we generate five stable polymorphs of VQIVYK fibrils, establish their relative free energy with umbrella sampling methods, and identify the side chain interactions that provide stability. The two most stable polymorphs, which have nearly equal free energy, are formed by interdigitation of the mostly hydrophobic VIY “face” sides of the β-sheets. Another stable polymorph is formed by interdigitation of the QVK “back” sides. When we turn to examine structures from cryo-electron microscopy experiments on Tau filaments taken from diseased patients or generated in vitro, we find that the pattern of side chain interactions found in the two most stable face-to-face as well as the back-to-back polymorphs are recapitulated in amyloid structures of the full protein. Thus, our studies suggest that the interactions stabilizing PHF6 fibrils explain the amyloidogenicity of the VQIVYK motif within the full Tau protein and provide justification for the use of VQIVYK fibrils as a test bed for the design of molecules that identify or inhibit amyloid structures.     

Genetic segregation of random amplified polymorphic DNA in diploid cultivated alfalfa.

Polymerase chain reaction was used, with single 10-mer primers of arbitrary sequence, to amplify random regions of genomic DNA from a diploid cultivated alfalfa backcross population. Segregation of the random amplified polymorphic DNA (RAPD) fragments was analysed to determine if RAPD markers are suitable for use as genetic markers. Of the 19 primers tested, 13 amplified a total of 37 polymorphic fragments, of which 28 (76%) segregated as dominant Mendelian traits. RAPD markers appear useful for the rapid development of genetic information in species like alfalfa where little information currently exists or is difficult to obtain.     

Cyclic AMP signaling in trypanosomatids

Curative interference with signal transduction pathways is a spectacularly successful concept in many domains of modern pharmacology; indeed, the 'wonder drug' Viagra is but a humble inhibitor of a cyclic GMP (cGMP)-specific phosphodiesterase and, thus, interferes with cGMP-signaling in a strategic organ. In fact, about half of the 100 most successful drugs currently on the market act through modulating cellular signal transduction. Despite these encouraging findings, signal transduction pathways as potential drug targets in trypanosomatids have remained largely unexplored. However, what little is known indicates that adenylyl cyclases of trypanosomatids, and probably other enzymes of the cyclic nucleotide signaling pathways, are significantly different from their mammalian counterparts. Here, Christina Naula and Thomas Seebeck summarize what is known about cAMP signal transduction in trypanosomatids.     

Programmed cell death in trypanosomatids

It has generally been assumed that apoptosis and other forms of programmed cell death evolved to regulate growth and development in multicellular organisms. However, recent work has shown that some parasitic protozoa have evolved a cell suicide pathway analogous to the process described as apoptosis in metazoa. In this review, Susan Welburn, Marcello Barcinski and Gwyn Williams discuss the possible implications of a cell suicide pathway in the vector-borne Trypanosomatids.