Dithiol Proteins as Guardians of the Intracellular Redox Milieu in Parasites: Old and New Drug Targets in Trypanosomes and Malaria-Causing Plasmodia

Parasitic diseases such as sleeping sickness, Chagas' heart disease, and malaria are major health problems in poverty-stricken areas. Antiparasitic drugs that are not only active but also affordable and readily available are urgently required. One approach to finding new drugs and rediscovering old ones is based on enzyme inhibitors that paralyze antioxidant systems in the pathogens. These antioxidant ensembles are essential to the parasites as they are attacked in the human host by strong oxidants such as peroxynitrite, hypochlorite, and H2O2. The pathogen-protecting system consists of some 20 thiol and dithiol proteins, which buffer the intraparasitic redox milieu at a potential of -250 mV. In trypanosomes and leishmania the network is centered around the unique dithiol trypanothione (N1,N8-bis(glutathionyl)spermidine). In contrast, malaria parasites have a more conservative dual antioxidative system based on glutathione and thioredoxin. Inhibitors of antioxidant enzymes such as trypanothione reductase are, indeed, parasiticidal but they can also delay or prevent resistance against a number of other antiparasitic drugs.

Rapid isolation of DNA from trypanosomatid protozoa using a simple 'mini-prep' procedure

Although several methods for isolating genomic DNA from trypanosomatid protozoa exist, all are time-consuming and cumbersome. Faster, simpler and efficient protocols for preparation of DNA from these protozoa are needed to ease the screening of mutants and transfectants. We describe the use of a bacterial lysis method to isolate chromosomal DNA from a wide range of trypanosomatids. The method is based on the finding reported by He et al., who noticed that phenol/chloroform treatment of Escherichia coli cells in the presence of LiCl and Triton X-100 solubilizes plasmid DNA, while precipitating unwanted chromosomal DNA and denatured cellular proteins. In applying this lysis method to the isolation of episomal DNA from transfected trypanosomatids, we found that, unlike bacterial genomic DNA, chromosomal DNA of trypanosomatids was soluble in the phenol/chloroform/Triton/LiCl mixture. This observation prompted us to use the bacterial lysis method as a routine protocol for extraction of DNA from trypanosomatids.

Detection and identification of Trypanosoma of African livestock through a single PCR based on internal transcribed spacer 1 of rDNA

Primers hybridising with the rDNA cistron have previously been evaluated for PCR diagnosis specific for kinetoplastids, and shown to detect and differentiate the Trypanosoma brucei complex and Trypanosoma cruzi. Kin1 and Kin2 primers, amplifying internal transcribed spacer 1, were subsequently evaluated for the diagnosis of African livestock trypanosomosis. Based on the size of the PCR products obtained, Kin primers allowed detection and identification of three Trypanosoma congolense types (savannah, forest and Kenya Coast), with distinction among themselves and from the subgenus Trypanozoon (T. brucei spp., Trypanosoma evansi and Trypanosoma equiperdum), Trypanosoma vivax, Trypanosoma simiae and Trypanosoma theileri. These primers were shown to be suitable for the sensitive and type-specific diagnosis of African livestock trypanosome isolates through a single PCR even in the case of multi-taxa samples. With field samples (buffy-coat from cattle blood) sensitivity was close to the sensitivity observed in single reactions with the classical specific primers for the Trypanozoon subgenus and T. congolense-type savannah, but was lower for detection of T. vivax. Additional reaction, improvement of DNA preparation, and/or new primers design are necessary to improve the sensitivity for detection of T. vivax in field samples. However, these primers are suitable for isolate typing through a single PCR.

Structure and mechanism of RNA ligase

T4 RNA ligase 2 (Rnl2) exemplifies an RNA ligase family that includes the RNA editing ligases (RELs) of Trypanosoma and Leishmania. The Rnl2/REL enzymes are defined by essential signature residues and a unique C-terminal domain, which we show is essential for sealing of 3'-OH and 5'-PO4 RNA ends by Rnl2, but not for ligase adenylation or phosphodiester bond formation at a preadenylated AppRNA end. The N-terminal segment Rnl2(1-249) of the 334 aa Rnl2 protein comprises an autonomous adenylyltransferase/AppRNA ligase domain. We report the 1.9 A crystal structure of the ligase domain with AMP bound at the active site, which reveals a shared fold, catalytic mechanism, and evolutionary history for RNA ligases, DNA ligases, and mRNA capping enzymes.

A novel and accurate diagnostic test for human African trypanosomiasis

INTRODUCTION

Human African trypanosomiasis (sleeping sickness) affects up to half a million people every year in sub-Saharan Africa. Because current diagnostic tests for the disease have low accuracy, we sought to develop a novel test that can diagnose human African trypanosomiasis with high sensitivity and specificity.

METHODS

We applied serum samples from 85 patients with African trypanosomiasis and 146 control patients who had other parasitic and non-parasitic infections to a weak cation exchange chip, and analysed with surface-enhanced laser desorption-ionisation time-of-flight mass spectrometry. Mass spectra were then assessed with three powerful data-mining tools: a tree classifier, a neural network, and a genetic algorithm.

FINDINGS

Spectra (2-100 kDa) were grouped into training (n=122) and testing (n=109) sets. The training set enabled data-mining software to identify distinct serum proteomic signatures characteristic of human African trypanosomiasis among 206 protein clusters. Sensitivity and specificity, determined with the testing set, were 100% and 98.6%, respectively, when the majority opinion of the three algorithms was considered. This novel approach is much more accurate than any other diagnostic test.

INTERPRETATION

Our report of the accurate diagnosis of an infection by use of proteomic signature analysis could form the basis for diagnostic tests for the disease, monitoring of response to treatment, and for improving the accuracy of patient recruitment in large-scale epidemiological studies.

A target within the target: probing cruzain's P1' site to define structural determinants for the Chagas' disease protease

BACKGROUND

Cysteine proteases of the papain superfamily are present in nearly all groups of eukaryotes and play vital roles in a wide range of biological processes and diseases, including antigen and hormone processing, bacterial infection, arthritis, osteoporosis, Alzheimer's disease and cancer-cell invasion. Because they are critical to the life-cycle progression of many pathogenic protozoa, they represent potential targets for selective inhibitors. Chagas' disease, the leading cause of death due to heart disease in Latin American countries, is transmitted by Trypanosoma cruzi. Cruzain is the major cysteine protease of T cruzi and has been the target of extensive structure-based drug design.

RESULTS

High-resolution crystal structures of cruzain bound to a series of potent phenyl-containing vinyl-sulfone, sulfonate and sulfonamide inhibitors have been determined. The structures show a consistent mode of interaction for this family of inhibitors based on a covalent Michael addition formed at the enzyme's active-site cysteine, hydrophobic interactions in the S2 substrate-binding pocket and a strong constellation of hydrogen bonding in the S1' region.

CONCLUSIONS

The series of vinyl-sulfone-based inhibitors examined in complex with cruzain was designed to probe recognition and binding potential of an aromatic-rich region of the enzyme. Analysis of the interactions formed shows that aromatic interactions play a less significant role, whereas the strength and importance of hydrogen bonding in the conformation adopted by the inhibitor upon binding to the enzyme was highlighted. A derivative of one inhibitor examined is currently under development as a therapeutic agent against Chagas' disease.

Grouping of trypanosome species in mixed infections in Glossina pallidipes

Trypanosomes in the dissection-positive proboscis of Glossina pallidipes were identified by PCR using species-specific primers. Of the 3741 flies dissected 643 were proboscis positive. PCR was performed on 406 dissection-positive probosces giving positive identifications in 352 (86.7%) and infection rates of 14.8% for congolense-type infections, 2.8% for vivax-type infections and 1.4% for the unidentified group. Of the 352 PCR identified infections 225 were single, 111 were double, 13 were triple infections and there were 3 quadruple infections. Statistical analysis suggests that mixed infections group into 3 largely separate divisions among the tsetse population (i) Trypanosoma congolense savannah and T. congolense Kenya coast, (ii) T. simiae, T. congolense Tsavo and T. godfreyi and (iii) T. vivax. We conclude that either differing feeding patterns among members of the fly population or the ability of the trypanosomes in each of the infection categories to significantly influence the maturation of trypanosomes in the other categories are the most likely causes of the groupings noted. Chi-squared analysis of dissection and PCR methods of trypanosome identification revealed profound differences (chi 2 = 19.1; D.F. = 1; P > 0.05). If confirmed in other studies these findings have serious implications for our understanding of trypanosome epidemiology in tsetse flies, much of which is founded on data from dissection-based trypanosome identifications.

Kinetoplastid membrane protein-11 (KMP-11) is differentially expressed during the life cycle of African trypanosomes and is found in a wide variety of kinetoplastid parasites

An abundant 11-kDa membrane protein was purified from African trypanosomes by organic solvent extraction and octyl-Sepharose chromatography. This protein cross-reacts with monoclonal antibodies originally generated against the lipophosphoglycan-associated protein of Leishmania donovani. Immunoblot analysis showed that the 11-kDa molecule was present in a variety of species of kinetoplastids. It was found in several species and subspecies of African trypanosomes and was present in low amounts in bloodstream forms and in larger amounts in procyclic, epimastigote and metacyclic life cycle stages. Expression of the 11-kDa molecule rapidly increased during transformation from bloodstream forms to procyclic forms, paralleling expression of the major surface glycoprotein of Trypanosoma congolense, the glutamic acid/alanine-rich protein, an analogue of T. brucei procyclin. The molecule was present in procyclic trypanosome membranes at approximately 2 x 10(5)-1 x 10(6) molecules per cell, suggesting it may have an important role in parasite membrane organization and function. Amino-acid analysis of the trypanosome 11-kDa protein showed it had a different composition than that of its leishmania counterpart. Its wide distribution in kinetoplastids and its membrane disposition suggest a name for this class of molecules: kinetoplastid membrane protein-11 (KMP-11).

Genetic relatedness among Trypanosoma evansi stocks by random amplification of polymorphic DNA and evaluation of a synapomorphic DNA fragment for species-specific diagnosis

In this study we employed randomly amplified polymorphic DNA patterns to assess the genetic relatedness among 14 Brazilian Trypanosoma evansi stocks from domestic and wild hosts, which are known to differ in biological characteristics. These akinetoplastic stocks were compared with one another, to three Old World (Ethiopia, China and Philippines) dyskinetoplastic stocks of T. evansi, and also with Trypanosoma equiperdum, Trypanosoma brucei brucei, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense. Randomly amplified polymorphic DNA analysis showed limited heterogeneity in T. evansi stocks from different hosts and geographical regions of the world, or in other species of the subgenus Trypanozoon. However, minor variations generated random amplification of polymorphic DNA analysis disclosed a pattern consisting of a unique synapomorphic DNA fragment (termed Te664) for the T. evansi cluster that was not detected in any other trypanosome species investigated. Pulsed field gel electrophoresis analysis demonstrated that the Te664 fragment is a repetitive sequence, dispersed in intermediate and minichromosomes of T. evansi. Based on this sequence, we developed a conventional PCR assay for the detection of T. evansi using crude preparations of blood collected either on glass slides or on filter paper as template DNA. Our results showed that this assay may be useful as a diagnostic tool for field-epidemiological studies of T. evansi.

The supportive role of complement in HIV pathogenesis

This review focuses on interactions of HIV with the first-line defence of native immunity, the complement system. In all body compartments tested so far, HIV meets complement. Activation of the complement system results in deposition of C3 fragments on the viral surface, but in contrast to other pathogens, most of HIV is not or is only poorly lysed by membrane attack complexes. To survive complement-mediated lysis, HIV has not only developed resistance mechanisms, but uses opsonisation with complement fragments for its own advantage. Opsonised virions interact with complement receptor-expressing cells, which are either subsequently infected with high efficiency or retain viral particles on their surface, which promotes transmission of virus to other permissive cells. Our knowledge of these mechanisms has increased enormously over the past few years. A complete understanding of these complex interactions of HIV with the complement system opens new perspectives for development of alternative therapeutic strategies.

beta-D-glucosyl-hydroxymethyluracil, a novel base in African trypanosomes and other Kinetoplastida

A novel base, beta-D-glucosyl-hydroxymethyluracil or J for short, was recently discovered in DNA of bloodstream form Trypanosoma brucei. The base is predominantly found in the hexameric repeat arrays of chromosome telomeres and in adjacent repetitive sub-telomeric DNA, and it is made by modification of specific thymines in DNA. J is present in inactive telomeric variant surface glycoprotein (VSG) genes, but not in active ones, suggesting a link between the presence of J and repression of the telomeric expression sites for VSG genes. The presence of J in DNA is specific for bloodstream form trypanosomes, as J is absent in insect form (procyclic) T. brucei. In addition to African trypanosomes, J has been found in DNA from other Kinetoplastida that do not undergo antigenic variation, such as Leishmania and Crithidia. The biological function of J remains to be deciphered.

Host specificity of Trypanosoma (Herpetosoma) species: evidence that bank voles (Clethrionomys glareolus) carry only one T. (H.) evotomys 18S rRNA genotype but wood mice (Apodemus sylvaticus) carry at least two polyphyletic parasites

The strongest evidence for host specificity of mammalian trypanosomes comes from parasites of the subgenus Trypanosoma (Herpetosoma). Laboratory studies have shown that T. (Herpetosoma) species will not infect an alternative host. However, this has not been demonstrated in wild populations. We screened 560 bank voles (Clethrionomys glareolus) and 148 wood mice (Apodemus sylvaticus) for trypanosomes by PCR amplification of the 18S rRNA gene. In total, 109 (19%) bank voles and 12 (8%) wood mice were infected. A HaeIII restriction site was discovered that could be used to discriminate between T. (H.) evotomys of the bank vole and T. (H.) grosi of the wood mouse. All the parasites in the bank voles were identified as T. (Herpetosoma) evotomys by RFLP-PCR. Out of the 12 wood mouse infections 10 were due to T. grosi. Two of the wood mice were infected with parasites with a novel genotype that was most similar to those of T. evotomys and T. microti of voles. Fifty-six fleas collected from the rodents were also screened for trypanosomes; 9 were infected with T. evotomys and 1 with T. grosi. One of the fleas infected with T. evotomys was collected from a wood mouse.

Phylogenetic relationships of Trypanosoma chelodina and Trypanosoma binneyi from Australian tortoises and platypuses inferred from small subunit rRNA analyses

Trypanosome infections are often difficult to detect by conventional microscopy and their pleomorphy often confounds differential diagnosis. Molecular techniques are now being used to diagnose infections and to determine phylogenetic relationships between species. Complete small subunit rRNA gene sequences were determined for isolates of Trypanosoma chelodina from the Brisbane River tortoise (Emydura signata), the saw-shelled tortoise (Elseya latisternum), and the eastern snake-necked tortoise (Chelodina longicollis) from southeast Queensland, Australia. Partial sequence data were also obtained for T. binneyi from a platypus (Ornithorhynchus anatinus) from Tasmania. Phylogenetic relationships between T. chelodina, T. binneyi and other species were examined by maximum parsimony and likelihood methods. The Australian tortoise and platypus trypanosomes did not exhibit any close phylogenetic relationships with those of mammals, reptiles or amphibians, but were closely related to each other, and to fish trypanosomes. This contra-indicates their co-evolution with their vertebrate hosts but does not exclude co-evolution with different groups of invertebrate vectors, notably insects and leeches.

A graph-topological approach to recognition of pattern and similarity in RNA secondary structures

Secondary and tertiary RNA structures play an important role in many biological processes. Therefore the necessity arises to find similar higher-order structures for different but functionally homologous RNA sequences. We propose here a graph-topological approach to the problem, which shows two main features: simplified graph representation which allows the recognition of similarity of RNA secondary structures with the same branching look despite minor differences. This allows comparison among foldings from different sequences, and "pruning" of the secondary structures not shared by all the sequences since the early stages of the search. (b) The graph representation is encoded by the Randić topological index, and the search for the folding similarity is reduced to checking the identity of single numbers. These characteristics make this approach significantly different, less depending on empirical criteria, and less computationally heavy then previous methods, where the folding consensus has been measured by an alignment procedure or correlation of strings representing the secondary structures. Some U2 snRNA and viroid sequences are studied by this approach, which is imbedded in our previous search method based on genetic algorithms.

An essential dimeric membrane protein of trypanosome glycosomes

Kinetoplastid parasites compartmentalize the first seven enzymes of glycolysis in a peroxisome-like microbody, the glycosome. Genes encoding the most abundant protein of the glycosomal membrane, GIM5, have been cloned and the protein characterized. Two genes, GIM5A and GIM5B, encode 26 kDa proteins. Although many microbody membrane proteins are conserved in evolution, the only homologues of GIM5 in the available databases are from the closely related kinetoplastids Trypanosoma cruzi and Leishmania. The N- and C-termini are conserved between the two genes, and between species, and are oriented towards the cytosol. They are separated by a short loop that is located between two transmembrane domains and shows almost no sequence conservation. This suggests that the N- and C-terminal domains are more important for function. GIM5 forms dimers in vivo. Overexpression of GIM5B inhibits growth, whereas depletion of GIM5 to below 10% of wild-type levels is very rapidly lethal. This novel organellar membrane protein is therefore essential for bloodstream trypanosome survival.

The fatty acids in unremodelled trypanosome glycosyl-phosphatidylinositols

Glycolipid A, the precursor of the glycosyl-phosphatidylinositol (GPI) anchor of the trypanosome variant surface glycoprotein, is constructed in two phases. First, the glycan is assembled on phosphatidylinositol (PI), yielding a glycolipid termed A'. Second, glycolipid A' undergoes fatty acid remodelling, by deacylation and reacylation, to become the dimyristoyl species glycolipid A. In this paper, we examine the fatty acid content of glycolipid A' and its cellular progenitors. A' contains exclusively stearate at the sn-1 position and a complex mixture of fatty acids (including 18:0, 18:1, 18:2, 20:4 and 22:6) at sn-2. Presumably these fatty acids derive from stearate-containing PI species which initially enter the biosynthetic pathway. We compared the diacylglycerol species from glycolipid A' with those from phosphatidylinositol to determine whether a subset of stearate-containing PIs is utilized for GPI biosynthesis. We found that the spectrum of stearate-containing diacylglycerols in PI is similar to that in A', although the proportions of each compound differ. Total PI in general was highly enriched in stearate-containing species. Differences in composition between glycosylated PI and total cellular PI may be due to the substrate specificity of the sugar transferase which initiates the GPI biosynthetic pathway. Alternatively, the species of PI present at the endoplasmic reticulum site of GPI biosynthesis may differ from those in total PI.

Proteomic fingerprinting for the diagnosis of human African trypanosomiasis

Papadopoulos et al. recently reported the discovery of a diagnostic serum proteomic signature for human African trypanosomiasis (HAT), using a combination of surface-enhanced laser desorption-ionization time-of-flight (SELDI-TOF) mass spectrometry and data-mining algorithms. This novel approach, coupled with biochemical characterization of the proteins that contribute to the signature, provides powerful new tools for the development of improved diagnostic tests, disease staging and identification of potential novel drug targets in HAT.

Characterization of antibodies to the glycosyl-phosphatidylinositol membrane anchors of mammalian proteins

Two polyclonal antisera were raised in rabbits to the phospholipase C-solubilized forms of pig renal dipeptidase (EC 3.4.13.11) and pig aminopeptidase P (EC 3.4.11.9). These antisera were purified and shown to cross-react with other glycosyl-phosphatidylinositol (G-PI)-anchored proteins isolated from pig, human and trypanosomes. The epitopes involved in this cross-reactivity were characterized by Western-blot analysis after mild acid or nitrous acid treatment of the G-PI-anchored proteins and by a competitive e.l.i.s.a. with other G-PI-anchored proteins and individual components of the anchor structure. These studies revealed that the primary epitope for both antisera is the inositol 1.2-(cyclic)monophosphate that is formed on phospholipase C cleavage of the intact G-PI anchor. Other minor epitopes, such as phosphoethanolamine, probably involve side-chain modifications to the core anchor structure that may be species-specific.

Unravelling the phylogenetic relationships of African trypanosomes of suids

African trypanosomes of the subgenera Nannomonas and Pycnomonas have been recorded from both wild and domestic suids. However, complete descriptions of some of these trypanosomes with regard to host range, pathogenicity, transmission and distribution are still lacking. Neither the recently described Trypanosoma (Nannomonas) godfreyi nor Trypanosoma (Nannomonas) congolense Tsavo have been isolated from mammalian hosts, while Trypanosoma (Pycnomonas) suis remains the rarest of the Salivarian trypanosomes. The only isolate presumed to be of the latter species is maintained at the Kenya Trypanosomiasis Research Institute, Nairobi. We present here the results of characterization of this isolate by morphology, tsetse transmission, the use of species-specific DNA probes and DNA sequence analysis. Morphology in stained blood smears revealed a small trypanosome with a free flagellum. Experimental transmission through Glossina morsitans morsitans showed a developmental cycle typical of subgenus Nannomonas A positive identification was obtained with species-specific PCR primers for T. congolense Tsavo; moreover, the sequence of the SSU rRNA gene was almost identical to that of T. congolense Tsavo on database. In phylogenetic analysis of the SSU rRNA genes of Salivarian trypanosomes, T. congolense Tsavo grouped with T. simiae rather than T. congolense, suggesting that the name T. simiae Tsavo is more appropriate.

Variant Surface Glycoprotein fromTrypanosomaevansiIs Partially Responsible for the Cross-Reaction betweenTrypanosomaevansiandTrypanosoma vivax†

Salivarian trypanosomes use antigenic variation of their variant-specific surface glycoprotein (VSG) coat as a defense against the host immune system. Although about 1000 VSG and pseudo-VSG genes are scattered throughout the trypanosome genome, each trypanosome expresses only one VSG, while the rest of the genes are transcriptionally silent. A 64-kDa glycosylated cross-reacting antigen between Trypanosoma evansi and Trypanosoma vivax (p64), which was purified from the TEVA1 T. evansi Venezuelan isolate, was proven here to represent the soluble form of a VSG. Initially, a biochemical characterization of p64 was carried out. Gel filtration chromatography, sedimentation, and chemical cross-linking provided evidences of the dimeric nature of p64. The hydrodynamic parameters indicated that p64 is asymmetrical with a frictional ratio f/fo = 1.57. Isoelectric focusing and two-dimensional polyacrylamide gel electrophoresis revealed that p64 contained two isoforms with isoelectric points of 6.8-6.9 and 7.1-7.2. When p64 and three p64 Staphylococcus aureus V8 proteolytic fragments were sequenced, the same N-termini sequence was obtained: Ala-Pro-Ile-Thr-Asp-Ala-Asp-Leu-Gly-Pro-Ala-Gln-Ile-Ala-Asp, which displayed a significant homology with a putative Trypanosoma brucei VSG gene located on chromosome 4. Additionally, immunofluorescence microscopy on T. evansi and T. vivax established that p64 and its T. vivax homologue were confined to the surface of both parasites. An immunological characterization of this antigen was also carried out using several Venezuelan T. evansi isolates expressing different VSGs, which were obtained from naturally infected animals. Although sera from animals infected with the various T. evansi isolates recognized p64, only one isolate, besides TEVA1, contained polypeptides that were recognized by anti-p64 antibodies. All these results together with prior evidences [Uzcanga, G. et al. (2002) Parasitology 124, 287-299] confirmed that p64 is the soluble form of a T. evansi VSG, containing common epitopes recognized by sera from animals infected with T. evansi or T. vivax. Despite the huge repertoire of VSG genes existing on bloodstream trypanosomes, our data also demonstrated the potential use of a VSG variant from the TEVA1 T. evansi isolate as a diagnostic reagent.

Analysis of the trypanosome flagellar proteome using a combined electron transfer/collisionally activated dissociation strategy

The use of electron-transfer dissociation as an alternative peptide ion activation method for generation of protein sequence information is examined here in comparison with the conventional method of choice, collisionally activated dissociation, using a linear ion trapping instrument. Direct comparability between collisionally and electron-transfer-activated product ion data were ensured by employing an activation-switching method during acquisition, sequentially activating precisely the same precursor ion species with each fragmentation method in turn. Sequest (Thermo Fisher Scientific, San Jose, CA) searching of product ion data generated an overlapping yet distinct pool of polypeptide identifications from the products of collisional and electron-transfer-mediated activation products. To provide a highly confident set of protein recognitions, identification data were filtered using parameters that achieved a peptide false discovery rate of 1%, with two or more independent peptide assignments required for each protein. The use of electron transfer dissociation (ETD) has allowed us to identify additional peptides where the quality of product ion data generated by collisionally activated dissociation (CAD) was insufficient to infer peptide sequence. Thus, a combined ETD/CAD approach leads to the recognition of more peptides and proteins than are achieved using peptide analysis by CAD- or ETD-based tandem mass spectrometry alone.

The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate

Guide RNAs bind antiparallel to their target pre-mRNAs to form editing substrates in reaction cycles that insert or delete uridylates (Us) in most mitochondrial transcripts of trypanosomes. The 5' end of each guide RNA has an anchor sequence that binds to the pre-mRNA by base-pair complementarity. The template sequence in the middle of the guide RNA directs the editing reactions. The 3' ends of most guide RNAs have ∼15 contiguous Us that bind to the purine-rich unedited pre-mRNA upstream of the editing site. The resulting U-helix is rich in G·U wobble base pairs. To gain insights into the structure of the U-helix, we crystallized 8 bp of the U-helix in one editing substrate for the A6 mRNA of Trypanosoma brucei. The fragment provides three samples of the 5'-AGA-3'/5'-UUU-3' base-pair triple. The fusion of two identical U-helices head-to-head promoted crystallization. We obtained X-ray diffraction data with a resolution limit of 1.37 Å. The U-helix had low and high twist angles before and after each G·U wobble base pair; this variation was partly due to shearing of the wobble base pairs as revealed in comparisons with a crystal structure of a 16-nt RNA with all Watson-Crick base pairs. Both crystal structures had wider major grooves at the junction between the poly(U) and polypurine tracts. This junction mimics the junction between the template helix and the U-helix in RNA-editing substrates and may be a site of major groove invasion by RNA editing proteins.

Glycoinositol phospholipids from American Leishmania and Trypanosoma spp: partial characterization of the glycan cores and the human humoral immune response to them

The glycoinositol phospholipid (GIPL) profiles of American Leishmania spp. (L. mexicana and L. braziliensis), Leishmania donovani, and American Trypanosoma spp. (T. cruzi and T. rangeli) were compared. The major GIPLs in these parasites include tetraglycosyl-, pentaglycosyl-, and hexaglycosylphosphatidylinositol. These were partially identified by their comigration by high-performance thin-layer chromatography with purified L. major GIPLs, gas-liquid chromatography of the monosaccharides released after aqueous HF treatment, N-acetylation and methanolysis, sensitivity to exoglycosidases, and antibody absorption on several specific natural haptens. Members of the genus Leishmania have two other highly polar glycolipids, while the T. rangeli glycolipid profile was quite different from those of other kinetoplastids that were studied. On a weight basis, the glycan core of L. major GIPL-1 is the most reactive, followed by GIPL-3 and GIPL-2. Antibodies to the core glycans of GIPL-1, GIPL-2, and GIPL-3 were present at a low titer in the serum of every normal individual studied, while elevated GIPL-2 antibody levels were present in 80 to 100% of T. cruzi-, T. rangeli-, or L. donovani-infected patients, with lower values being found for GIPL-3 (30 to 60%) and GIPL-1 (30 to 50%). Except for GIPL-2 antibodies, which were mainly located on immunoglobulin G (IgG) and IgM, GIPL-1 and GIPL-3 antibodies were mainly distributed in IgM, with lower reactivity present in IgG. Antigen-antibody binding was very selectively blocked with Gal(alpha 1-3)Man, or Gal(beta 1-4)Man, Gal(alpha 1-3)Gal, and Gal(alpha 1-6)Gal for GIPL-1, GIPL-2, and GIPL-3 antibodies, respectively.