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Free-living amoeba (FLA) group includes the potentially pathogenic genera Acanthamoeba, Naegleria, Balamuthia, Sappinia, and Vermamoeba, causative agents of human infections (encephalitis, keratitis, and disseminated diseases). In Brazil, the first report on pathogenic FLA was published in the 70s and showed meningoencephalitis caused by Naegleria spp. FLA studies are emerging, but no literature review is available to investigate this trend in Brazil critically. Thus, the present work aims to integrate and discuss these data. Scopus, PubMed, and Web of Science were searched, retrieving studies from 1974 to 2020. The screening process resulted in 178 papers, which were clustered into core and auxiliary classes and sorted into five categories: wet-bench studies, dry-bench studies, clinical reports, environmental identifications, and literature reviews. The papers dating from the last ten years account for 75% (134/178) of the total publications, indicating the FLA topic has gained Brazilian interest. Moreover, 81% (144/178) address Acanthamoeba-related matter, revealing this genus as the most prevalent in all categories. Brazil’s Southeast, South, and Midwest geographic regions accounted for 96% (171/178) of the publications studied in the present work. To the best of our knowledge, this review is the pioneer in summarising the FLA research history in Brazil.

Several molecular mechanisms are involved in the genetic code interpretation during translation, as codon degeneration for the incorporation of rare amino acids. One mechanism that stands out is selenocysteine (Sec), which requires a specific biosynthesis and incorporation pathway. In Bacteria, the Sec biosynthesis pathway has unique features compared with the eukaryote pathway as Ser to Sec conversion mechanism is accomplished by a homodecameric enzyme (selenocysteine synthase, SelA) followed by the action of an elongation factor (SelB) responsible for delivering the mature Sec-tRNA

Made available in DSpace on 2022-04-29T08:35:27Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-11-19 Several molecular mechanisms are involved in the genetic code interpretation during translation, as codon degeneration for the incorporation of rare amino acids. One mechanism that stands out is selenocysteine (Sec), which requires a specific biosynthesis and incorporation pathway. In Bacteria, the Sec biosynthesis pathway has unique features compared with the eukaryote pathway as Ser to Sec conversion mechanism is accomplished by a homodecameric enzyme (selenocysteine synthase, SelA) followed by the action of an elongation factor (SelB) responsible for delivering the mature Sec-tRNASec into the ribosome by the interaction with the Selenocysteine Insertion Sequence (SECIS). Besides this mechanism being already described, the sequential events for Sec-tRNASec and SECIS specific recognition remain unclear. In this study, we determined the order of events of the interactions between the proteins and RNAs involved in Sec incorporation. Dissociation constants between SelB and the native as well as unacylated-tRNASec variants demonstrated that the acceptor stem and variable arm are essential for SelB recognition. Moreover, our data support the sequence of molecular events where GTP-activated SelB strongly interacts with SelA.tRNASec. Subsequently, SelB.GTP.tRNASec recognizes the mRNA SECIS to deliver the tRNASec to the ribosome. SelB in complex with its specific RNAs were examined using Hydrogen/Deuterium exchange mapping that allowed the determination of the molecular envelopes and its secondary structural variations during the complex assembly. Our results demonstrate the ordering of events in Sec incorporation and contribute to the full comprehension of the tRNASec role in the Sec amino acid biosynthesis, as well as extending the knowledge of synthetic biology and the expansion of the genetic code. Physics Institute of Sao Carlos University of Sao Paulo, Trabalhador Sao Carlense Av., 400 Department of Chemistry and Biochemistry University California – Santa Cruz, 1156 High St. Physical Sciences Laboratory State University of Northern Rio de Janeiro Darcy Ribeiro – UENF, Av. Alberto Lamego, 2000 Faculty of Science Philosophy and Letters University of Sao Paulo Department of Biochemistry and Molecular Biology University of British Columbia, 2350 Health Science Mall Department of Physical Chemistry Chemistry Institute of the São Paulo State University – UNESP Physics Department Institute of Biosciences Letters and Exact Sciences (IBILCE) São Paulo State University – UNESP Department of General and Applied Biology Institute of Biosciences of Rio Claro São Paulo State University – UNESP Bioscience Institute of Universidade Estadual Paulista, Rubião Jr. Department of Genetics and Evolution Federal University of São Carlos – UFSCar Department of Physical Chemistry Chemistry Institute of the São Paulo State University – UNESP Physics Department Institute of Biosciences Letters and Exact Sciences (IBILCE) São Paulo State University – UNESP Department of General and Applied Biology Institute of Biosciences of Rio Claro São Paulo State University – UNESP Bioscience Institute of Universidade Estadual Paulista, Rubião Jr.

Protein tyrosine phosphatases (PTPs) are key virulence factors in pathogenic bacteria, consequently, they have become important targets for new approaches against these pathogens, especially in the fight against antibiotic resistance. Among these targets of interest YopH (Yersinia outer protein H) from virulent species of Yersinia is an example. PTPs can be reversibly inhibited by nitric oxide (NO) since the oxidative modification of cysteine residues may influence the protein structure and catalytic activity. We therefore investigated the effects of NO on the structure and enzymatic activity of Yersinia enterocolitica YopH in vitro. Through phosphatase activity assays, we observe that in the presence of NO YopH activity was inhibited by 50%, and that this oxidative modification is partially reversible in the presence of DTT. Furthermore, YopH S-nitrosylation was clearly confirmed by a biotin switch assay, high resolution mass spectrometry (MS) and X-ray crystallography approaches. The crystal structure confirmed the S-nitrosylation of the catalytic cysteine residue, Cys403, while the MS data provide evidence that Cys221 and Cys234 might also be modified by NO. Interestingly, circular dichroism spectroscopy shows that the S-nitrosylation affects secondary structure of wild type YopH, though to a lesser extent on the catalytic cysteine to serine YopH mutant. The data obtained demonstrate that S-nitrosylation inhibits the catalytic activity of YopH, with effects beyond the catalytic cysteine. These findings are helpful for designing effective YopH inhibitors and potential therapeutic strategies to fight this pathogen or others that use similar mechanisms to interfere in the signal transduction pathways of their hosts.

Made available in DSpace on 2020-12-10T17:34:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-08-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) The selenocysteine (Sec) incorporation is a co-translational event taking place at an in-frame UGA-codon and dependent on an organized molecular machinery. Selenium delivery requires mainly two enzymes, the selenocysteine lyase (CsdB) is essential for Sec recycling and conversion to selenide, further used by the selenophosphate synthetase (SelD), responsible for the conversion of selenide in selenophosphate. Therefore, understanding the catalytic mechanism involved in selenium compounds delivery, such as the interaction between SelD and CsdB (EcCsdB.EcSelD), is fundamental for the further comprehension of the selenocysteine synthesis pathway and its control. In Escherichia coli, EcCsdB.EcSelD interaction must occur to prevent cell death from the release of the toxic intermediate selenide. Here, we demonstrate and characterize the in vitro EcSelD.EcCsdB interaction by biophysical methods.The EcSelD.EcCsdB interaction occurs with a stoichiometiy of 1:1 in presence of selenocysteine and at a low-nanomolar affinity (similar to 1.8 nM). The data is in agreement with the small angle X-ray scattering model fitted using available structures. Moreover, yeast-2-hybrid assays supported the macromolecular interaction in the cellular environment. This is the first report that demonstrates the interaction between EcCsdB and EcSelD supporting the hypothesis that EcSelD.EcCsdB interaction is necessary to sequester the selenide during the selenocysteine incorporation pathway in Bacteria. (C) 2020 Elsevier B.V. All rights reserved. Univ Sao Paulo, Phys Inst Sao Carlos, Trabalhador Sao Carlense Av 400, BR-13566590 Sao Carlos, SP, Brazil Univ British Columbia, Dept Biochem & Mol Biol, 2350 Hlth Sci Mall, Vancouver, BC V6T 1Z3, Canada Univ Toronto, Lab Med & Pathobiol, 1 Kings Coll Circle, Toronto, ON M5S 1A8, Canada Univ Sao Paulo, Fac Sci Philosophy & Letters, BR-14040901 Ribeirao Preto, SP, Brazil Univ Estadual Paulista, Biosci Inst, BR-18618000 Botucatu, SP, Brazil Fed Univ Sao Carlos UFSCar, Dept Genet & Evolut, BR-13565905 Sao Carlos, SP, Brazil Univ Estadual Paulista, Biosci Inst, BR-18618000 Botucatu, SP, Brazil FAPESP: 2013/17791-0 FAPESP: 2014/16005-4 FAPESP: 2016/20977-7 FAPESP: JFS 2012/23730-1 FAPESP: 2014/00206-0 CNPq: 420226/2016-8

Selenium is an essential trace element which, at adequate levels, presents different beneficial biological effects, such as cancer regression, tissue development and protection against oxidative damage. The positive effects of this element are related to the expression of selenoproteins and their ability to modulate the immune system and the oxidative stress response. In Chagas disease and sleeping sickness, selenium supplementation has shown blood parasitism reduction and the alleviation of specific aspects of the diseases, such as diminishing anemia in sleeping sickness or minimization of myocardial and right ventricular chamber damage in Chagasdisease. Although the influence of selenium in trypanosomiasis has been investigated, the direct effects of sodium selenite supplementation on trypanosome cells are poorly understood. Treatment of Trypanosoma cruzi cultures with low selenium doses demonstrated different results, according to the parasite evolutive form analyzed. Epimastigote cultures supplemented with 100 nM of sodium selenite presented cell growth increment, which varies from 10 to 40% according to the parasite strain assayed. Selenium concentration around 600nM leads to a 30% increase in the amastigote form number, whereas, at the same dose, the mammal host cell presented no cellular growth alteration. For the bloodstream form, the results agree with theliterature, and all sodium selenite concentrations tested, demonstrated a reduction in parasite viability. The data suggest that selenium supplementation, under specific conditions, could increase T. cruzi viability, demonstrating that a strategy for using selenium as an adjuvant in Chagas disease treatment requires additional experimentation. KEY WORDS: Selenium; trypanosomiasis; Chagas disease; Trypanosoma cruzi.

tRNA synthetases are responsible for decoding the molecular information, from codons to amino acids. Seryl-tRNA synthetase (SerRS), besides the five isoacceptors of tRNA

The genus Naegleria, of the free-living amoeba (FLA) group, has been investigated mainly due to its human health impact, resulting in deadly infections and their worldwide distribution on freshwater systems. Naegleria fowleri, colloquially known as the &ldquo, brain-eating amoeba,&rdquo, is the most studied Naegleria species because it causes primary amoebic meningoencephalitis (PAM) of high lethality. The assessment of FLA biodiversity is fundamental to evaluate the presence of pathogenic species and the possibility of human contamination. However, the knowledge of FLA distribution in Brazil is unknown, and to rectify this situation, we present research on identifying Naegleria spp. in the Monjolinho River as a model study. The river is a public Brazilian freshwater source that crosses the city of S&atilde, o Carlos, in S&atilde, o Paulo state, Brazil. Five distinct sampling sites were examined through limnological features, trophozoites culturing, and PCR against internal transcribed spacer (ITS) regions and 5.8S rRNA sequences. The results identified N. philippinensis, N. canariensisi, N. australiensis, N. gruberi, N. dobsoni sequences, as well as a Hartmannella sequence. The methodology delineated here represents the first Brazilian Naegleria spp. study on a freshwater system. Our results stress the urgency of a large scale evaluation of the presence of free-living amoebas in Brazil.

The genus Naegleria, of free-living amoeba (FLA) group, has been investigated mainly due to its human health impact resulting in deadly infections and their worldwide distribution on freshwater systems. Naegleria fowleri, colloquially known as the “brain-eating amoeba”, is the most studied Naegleria species because it causes Primary Amoebic Meningoencephalitis (PAM) of high lethality. The assessment of FLA biodiversity is fundamental to evaluate the presence of pathogenic species and the possibility of human contamination. However, the knowledge of FLA distribution in Brazil is unknown, and to rectify this situation we present a research on identifying Naegleria spp. in the Monjolinho River, as a model study. The river is a public Brazilian freshwater source that crosses the city of São Carlos. Five distinct sampling sites were examined through limnological features, trophozoites culturing and PCR against internal transcribed spacers (ITS) regions and 5.8S rRNA sequence. The results identified N. philippinensis, N. canariensisi, N. australiensis, N.gruberi, N. dobsoni sequences, as well as a Vahlkampfia sequence. The methodology delineated here represents the first Brazilian Naegleria spp. study on a freshwater system. Our result stresses the urgency of a large scale evaluation of the presence of free-living amoebas in Brazil.

Naegleria fowleri is a pathogenic amoeboflagellate most prominently known for its role as the etiological agent of the Primary Amoebic Meningoencephalitis (PAM), a disease that afflicts the central nervous system and is fatal in more than 95% of the reported cases. Although being fatal and with potential risks for an increase in the occurrence of the pathogen in populated areas, the organism receives little public health attention. A great underestimation in the number of PAM cases reported is assumed, taking into account the difficulty in obtaining an accurate diagnosis. In this review, we summarize different techniques and methods used in the identification of the protozoan in clinical and environmental samples. Since it remains unclear whether the protozoan infection can be successfully treated with the currently available drugs, we proceed to discuss the current PAM therapeutic strategies and its effectiveness. Finally, novel compounds for potential treatments are discussed as well as research on vaccine development against PAM.

tRNA synthetases are responsible for decoding the molecular information, from codons to amino acids. Seryl-tRNA synthetase (SerRS), besides the five isoacceptors of tRNASer, recognizes tRNA[Ser]Sec for the incorporation of selenocysteine (Sec, U) into selenoproteins. The selenocysteine synthesis pathway is known and is dependent on several protein-protein and protein-RNA interactions. Those interactions are not fully described, in particular, involving tRNA[Ser]Sec and SerRS. Here we describe the molecular interactions between the Escherichia coli Seryl-tRNA synthetase (EcSerRS) and tRNA[Ser]Sec in order to determine their specificity, selectivity and binding order, leading to tRNA aminoacylation. The dissociation constant of EcSerRS and tRNA[Ser]Sec was determined as (126 ± 20) nM. We also demonstrate that EcSerRS binds initially to tRNA[Ser]Sec in the presence of ATP for further recognition by E. coli selenocysteine synthetase (EcSelA) for Ser to Sec conversion. The proposed studies clarify the mechanism of tRNA[Ser]Sec incorporation in Bacteria as well as of other domains of life.

Selenium (Se) is an essential trace element for several organisms and is mostly present in proteins as L-selenocysteine (Sec or U). Sec is synthesized on its L-seryl-tRNA

Chromatin associated proteins are key regulators of many important processes in the cell. Trypanosoma cruzi, a protozoa flagellate that causes Chagas disease, alternates between replicative and nonreplicative forms accompanied by a shift on global transcription levels and by changes in its chromatin architecture. Here, we investigated the T. cruzi chromatin proteome using three different protocols and compared it between replicative (epimastigote) and nonreplicative (trypomastigote) forms by high-resolution mass spectrometry. More than 2000 proteins were identified and quantified both in chromatin and nonchromatin extracts. Besides histones and other known nuclear proteins, trypanosomes chromatin also contains metabolic (mainly from carbohydrate pathway), cytoskeleton and many other proteins with unknown functions. Strikingly, the two parasite forms differ greatly regarding their chromatin-associated factors composition and amount. Although the nucleosome content is the same for both life forms (as seen by MNase digestion), the remaining proteins were much less detected in nonreplicative forms, suggesting that they have a naked chromatin. Proteins associated to DNA proliferation, such as PCNA, RPA, and DNA topoisomerases were exclusively found in the chromatin of replicative stages. On the other hand, the nonreplicative stages have an enrichment of a histone H2B variant. Furthermore, almost 20% of replicative stages chromatin-associated proteins are expressed in nonreplicative forms, but located at nonchromatin space. We identified different classes of proteins including phosphatases and a Ran-binding protein, that may shuttle between chromatin and nonchromatin space during differentiation. Seven proteins, including those with unknown functions, were selected for further validation. We confirmed their location in chromatin and their differential expression, using Western blotting assays and chromatin immunoprecipitation (ChIP). Our results indicate that the replicative state in trypanosomes involves an increase of chromatin associated proteins content. We discuss in details, the qualitative and quantitative implication of this chromatin set in trypanosome chromatin biology. Because trypanosomes are early-branching organisms, this data can boost our understanding of chromatin-associated processes in other cell types.

Selenophosphate synthetase (SPS) plays an indispensable role in selenium metabolism, being responsible for catalyzing the activation of selenide with adenosine 5'-triphosphate (ATP) to generate selenophosphate, the essential selenium donor for selenocysteine synthesis. Recombinant full-length Leishmania major SPS (LmSPS2) was recalcitrant to crystallization. Therefore, a limited proteolysis technique was used and a stable N-terminal truncated construct (ΔN-LmSPS2) yielded suitable crystals. The Trypanosoma brucei SPS orthologue (TbSPS2) was crystallized by the microbatch method using paraffin oil. X-ray diffraction data were collected to resolutions of 1.9 Å for ΔN-LmSPS2 and 3.4 Å for TbSPS2.

Histones are well-conserved proteins that form the basic structure of chromatin in eukaryotes and undergo several post-translational modifications, which are important for the control of transcription, replication, DNA damage repair, and chromosome condensation. In early branched organisms, histones are less conserved and appear to contain alternative sites for modifications, which could reveal evolutionary unique functions of histone modifications in gene expression and other chromatin-based processes. Here, by using high-resolution mass spectrometry, we identified and quantified histone post-translational modifications in two life cycle stages of Trypanosoma cruzi, the protozoan parasite that causes Chagas disease. We detected 44 new modifications, namely: 18 acetylations, seven monomethylations, seven dimethylations, seven trimethylations, and four phosphorylations. We found that replicative (epimastigote stage) contains more histone modifications than nonreplicative and infective parasites (trypomastigote stage). Acetylations of lysines at the C-terminus of histone H2A and methylations of lysine 23 of histone H3 were found to be enriched in trypomastigotes. In contrast, phosphorylation in serine 23 of H2B and methylations of lysine 76 of histone H3 predominates in proliferative states. The presence of one or two methylations in the lysine 76 was found in cells undergoing mitosis and cytokinesis, typical of proliferating parasites. Our findings provide new insights into the role of histone modifications related to the control of gene expression and cell-cycle regulation in an early divergent organism.

Phosphoglycerate mutases (PGAMs) participate in both the glycolytic and the gluconeogenic pathways in reversible isomerization of 3-phosphoglycerate and 2-phosphoglycerate. PGAMs are members of two distinct protein families: enzymes that are dependent on or independent of the 2,3-bisphosphoglycerate cofactor. We determined the X-ray structure of the monomeric Trypanosoma brucei independent PGAM (TbiPGAM) in its apoenzyme form, and confirmed this observation by small angle X-ray scattering data. Comparing the TbiPGAM structure with the Leishmania mexicana independent PGAM structure, previously reported with a phosphoglycerate molecule bound to the active site, revealed the domain movement resulting from active site occupation. The structure reported here shows the interaction between Asp319 and the metal bound to the active site, and its contribution to the domain movement. Substitution of the metal-binding residue Asp319 by Ala resulted in complete loss of independent PGAM activity, and showed for the first time its involvement in the enzyme's function. As TbiPGAM is an attractive molecular target for drug development, the apoenzyme conformation described here provides opportunities for its use in structure-based drug design approaches. Database Structural data for the Trypanosoma brucei 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM) has been deposited with the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank under code 3NVL.

Selenoproteins are characterized by the incorporation of at least one amino acid selenocysteine (Sec-U) encoded by in-frame UGA stop codons. These proteins, as well as the components of the Sec synthesis pathway, are present in members of the bacteria, archaea and eukaryote domains. Although not a ubiquitous pathway in all organisms, it was also identified in several protozoa, including the Kinetoplastida. Genetic evidence has indicated that the pathway is non-essential to the survival of Trypanosoma growing in non-stressed conditions. By analyzing the effects of RNA interference of the Trypanosoma brucei selenophosphate synthetase SPS2, we found a requirement under sub-optimal growth conditions. The present work shows that SPS2 is involved in oxidative stress protection of the parasite and its absence severely hampers the parasite survival in the presence of an oxidizing environment that results in an apoptotic-like phenotype and cell death.

Phosphoribosyl pyrophosphate synthetase (PRS—EC:2.7.6.1) is an important enzyme present in several metabolic pathways, thus forming a complex family of isoenzymes. However, plant PRS enzymes have not been extensively investigated. In this study, a sugarcane prs gene has been characterized from the Sugar Cane Expressed Sequence Tag Genome Project. This gene contains a 984-bp open reading frame encoding a 328-amino acid protein. The predicted amino acid sequence has 77% and 78% amino acid sequence identity to Arabidopsis thaliana and Spinacia oleracea PRS4, respectively. The assignment of sugarcane PRS as a phosphate-independent PRS isoenzyme (Class II PRS) is verified following enzyme assay and phylogenetic reconstruction of PRS homologues. To gain further insight into the structural framework of the phosphate independence of sugarcane PRS, a molecular model is described. This model reveals the formation of two conserved domains elucidating the structural features involved in sugarcane PRS phosphate independence. The recombinant PRS retains secondary structure elements and a quaternary arrangement consistent with known PRS homologues, based on circular dichroism measurements.

Adenine phosphoribosyltransferase (APRT) is an important enzyme component of the purine recycling pathway. Parasitic protozoa of the order Kinetoplastida are unable to synthesize purines de novo and use the salvage pathway for the synthesis of purine bases rendering this biosynthetic pathway an attractive target for antiparasitic drug design. The recombinant human adenine phosphoribosyltransferase (hAPRT) structure was resolved in the presence of AMP in the active site to 1.76 A resolution and with the substrates PRPP and adenine simultaneously bound to the catalytic site to 1.83 A resolution. An additional structure was solved containing one subunit of the dimer in the apo-form to 2.10 A resolution. Comparisons of these three hAPRT structures with other 'type I' PRTases revealed several important features of this class of enzymes. Our data indicate that the flexible loop structure adopts an open conformation before and after binding of both substrates adenine and PRPP. Comparative analyses presented here provide structural evidence to propose the role of Glu104 as the residue that abstracts the proton of adenine N9 atom before its nucleophilic attack on the PRPP anomeric carbon. This work leads to new insights to the understanding of the APRT catalytic mechanism.

A total of 39 endophytic fungi have been isolated from Viguiera arenaria and Tithonia diversifolia, both collected in São Paulo State, Brazil. The isolates were identified based on their ribosomal DNA sequences. The ethyl acetate (EtOAc) extracts of all endophytic fungi were evaluated for their antimicrobial, antiparasitic and antitumoral activity. Antimicrobial screening was conducted using an agar diffusion assay against three pathogenic microorganisms: Staphylococcus aureus, Escherichia coli and Candida albicans. Antiparasitic activity was determined by enzymatic inhibition of gGAPDH of Trypanosoma cruzi and adenine phosphorybosiltransferase (APRT) of Leishmania tarentolae. Antitumoral activity was tested against human T leukemia cells by the Mosmann colorimetric method. All extracts showed activity in at least one assay: 79.5% of the extracts were cytotoxic against leukemia cells, 5.1% of the extracts were active against S. aureus, 25.6% against E. coli and 64.1% against Candida albicans. Only one extract showed promising results in the inhibition of parasitic enzymes gGAPDH (95.0%) and three were found to inhibit APRT activity. The cytotoxic extract produced by the strain VA1 (Glomerella cingulata) was fractionated and yielded nectriapyrone and tyrosol. Nectriapyrone showed relevant cytotoxic activity against both human T leukemia and melanoma tumor cell lines.

The investigation of extracts from six species of marine invertebrates yielded one new and several known natural products. Isoptilocaulin from the sponge Monanchora aff. arbuscula displayed antimicrobial activity at 1.3 mg/mL against an oxacillin-resistant strain of Staphylococcus aureus. Five inactive known dibromotyrosine derivatives, 2 6, were isolated from a new species of marine sponge, Aplysina sp. The sponges Petromica ciocalyptoides and Topsentia ophiraphidites yielded the known halistanol sulfate A (7) as an inhibitor of the antileishmanial target adenosine phosphoribosyl transferase. The ascidian Didemnum ligulum yielded asterubin (10) and the new N,N-dimethyl-O-methylethanolamine (11). The octocoral Carijoa riisei yielded the known 18-acetoxypregna-1,4,20-trien-3-one (12), which displayed cytotoxic activity against the cancer cell lines SF295, MDA-MB435, HCT8 and HL60.

The dichloromethane extract of Calea uniflora afforded a mixture of two novel chromanones, uniflorol-A (1) and uniflorol-B (2), and one known chromanone, 2,2-dimethyl-6- (1-hydroxyethyl)-chroman-4-one (3). The structures of these compounds were determined by spectroscopic methods. Biological activity of the compounds against Leishmania major promastigotes was evaluated. Mixture of the novel chromanones 1 and 2 showed significant growth inhibition of the parasite in the micrograms per milliliter range.

Proline is crucial for energizing critical events throughout the life cycle of Trypanosoma cruzi, the etiological agent of Chagas disease. The proline breakdown pathway consists of two oxidation steps, both of which produce reducing equivalents as follows: the conversion of proline to Δ(1)-pyrroline-5-carboxylate (P5C), and the subsequent conversion of P5C to glutamate. We have identified and characterized the Δ(1)-pyrroline-5-carboxylate dehydrogenase from T. cruzi (TcP5CDH) and report here on how this enzyme contributes to a central metabolic pathway in this parasite. Size-exclusion chromatography, two-dimensional gel electrophoresis, and small angle x-ray scattering analysis of TcP5CDH revealed an oligomeric state composed of two subunits of six protomers. TcP5CDH was found to complement a yeast strain deficient in PUT2 activity, confirming the enzyme's functional role; and the biochemical parameters (Km, kcat, and kcat/Km) of the recombinant TcP5CDH were determined, exhibiting values comparable with those from T. cruzi lysates. In addition, TcP5CDH exhibited mitochondrial staining during the main stages of the T. cruzi life cycle. mRNA and enzymatic activity levels indicated the up-regulation (6-fold change) of TcP5CDH during the infective stages of the parasite. The participation of P5C as an energy source was also demonstrated. Overall, we propose that this enzymatic step is crucial for the viability of both replicative and infective forms of T. cruzi.

Selenoproteins result from the incorporation of selenocysteine (Sec-U) at an UGA-stop codon positioned within a gene's open reading frame and directed by selenocysteine insertion sequence (SECIS) elements. Although the selenocysteine incorporation pathway has been identified in a wide range of organisms it has not yet been reported in the Kinetoplastida Leishmania and Trypanosoma. Here we present evidence consistent with the presence of a selenocysteine biosynthetic pathway in Kinetoplastida. These include the existence of SECIS-containing coding sequences in Leishmania major and Leishmania infantum, the incorporation of (75)Se into Leishmania proteins, the occurrence of selenocysteine-tRNA (tRNA (sec) (uca)) in both Leishmania and Trypanosoma and in addition the finding of all genes necessary for selenocysteine synthesis such as SELB, SELD, PSTK and SECp43. As in other eukaryotes, the Kinetoplastids have no identifiable SELA homologue. To our knowledge this is the first report on the identification of selenocysteine insertion machinery in Kinetoplastida, more specifically in Leishmania, at the sequence level.

Glucose-6-phosphate isomerase catalyzes the reversible aldose-ketose isomerization of D-glucose-6-phosphate to D-fructose-6-phosphate in glycolysis and gluconeogenesis, and in the recycling of hexose-6-phosphate in the pentose phosphate pathway. The unicellular protozoans, Trypanosoma brucei, T. cruzi and Leishmania spp., of the order Kinetoplastida are important human parasites responsible for African sleeping sickness, Chagas' disease and leishmaniases, respectively. In these parasites, glycolysis is an important (and in some cases the only) metabolic pathway for ATP supply. The first seven of the 10 enzymes that participate in glycolysis, as well as an important fraction of the enzymes of the pentose phosphate pathway, are compartmentalized in peroxisome-like organelles called glycosomes. The dependence of the parasites on glycolysis, the importance of the pentose phosphate pathway in defense against oxidative stress, and the unique compartmentalization of these pathways, point to the enzymes contained in the glycosome as potential targets for drug design. The present report describes the first crystallographic structure of a parasite (Leishmania mexicana) glucose-6-phosphate isomerase. A comparison of the atomic structure of L. mexicana, human and other mammalian PGIs, which highlights unique features of the parasite's enzyme, is presented.

Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.

The three-dimensional structure of Leishmania tarentolae adenine phosphoribosyltransferase (APRT) in complex with adenosine-5-monophosphate (AMP) and a phosphate ion has been solved. Refinement against X-ray diffraction data extending to 2.2-A resolution led to a final crystallographic R factor of 18.3%. Structural comparisons amongst this APRT enzyme and other 'type I' PRTases whose structures have been determined reveal several important features of the PRTases catalytic mechanism. Based on structural superpositions and molecular interaction potential calculations, it was possible to suggest that the PRPP is the first substrate to bind, while the AMP is the last product to leave the active site, in accordance to recent kinetic studies performed with the Leishmania donovani APRT.

Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) (EC 2.4.2.8) is an important enzyme involved in the recycling of purine nucleotides in all cells. Parasitic protozoa of the order Kinetoplastida are unable to synthesize purines de novo and use the salvage pathway for the synthesis of nucleotides; therefore, this pathway is an attractive target for antiparasitic drug design. The hgprt gene was cloned from a Leishmania tarentolae genomic library and the sequence determined. The L. tarentolae hgprt gene contains a 633-nucleotide open reading frame that encodes a 23.4-kDa protein. A pairwise alignment of the different HGPRT's sequences revealed a 26%-53% sequence identity with the Leishmania sequences and 87% identity to the HGPRT of Leishmania donovani. A recombinant protein was expressed in Escherichia coli, purified to homogeneity and found to retain enzymatic activity. The steady-state kinetic parameters were determined for the recombinant enzyme and the enzyme is active as a homodimer in solution. Single crystals were obtained for the L. tarentolae HGPRT representing the first Leishmania HGPRT crystallized and initial crystallographic data were collected. The crystals obtained belong to the orthorhombic space group (P2(1)2(1)2(1)) with unit cell parameters a=58.104 A, b=85.443 A and c=87.598 A and diffract to a resolution of 2.3 A. The availability of the HGPRT enzyme from Leishmania and its crystallization suitable for X-ray diffraction data collection should provide the basis for a functional and structural analysis of this enzyme, which has been proposed as a potential target for rational drug design, in a Leishmania model system.

The synthesis of selenocysteine-containing proteins (selenoproteins) involves the interaction of selenocysteine synthase (SelA), tRNA (tRNA(Sec)), selenophosphate synthetase (SelD, SPS), a specific elongation factor (SelB), and a specific mRNA sequence known as selenocysteine insertion sequence (SECIS). Because selenium compounds are highly toxic in the cellular environment, the association of selenium with proteins throughout its metabolism is essential for cell survival. In this study, we demonstrate the interaction of SPS with the SelA-tRNA(Sec) complex, resulting in a 1.3-MDa ternary complex of 27.0 ± 0.5 nm in diameter and 4.02 ± 0.05 nm in height. To assemble the ternary complex, SPS undergoes a conformational change. We demonstrated that the glycine-rich N-terminal region of SPS is crucial for the SelA-tRNA(Sec)-SPS interaction and selenoprotein biosynthesis, as revealed by functional complementation experiments. Taken together, our results provide new insights into selenoprotein biosynthesis, demonstrating for the first time the formation of the functional ternary SelA-tRNA(Sec)-SPS complex. We propose that this complex is necessary for proper selenocysteine synthesis and may be involved in avoiding the cellular toxicity of selenium compounds.

Chagas disease, Sleeping Sickness, Nagana and Leishmaniasis are serious infections caused by protozoa of the order Kinetoplastidae. They were described over a century ago by seminal work of different physician-researchers and, despite the initial discoveries, few drugs have been made available for the treatment of these infections. The drugs available present serious efficacy and toxicity problems. Moreover, the emergence of resistant strains has rendered the development of novel chemotherapeutic strategies a priority. Auranofin is currently in use to treat rheumatoid arthritis in humans. Previous reports showed that this compound presents activity against Trypanosoma brucei and Leishmania cells. In Trypanosoma cruzi cells, auranofin resulted in a more potent compound than benznidazole in vitro when tested in different DTUs. In vivo experiments, although not decreasing T. cruzi parasitemia, decreases host mortality. Therefore, we propose auranofin as a potential alternative for a new chemotherapy in Chagas disease with the added advantage of already being approved for use in humans.

The cyclohexane-1,2,3,4,5-pentol,C6H12O5 is a natural product extracted from Adiscanthus fusciflorus (Rutaceae). It crystallizes in the non-centrosymmetric space group P21 with one molecule in the asymmetric unit and it has been postulated to have at least ten strong O-H…O intermolecular interactions, two per each OH group of one molecule, producing a three-dimensional network. The crystal packing is defined by O-H…O hydrogen bonds. Due to the crucial role of the hydrogen bonds in defining the crystal structure, theoretical investigations in the gas phase have been carried out in order to explore the hydrogenbonding mechanism through a quantitative Kohn-Sham molecular orbital and corresponding energy decomposition analyses. The existence of a covalent component in hydrogen bonds has been proved which originates from donor-acceptor orbital interactions in the σ-electron system. Our analyses show that the stability of the crystal structure is enhanced by the formation of two hydrogen bonds with two vicinal molecules for each OH group in C6H12O5 molecule with respect to the formation of one or two hydrogen bonds with only one vicinal molecule, thus confirming the proposed existence of ten strong O-H…O intermolecular interactions for each molecule in the asymmetric unit. The presence of a cooperativity effect is observed which originates from a charge separation induced by the two vicinal molecules hydrogenbonded to an OH group in C6H12O5 molecule.

Leishmaniasis and Chagas disease, caused by the kinetoplastid parasites Leishmania spp and Trypanosoma cruzi, respectively, are among the most important parasitic diseases, affecting millions of people and considered to be within the most relevant group of neglected tropical diseases. Chemotherapy is the main alternative to control such parasites, nevertheless, current treatments are far from satisfactory. This review outlines the current understanding on different drugs against leishmaniasis and Chagas disease and their mechanism of action. Recent approaches in the area of anti-leishmanial and trypanocidal therapies are also enumerated, as well as the search for new drugs. Leishmaniose e doença de Chagas, causadas pelos parasitas kinetoplastideos Leishmania spp e Trypanosoma cruzi, respectivamente, estão entre as doenças parasitárias mais importantes, afetando milhões de pessoas e consideradas dentro do grupo mais relevante de doenças tropicais negligenciadas. A principal alternativa para controlar essas parasitoses é a quimioterapia. No entanto, os atuais tratamentos quimioterápicos estão longe de serem satisfatórios. Esta revisão delineia o entendimento atual de diferentes fármacos contra leishmaniose e doença de Chagas e seus mecanismos de ação. As abordagens recentes na área de terapias anti-Leishmania e tripanocida também são enumerados, assim como a busca por novas drogas.

Nucleotide synthesis is of central importance to all cells. In most organisms, the purine nucleotides are synthesized de novo from non-nucleotide precursors such as amino acids, ammonia and carbon dioxide. An understanding of the enzymes involved in sugarcane purine synthesis opens the possibility of using these enzymes as targets for chemicals which may be effective in combating phytopathogen. Such an approach has already been applied to several parasites and types of cancer. The strategy described in this paper was applied to identify sugarcane clusters for each step of the de novo purine synthesis pathway. Representative sequences of this pathway were chosen from the National Center for Biotechnology Information (NCBI) database and used to search the translated sugarcane expressed sequence tag (SUCEST) database using the available basic local alignment search tool (BLAST) facility. Retrieved clusters were further tested for the statistical significance of the alignment by an implementation (PRSS3) of the Monte Carlo shuffling algorithm calibrated using known protein sequences of divergent taxa along the phylogenetic tree. The sequences were compared to each other and to the sugarcane clusters selected using BLAST analysis, with the resulting table of p-values indicating the degree of divergence of each enzyme within different taxa and in relation to the sugarcane clusters. The results obtained by this strategy allowed us to identify the sugarcane proteins participating in the purine synthesis pathway.A via de síntese de purino nucleotídeos é considerada uma via de central importância para todas as células. Na maioria dos organismos, os purino nucleotídeos são sintetizados ''de novo'' a partir de precursores não-nucleotídicos como amino ácidos, amônia e dióxido de carbono. O conhecimento das enzimas envolvidas na via de síntese de purinas da cana-de-açúcar vai abrir a possibilidade do uso dessas enzimas como alvos no desenho racional de inibidores no combate a agentes fitopatogênicos, como esta sendo feita com diversos parasitos e células cancerosas. A seguinte estratégia esta sendo utilizada na identificação de genes de cana-de-açúcar para cada membro da via de síntese de purinas: Seqüências representativas dos genes que compões a via foram escolhidas do banco de dados NCBI. Essas seqüências de peptídeos estão sendo utilizadas em buscas ao banco de dados gerado pelo SUCEST pelo programa BLAST (implementação tBLASTn). Alinhamentos com os clusters de cana-de-a��úcar são posteriormente analisados para sua significância estatística pela implementação PRSS3 do algoritmo conhecido como Monte Carlo shuffling. Para calibrar a análise dos resultados de PRSS3, foram empregadas seqüências conhecidas de diferentes taxas ao longo da arvore filogenética. Essas seqüências são comparadas duas a duas e com o cluster da cana-de-açúcar. A tabela de valores-p resultante indica o grau estatístico de similaridade e divergência entre as seqüências já descritas e entre essas e os clusters de cana-de-açúcar. Os resultados obtidos dessas análises estão descritos neste artigo.

a Howard Hughes Medical Institute, UCLA School of Medicine, Los Angles, CA 90095-1662, USA b Laboratory of Protein Crystallography and Structural Biology, Physics Institute of San Carlos, Uni6ersity of Sao Paulo, A6. Dr. Carlos Botelho 1465, P.O. Box 369, San Carlos, SP 13560-970, Brazil c Department of Microbiology, Immunology and Molecular Genetics, 6780 MacDonald Building, 675 Charles Young Dri6e, Los Angeles, CA S 90095-1662, USA

Uridine insertion/deletion RNA editing is a post-transcriptional RNA modification occurring in the mitochondria of kinetoplastid protozoa. The U-insertion/deletion Edited Sequence Database is a compilation of mitochondrial genes and edited mRNAs from five kinetoplastid species. It contains separate files with the DNA, mRNA (both unedited and edited) and predicted protein sequences, as well as alignments of the Leishmania tarentolae and Trypanosoma brucei protein sequences from edited and unedited genes. The sequence files are in GCG format. A 'map' sequence file showing the location of U-deletions, U-insertions and the translated amino acid sequences is also provided for each gene. Genomic maps for each species are also provided with clickable genes, including maxicircle-encoded gRNAs. Sets of aligned nuclear rRNA sequences from kinetoplastid protozoa are also provided, which were used for phylogenetic reconstructions in an analysis of the origin of RNA editing. The database is available through the World Wide Web as an HTML document at the URLhttp://www.lifesci.ucla.edu/RNA/trypanosome/ database.html

Recent advances in in vitro systems and identification of putative enzymatic activities have led to the acceptance of a modified ‘enzyme cascade’ model for U insertion/deletion RNA editing in kinetoplastid mitochondria. Models involving the transfer of uridines (Us) from the 34-end of gRNA to the editing site appear to be untenable. Two types of in vitro systems have been reported: (i) a gRNA-independent U insertion activity that is dependent on the secondary structure of the mRNA; (ii) a gRNA-dependent U insertion activity that requires addition of a gRNA that can form an anchor duplex with the pre-edited mRNA and which contains guiding A and G nucleotides to base pair with the added Us. In the case of the gRNA-mediated reaction, the precise site of cleavage is at the end of the gRNA‐mRNA anchor duplex, as predicted by the original model. The model has been modified to include the addition of multiple Us to the 34-end of the 54-cleavage fragment, followed by the formation of base pairs with the guiding nucleotides and trimming back of the single-stranded oligo(U) 34-overhang. The two fragments, which are held together by the gRNA ‘splint’, are then ligated. Circumstantial in vitro evidence for involvement of an RNA ligase and an endoribonuclease, which are components of a 20S complex, was obtained. Efforts are underway in several laboratories to isolate and characterize specific components of the editing machinery.

Leishmania RNA Virus (LRV, Totiviridae) infect Leishmania cells and subvert mice immune response, probably promoting parasite persistence, suggesting significant roles for LRV in host-parasite interaction. Here we describe a new LRV1-4 purification protocol, enabling capsid visualization by negatively stained electron microscopy representing a significant contribution to future LRV investigations.

Phosphoribosylpyrophosphate synthases (PRS; EC 2.7.6.1) are enzymes that are of central importance in several metabolic pathways in all cells. The sugar cane PRS enzyme contains 328 amino acids with a molecular weight of 36.6 kDa and represents the first plant PRS to be crystallized, as well as the first phosphate-independent PRS to be studied in molecular detail. Sugar cane PRS was overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. Using X-ray diffraction experiments it was determined that the crystals belong to the orthorhombic system, with space group P2(1)2(1)2 and unit-cell parameters a = 213.2, b = 152.6, c = 149.3 A. The crystals diffract to a maximum resolution of 3.3 A and a complete data set to 3.5 A resolution was collected and analysed.

The title acid, C16H20O5, was extracted from Adiscanthus fusciflorus (Rutaceae) and is shown to inhibit adenine phospho­ribosyl­transferase (APRT) enzyme activity. This compound crystallizes in the centrosymmetric space group C2/c with one mol­ecule in the asymmetric unit. There is one strong hydrogen bond, with OD⋯OA = 2.6238 (12) A and OD—H⋯OA = 171.1 (17)° involving the COOH group, forming a cyclic dimer about a center of symmetry. The packing of the mol­ecules is additionally stabilized by one C—H⋯O [CD⋯OA = 2.9820 (16) A and CD—H⋯OA = 101.8 (10)°] and two C—H⋯π intermolecular hydrogen bonds.

The title compound (alternative name 5,8-di­methoxy­psoralen), C13H10O5, is a natural product extracted from Adiscanthus fusciflorus (Rutaceae). Our biochemical tests show that this compound has inhibitory activity against the enzyme adenine phospho­ribosyl­transferase (APRT) from Leishmania, a tropical parasite causing endemic disease in poor countries. It crystallizes in the centrosymmetric space group P21/c, with one mol­ecule in the asymmetric unit, and has at least two C—H⋯O intermolecular interactions, leading to the formation of centrosymmetric dimers.

The title compound (alternative names 7,8-di­methoxy­dictam­mine and 4,7,8-tri­methoxy­furo­[2,3-b]­quinoline), C14H13NO4, is a natural product extracted from Adiscanthus fusciflorus (Ruta­ceae). Our biochemical tests show that it has inhibitory activity against the enzyme adenine phospho­ribosyl­transferase (APRT) from Leishmania, a tropical parasite causing endemic disease in poor countries. It crystallizes in the centrosymmetric space group P21/c, with one mol­ecule in the asymmetric unit, and has at least two C—H⋯O intermolecular interactions, leading to the formation of centrosymmetric dimers.

Xylella fastidiosa is responsible for a wide range of economically important plant diseases. We report here the crystal structure and kinetic data of Xylellain, the first cysteine protease characterized from the genome of the pathogenic X. fastidiosa strain 9a5c. Xylellain has a papain-family fold, and part of the N-terminal sequence blocks the enzyme active site, thereby mediating protein activity. One novel feature identified in the structure is the presence of a ribonucleotide bound outside the active site. We show that this ribonucleotide plays an important regulatory role in Xylellain enzyme kinetics, possibly functioning as a physiological mediator.Structured summary of protein interactionsXylellain and Xylellain bind by X-ray crystallography (View interaction)

RNA editing in kinetoplastids appears to be a labile genetic trait that is affected by prolonged cell culture. The transcripts of the G1-G5 cryptogenes are pan-edited in the recently isolated LEM125 strain of Leishmania tarentolae, but not in the UC strain which has been in culture for 55 years. At least 32 minicircle-encoded guide RNAs (gRNAs) for the editing of G1-G5 transcripts are present in LEM125 and absent in UC. We hypothesize that specific minicircle sequence classes encoding gRNAs for the editing of these transcripts were lost during the long culture history of the UC strain. The protein products, which include components of complex I of the respiratory chain, are probably not required during the culture stage of the Leishmania life cycle.

RNA editing in the mitochondrion (kinetoplas0 of trypanosomatid protozoa involves a post-transcriptional addition and deletion of uridilate residues [14]. The sites of editing are specified by small guide RNA transcripts (gRNAs), which are encoded in both kinetoplast DNA minicircles and maxicircles. The process initiates with a short region of base-pairing (anchor formation) between a specific gRNA and a pre-edited mRNA, and generally proceeds in a 5' direction with the insertion and deletion of uridilate (U) residues. The precise sites and number of Us inserted and/or deleted is determined by base-pairing with guide adenine or guanine nucleotides in the gRNA. Two basic models have been proposed for the mechanism of this process, one involving two