Sequence of the 24S alpha ribosomal RNA gene and characterization of a corresponding pseudogene from Trypanosoma cruzi

Trypanosomatid Richness in Wild and Synanthropic Small Mammals from a Biological Station in Rio de Janeiro, Brazil

Trypanosomatids are diverse and can infect several host species, including small mammals (rodents and marsupials). Between 2012 and 2014, 91 small mammals were surveyed for trypanosomatid infection in the Estação Biológica FIOCRUZ Mata Atlântica (EFMA), an Atlantic Forest area in Rio de Janeiro that presents different levels of conserved and degraded areas. Blood, skin, liver, and spleen samples were submitted to parasitological, serological, and molecular assays to detect the infection and determine the taxonomic status of their parasites. Sixty-eight individuals (74.7%; n = 91) were infected by trypanosomatids, including fourteen mixed infected by different trypanosomatid parasites. These hosts were infected by: T. cruzi DTU TcI (n = 12), T. cruzi DTU TcIV (n = 2), T. janseni (n = 15), T. dionisii (n = 1), and T. rangeli A (n = 1) detected in blood or tissue cultures, in addition to T. cruzi DTU TcI (n = 9) and Leishmania sp. (n = 1) only by the molecular diagnosis. Serological diagnosis was positive in 38 (71.6%) individuals for T. cruzi, the same amount for Leishmania spp., and 23 (43.3%) individuals were mixed infected. These data indicate a remarkable richness of trypanosomatid species/genotypes infecting small mammals, even in a disturbed area with low mammal species diversity—as is the case of the EFMA—reinforcing the generalist aspect of these parasites.

Trypanosoma rangeli 28Sβ Ribosomal Gene Allows Intra and Interspecific Molecular Differentiation

Trypanosoma rangeli is an avirulent flagellate protozoan that could mislead correct diagnosis of Trypanosoma cruzi infection, the causative agent of Chagas' disease, given their high similarity. Besides, T. rangeli presents two genetic groups, whose differentiation is achieved mainly by molecular approaches. In this context, ribosomal DNA (rDNA) is a useful target for intra and interspecific molecular differentiation. Analyzing the rDNA of T. rangeli and comparison with other trypanosomatid species, two highly divergent regions (Trβ1 and Trβ2) within the 28Sβ gene were found. Those regions were amplified and sequenced in KP1(+) and KP1(-) strains of T. rangeli, revealing group-specific polymorphisms useful for intraspecific distinction through restriction fragment length polymorphism technique. Also, amplification of Trβ1 allowed differentiation between T. rangeli and T. cruzi. Trβ2 predicted restriction length profile, allowed differentiation between T. rangeli, T. cruzi, Trypanosoma brucei, and Leishmania braziliensis, increasing the use of Trβ1 and Trβ2 beyond a molecular approach for T. rangeli genotyping, but also as a useful target for trypanosomatid classification.

Genetic Variability of Trypanosoma cruzi:Implications for the Pathogenesis of Chagas Disease

Chagas disease, caused by the protozoan Trypanosoma cruzi, has a variable clinical course, ranging from symptomless infection to severe chronic disease with cardiovascular or gastrointestinal involvement or even overwhelming acute episodes. The factors influencing this clinical variability have not been elucidated, but genetic variation of both the host and parasite is likely to be important. Here, Andréa M. Macedo and Sérgio D.J. Pena review the evidence showing a role for the genetic constitution of T. cruzi in determining the clinical characteristics of Chagas disease, and propose a ;clonal-histotropic model' for the pathogenesis of this disease.

Genomic repetitive DNA elements of Trypanosoma cruzi

Repetitive DNA sequences are interspersed throughout the genomes of mammals and other higher eukaryotes, and represent a substantial portion of the genome. Although it has been generally assumed that the redundant DNA is present only in the complex genomes of high order organisms, over the past few years a number of repetitive DNA sequences have been also detected in the protozoan parasite Trypanosoma cruzi. A compilation of the repetitive DNA sequences found in the T. cruzi genome is here presented by Jose Maria Requena, Manuel Carlos López and Carlos Alonso, who also speculate on their possible origin and functional implications regarding retrotransposition and gene regulation.

Trypanosoma cruzi: genetic structure of populations and relevance of genetic variability to the pathogenesis of chagas disease

Chagas disease, caused by the protozoan Trypanosoma cruzi, has a variable clinical course, ranging from symptomless infection to severe chronic disease with cardiovascular or gastrointestinal involvement or, occasionally, overwhelming acute episodes. The factors influencing this clinical variability have not been elucidated, but it is likely that the genetic variability of both the host and the parasite are of importance. In this work we review the the genetic structure of T. cruzi populations and analyze the importance of genetic variation of the parasite in the pathogenesis of the disease under the light of the histotropic-clonal model.

Evaluation of Trypanosoma cruzi hybrid stocks based on chromosomal size variation

Although all classical lines of evidence point to the fact that Trypanosoma cruzi has a predominantly clonal evolution, accumulating data show that some T. cruzi stocks are the result of hybridisation events. We evaluated whether chromosomal polymorphism would give evolutionary information on hybrid isolates. Twenty-three coding sequences were mapped on the chromosomes of nine parasite stocks, four of which are putative hybrids (CL Brener and rDNA group 1/2). Phenetic analyses of karyotype data were based on the absolute chromosomal size difference index (aCSDI), a method that assumes that the genomic distance between two organisms is the sum of the size differences between their homologous chromosomes. aCSDI-based dendrograms obtained from a variable number of probes (3-18 probes) defined in all the cases three clusters: two corresponding, respectively, to T. cruzi I and T. cruzi II groups; and a third one, to rDNA group 1/2. CL Brener was alternatively positioned in T. cruzi II or rDNA group 1/2 clusters. Three clusters were also observed in the dendrogram constructed with restriction fragment length polymorphism (RFLP) data from 18 probes. The topology of the chromosome and RFLP dendrograms is similar, with a significant correlation coefficient (r=0.86062; P<0.0001), supporting a strong structuring of the clusters. This study also revealed that hybrid stocks have a larger proportion of two different-sized homologous chromosomes, as compared with non-hybrid strains. Overall, our results show that chromosomes are valuable characters for identification of evolutionary groups, in particular, T. cruzi hybrid organisms.

Two types of ribosomal RNA genes in hybrid Trypanosoma cruzi strains

Trypanosoma cruzi isolates can be divided into two major phylogenetic lineages-T. cruzi I and T. cruzi II. The population structure is predominantly clonal, with sexuality having no or limited influence on the evolution of the parasite. Isoenzymes and nuclear gene sequences have provided evidence that some T. cruzi strains are hybrids. Previous work of our group has shown that the putative hybrid strains designated as group 1/2 contain two types of rDNA units, corresponding to those found in T. cruzi I and T. cruzi II. In this study, the presence and transcription of the two types of ribosomal RNA (rRNA) cistrons were investigated in epimastigotes, metacyclic and tissue culture trypomastigotes of group 1/2 isolates. PCR and RT-PCR assays indicate that both types of cistrons are present in group 1/2 strains, but only type-2 genes are transcribed in all developmental stages. The structure of the promoter regions of group 1/2 was compared to reference T. cruzi I and T. cruzi II strains. In all cases, the transcription start point was mapped to a conserved A residue located approximately 1800 bp upstream the 18S rRNA gene. The distribution of rDNA clusters in chromosomal bands of group 1/2 was evaluated by pulsed-field gel electrophoresis (PFGE). The majority of type-2 rDNA genes are localized in a 1.5 Mbp band, whereas type-1 cistrons are mostly concentrated in a 1.1 Mbp band. The structural and functional studies of group 1/2 ribosomal cistrons described here may shed light on the evolutionary processes that took place during the generation of such hybrid organisms.

A Trypanosoma cruzi small surface molecule provides the first immunological evidence that Chagas' disease is due to a single parasite lineage

Chagas' disease is a major health and economic problem caused by the protozoan Trypanosoma cruzi. Multiple independently evolving clones define a complex parasite population that can be arranged into two broad genetic lineages termed T. cruzi I and II. These lineages have different evolutionary origin and display distinct ecological and biological traits. Here we describe a novel molecule termed TSSA for trypomastigote small surface antigen that provides the first immunological marker allowing discrimination between lineages. TSSA is a surface, glycosylphosphatidyl inositol (GPI)-anchored mucin-like protein, highly antigenic during the infection. TSSA sequences from different parasite isolates reveal a population dimorphism that perfectly matches with the two T. cruzi lineages. Interestingly, this dimorphism is restricted to the central region of the molecule, which comprises the immunodominant B cell epitopes. This sequence variability has a major impact on TSSA antigenicity, leading to no immunological cross-reactivity between both isoforms for antibodies present either in immunization or infection sera. Furthermore, the absolute seroprevalence for TSSA in confirmed Chagasic patients is restricted to T. cruzi II isoform, strongly suggesting that human infections are due to this particular subgroup. Even though association of T. cruzi II with Chagas' disease has been proposed based on molecular markers, this is the first immunological evidence supporting this hypothesis. The implications of these results for the future research on Chagas' disease could be envisaged.

MRNA encoding a putative RNA helicase of the DEAD-box gene family is up-regulated in trypomastigotes of Trypanosoma cruzi

Differential display of mRNAs from Trypanosoma cruzi epimastigote and metacyclic trypomastigote stages showed several mRNA species differing in their expression level. The cDNA corresponding to one of these mRNAs was used as a probe in Northern blots and identified a RNA product of 2.6 kb with an expression level eight or more times higher in trypomastigotes than in epimastigotes. This probe was also used to screen a genomic library of T. cruzi CL Brener clone prepared in lambda FIX. A clone of about 15 kb was selected that, after partial sequencing, revealed an open reading frame of 688 amino acids encoding a deduced protein with similarity to RNA helicases of the DEAD-box gene family. The presence of the eight conserved motifs characteristic of the DEAD protein family was observed in the T. cruzi sequence, indicating that it corresponds to a putative RNA helicase gene, which we named HelTc. Southern blot analysis indicated that HelTc is a single-copy gene. Pulsed-field gel electrophoresis separation of chromosomes of several isolates of T. cruzi showed that this gene was localized in one or two chromosomal bands.

Genomic clustering of the Trypanosoma cruzi nonlong terminal L1Tc retrotransposon with defined interspersed repeated DNA elements

We have analyzed the genomic distribution and organization of the long interspersed nucleotide element (LINE) L1Tc, a nonlong terminal repeat (LTR) retrotransposon of Trypanosoma cruzi. The results indicate that the L1Tc element is dispersed along the parasite genome and that in some regions it is organized in tandem repeats. The data allowed us to define the existence of short direct-repeated sequences flanking the genomic L1Tc elements. Relevant is the finding that the LINE L1Tc is located in genomic regions rich in short interspersed nucleotide elements (SINE)-like sequences. In particular, the L1Tc element is found associated to E13-related sequences, redefined in this work and renamed RS13Tc, and to a newly described RS1Tc sequence. The RS1Tc sequence is present, per haploid genome, in about 3,200 copies. Northern blot analysis showed that the RS1Tc is being transcribed into RNAs of different sizes. The analysis of the chromosomal distribution of these elements in various strains of T. cruzi suggested that this type of clustering might be a common feature of the genome of these parasites.

The short interspersed repetitive element of Trypanosoma cruzi, SIRE, is part of VIPER, an unusual retroelement related to long terminal repeat retrotransposons

The short interspersed repetitive element (SIRE) of Trypanosoma cruzi was first detected when comparing the sequences of loci that encode the TcP2beta genes. It is present in about 1,500-3,000 copies per genome, depending on the strain, and it is distributed in all chromosomes. An initial analysis of SIRE sequences from 21 genomic fragments allowed us to derive a consensus nucleotide sequence and structure for the element, consisting of three regions (I, II, and III) each harboring distinctive features. Analysis of 158 transcribed SIREs demonstrates that the consensus is highly conserved. The sequences of 51 cDNAs show that SIRE is included in the 3' end of several mRNAs, always transcribed from the sense strand, contributing the polyadenylation site in 63% of the cases. This study led to the characterization of VIPER (vestigial interposed retroelement), a 2,326-bp-long unusual retroelement. VIPER's 5' end is formed by the first 182 bp of SIRE, whereas its 3' end is formed by the last 220 bp of the element. Both SIRE moieties are connected by a 1,924-bp-long fragment that carries a unique ORF encoding a complete reverse transcriptase-RNase H gene whose 15 C-terminal amino acids derive from codons specified by SIRE's region II. The amino acid sequence of VIPER's reverse transcriptase-RNase H shares significant homology to that of long terminal repeat retrotransposons. The fact that SIRE and VIPER sequences are found only in the T. cruzi genome may be of relevance for studies concerning the evolution and the genome flexibility of this protozoan parasite.

Functional analysis of the intergenic regions of TcP2beta gene loci allowed the construction of an improved Trypanosoma cruzi expression vector

TcP2beta ribosomal protein genes in Trypanosoma cruzi are encoded by four different loci, H6.4, H1.8, H1.5 and H1.3. All loci have a similar organization, except for H1.8 that harbors two TcP2beta genes arranged in tandem and separated by a short repetitive sequence, named SIRE (short interspersed repetitive element), which is also found upstream of the first gene of the tandem and downstream of the second. In this locus the trans-splicing signal of TcP2beta is located within the SIRE element, while in the other loci it is positioned within the first 50bases upstream of the AUG with an AG acceptor site at position -12 respective to the initiation codon. Transient transfection experiments were used to evaluate the efficiency of these two different trans-splicing regions to drive CAT activity. The region named HX1 located upstream the TcP2beta H1. 8 gene was clearly more efficient than the SIRE sequence contained in the region named HX2. Therefore, we decided to use the HX1 region to ameliorate the performance of the cryptic trans-splicing signal present in the T. cruzi expression vector pRIBOTEX (Martinez-Calvillo, S., López, I., Hernandez, H., 1997. pRIBOTEX expression vector: a pTEX derivative for a rapid selection of Trypanosoma cruzi transfectants. Gene 199, 71-76). By insertion of the region HX1 downstream of the ribosomal promoter of pRIBOTEX, we constructed pRHX1CAT40 that, in stable transfected cells, was able to drive CAT activity 2760 times more efficiently than the control plasmids. Based on this, a novel plasmid vector was conceived, named pTREX-n, which retains the neo gene of pRIBOTEX as a positive selectable marker and replaces the CAT-SV40 cassette in pRHX1CAT40 by a multiple cloning site.

Virulence in Trypanosoma cruzi infection correlates with the expression of a distinct family of sialidase superfamily genes

The overall success of Trypanosoma cruzi depends on its ability to invade the host and establish a long-term infection. Little is known of the genetic factors responsible for observed differences in virulence from strain to strain in T. cruzi. A virulent T. cruzi line was derived from an attenuated parental line by two passages through mice. To identify virulence genes a subtraction library was constructed and screened for cDNA expressed exclusively in the virulent line. One cDNA hybridized to 3.5 and 4.5 Kb RNA present in virulent trypomastigotes but absent in attenuated trypomastigotes. Sequence analysis showed the cDNA to encode an 85 kDa protein with homology to members of the sialidase/trans-sialidase superfamily and has been designated vp85.1. The highest amino acid sequence similarity was to a previously described T. cruzi sialidase-homologue pseudogene [Takle, G.B., O'Conner, J., Young, A.J. and Cross, G.A.M. (1992) Mol. Biochem. Parasitol. 56, 117-128]. The vp85.1 amino acid sequence has higher homology to members of the 160 kDa flagellar-associated antigen family, FL-160, than to other 85 kDa expressed sialidase superfamily members. Southern blot analysis of virulent and attenuated lines demonstrated a complex hybridization pattern consistent with a multiple gene copy family that was identical in both lines. Antibody directed against recombinant vp85.1 peptide recognized proteins between 95 and 115 kDa in total virulent parasite lysates which were absent in attenuated lysates. Peptide N-glycosidase F treatment reduced the high molecular weight bands to 85 kDa, indicating vp85 is an N-linked glycoprotein. Immunofluorescence with anti-vp85.1 demonstrated surface localization of vp85.1 on virulent, but not attenuated, trypomastigotes. We postulate this new subfamily of trans-sialidases may play a role in virulence.

Control mechanisms of the H2A genes expression in Trypanosoma cruzi

In a previous report we have described that the T. cruzi histone H2A gene is encoded in two independent gene clusters located in a single chromosome. In the present paper we show that both gene cluster are actively transcribed as two sized classes of polyadenylated mRNAs demonstrating, moreover, the existence of alternative splicing sites and microheterogeneities at the polyadenylation site. We also describe that while the expression of the H2A genes in the non replicative trypomastigote forms is only residual, in the replicative forms there is constitutive transcription of these genes and that the transcription is not associated to DNA replication. The data show, moreover, that in the replicative forms the steady state levels of the H2A mRNAs are controlled at a post-transcriptional level which is associated to DNA replication.

The Trypanosoma cruzi genome project: nuclear karyotype and gene mapping of clone CL Brener

By using improved pulsed field gel electrophoresis conditions, the molecular karyotype of the reference clone CL Brener selected for Trypanosoma cruzi genome project was established. A total of 20 uniform chromosomal bands ranging in size from 0.45 to 3.5 Megabase pairs (Mbp) were resolved in a single run. The weighted sum of the chromosomal bands was approximately 87 Mbp. Chromoblots were hybridized with 39 different homologous probes, 13 of which identified single chromosomes. Several markers showed linkage and four different linkage groups were identified, each comprising two markers. Densitometric analysis suggests that most of the chromosomal bands contain two or more chromosomes representing either homologous chromosomes and/or heterologous chromosomes with similar sizes.

Leishmania major: comparison of the cathepsin L- and B-like cysteine protease genes with those of other trypanosomatids

Cysteine proteases play important roles in the pathogenesis of several parasitic infections and have been proposed as targets for the structure-based strategy of drug design. As a first step toward applying this strategy to design inhibitors as antiparasitic agents for leishmaniasis, we have isolated and sequenced the full-length clones of two cysteine protease genes from Leishmania major. One of the genes is structurally similar to the cathepsin L-like family and the other is similar to the cathepsin B-like family of cysteine proteases. The L. major cathepsin L-like sequence has a proregion that shares high sequence similarity with other cathepsin L sequences but not cathepsin B sequences and has a proline/threonine-rich C-terminal extension. The cathepsin L-like gene occurs in multiple copies, whereas there may be only one copy of the cathepsin B-like gene. Northern blot analyses show that both genes are expressed in the promastigote and amastigote stages, and pulse field gel electrophoresis revealed that the cathepsin L- and B-like genes are each found on two nonhomologous chromosomes. The L. major L-like amino acid sequence is 75% identical to the L. mexicana sequence, 74% identical to the L. pifanoi sequence, 47% identical with the Trypanosoma cruzi sequence, 47% identical with the T. congolense sequence, and 45% identical with the T. brucei sequence. L. major is one of two trypanosomatid species for which a cathepsin B-like gene has been identified and sequenced; its amino acid sequence is 82% identical to the one from L. mexicana. Tree inference based on distance and parsimony methods of kinetoplastid cathepsin L proteins yielded independent support for phylogenetic hypotheses inferred from analyses of ribosomal RNA genes. Because the cathepsin L locus has a high level of phylogenetic signal with respect to trypanosomatid taxa, this locus has great potential utility for investigating the evolutionary history of trypanosomatids and related organisms.

Post-transcriptional elements regulating expression of mRNAs from the amastin/tuzin gene cluster of Trypanosoma cruzi

The genome of Trypanosoma cruzi contains tandemly arrayed copies of the gene encoding amastin, an abundant protein on the surface of the amastigote stage of the parasite. The transcription rate of the amastin genes is the same in the different developmental stages, but the steady state level of the 1.4-kilobase amastin mRNA is 50-85 times higher in amastigotes than in epimastigotes or trypomastigotes (1). Here we show that the amastin genes alternate with genes encoding another protein, called tuzin, whose 1.7-kilobase mRNA is much less abundant in amastigotes. The 3'-untranslated region (UTR) of tuzin mRNA is only a few nucleotides in length or even nonexistent, in contrast with the 630-nucleotide 3'-UTR of amastin mRNA. No promoter elements were found upstream or within the amastin/tuzin gene cluster. However, in amastigotes, the protein synthesis inhibitor cycloheximide caused a 3-fold decrease in amastin mRNA and a 7-fold increase in tuzin mRNA. Furthermore, when the amastin 3'-UTR plus its downstream intergenic region were fused behind the luciferase coding region in a chimeric plasmid for transient transfections, luciferase activity increased 7-fold in amastigotes and decreased 5-fold in epimastigotes. Thus, developmental expression of these alternating genes is regulated by different mechanisms.

A short interspersed repetitive element provides a new 3' acceptor site for trans-splicing in certain ribosomal P2 beta protein genes of Trypanosoma cruzi

Four Trypanosoma cruzi genomic DNA fragments carrying different TcP2 beta genes have been isolated and sequenced. Three of them had a single TcP2 beta gene, while the 3.8-kb-long DNA segment encoding the TcP2 beta-H1.8 locus showed two TcP2 beta genes arranged in tandem. These genes were physically connected by a 428-bp-long DNA sequence that was also located immediately 5' to the first gene and immediately 3' to the second. Comparison of the 4 TcP2 beta gene loci, suggested that the insertion of this repeated element originated the duplication of its target sequence, a poly(dT) stretch. Approximately 1200 copies of this short sequence, named short interspersed repetitive element (SIRE), were found scattered in the genome. Analysis of the 5' non-coding regions of different TcP2 beta mRNAs, and RNA-PCR experiments suggested that the insertion of a SIRE upstream of a TcP2 beta-H1.8 gene introduced a new 3' spliced leader (SL) acceptor site in the TcP2 beta-H1.8 pre-mRNAs, encoded within the SIRE. Consequently, in the mature H1.8 mRNA the SL sequence is followed by 38 bases directly transcribed from the SIRE. Structural and functional features of this repeated element reveal similarity to the short interspersed repetitive DNA sequences detected in the genomes of several microorganisms.

Sensitive detection and strain classification of Trypanosoma cruzi by amplification of a ribosomal RNA sequence

A sequence of about 100 bp of the 24S alpha ribosomal RNA was investigated for sensitive detection of Trypanosoma cruzi. It was shown that the target sequence is specific for this parasite and no cross-reactivity was observed with different species of pathogenic Leishmania, two strains of Trypanosoma rangeli or human RNA. Amplification of the sequence was obtained by reverse transcription coupled to polymerase chain reaction. Following this procedure the equivalent to 0.1% of the nucleic acid content of a single parasite cell could be detected either by ethidium staining or blot hybridization. The distribution of the target sequence in sixteen strains of T. cruzi was investigated. Positive amplification was obtained for all samples employing the same oligonucleotides as primers. However, amplified fragments of 125 bp were obtained in eight strains, while fragments of 110 bp were detected in the remaining eight isolates. No amplification of both classes of fragments has been detected in any of the strains examined. Dimorphism in the target region was confirmed by hybridization to specific internal probes and sequencing, allowing the division of T. cruzi strains in two groups. It is proposed that sensitive parasite detection could be achieved by rRNA amplification followed by hybridization to two probes derived from the target sequences of both groups of T. cruzi strains. Furthermore, the sequence dimorphism found in this sequence opens the perspective of strain typing simultaneous with parasite detection.

Repetitive sequences in the ribosomal intergenic spacer of Trypanosoma cruzi

A fragment of Trypanosoma cruzi ribosomal intergenic spacer (IGS) located at 6.7 kb from the 3' end of the 24S rRNA gene was analyzed. This IGS fragment is characterized by the presence of three types of repetitive elements (designated Spacer Repetitive Elements, SRE), short direct repeats (5-6 bp) and chi-like recombinational sequences. SRE elements are composed of relatively short repeats (43-145 bp) which show variabilities consisting of nucleotide changes, insertions and deletions. SRE-1 element (145 bp) has a short oligo(dA) tail at the end of the repeat and can be found flanked by other SRE elements. SRE elements are species-specific, suggesting that probes based on them may be diagnostic for Trypanosoma cruzi.