Circular DNA of Entamoeba histolytica encodes ribosomal RNA

Molecular screening of Entamoeba spp. (E. histolytica, E. dispar, E. coli, and E. hartmanni) and Giardia intestinalis using PCR and sequencing

A wide range of intestinal protozoan parasites inhabit the human gut. To establish a more comprehensive molecular screening, we designed PCR-sequencing screening methods for Entamoeba spp., including commensal species, and Giardia intestinalis, and performed such methods using 174 stool samples collected from Kenyan children. The prevalences of the target species were as follows: E. histolytica (2/174, 1.1%), E. dispar (20/174, 11.5%), E. coli (107/174, 61.5%), E. hartmanni (77/174, 44.3%), and G. intestinalis (54/174, 31.0%). PCR amplicons specific to G. intestinalis was differentiated to assemblages A (8/174, 4.6%) and B (46/174, 26.4%). PCR specificity for Entamoeba spp. was quite high, except for some cross-reactions between E. hartmanni detection primers and G. intestinalis, although the false-positive amplicons were discernible by the band size. The 18S rRNA PCR primers that was designed by Monis et al. in 1999 for G. intestinalis, have specificity issue, therefore amplicon sequencing was essential not only to determine assemblage classifications but also to confirm the positive results by eliminating potential non-specific reactions. The detection sensitivity of both the Entamoeba universal PCR and the G. intestinalis PCR was more than 100 copies of the target loci, which is sufficient for detecting a single trophozoite or cyst of both species.

Amplicon-based next-generation sequencing of eukaryotic nuclear ribosomal genes (metabarcoding) for the detection of single-celled parasites in human faecal samples

Comprehensive detection and differentiation of intestinal protists mostly rely on DNA-based methods. Here, we evaluated next-generation sequencing of eukaryotic nuclear ribosomal genes (metabarcoding) for the detection and differentiation of intestinal eukaryotic protists in the stool of healthy Tunisian individuals.

Thirty-six faecal DNA samples previously evaluated by microscopy and ameboid species-specific PCRs were tested. The hypervariable regions V3-V4 and V3-V5 of the 18S rRNA gene were amplified using three universal eukaryotic primer sets and sequenced using Illumina®MiSeq sequencing. In addition, real-time PCR assays were used to detect Dientamoeba fragilis, Giardia duodenalis, and Cryptosporidium spp.

The metabarcoding assay detected Blastocystis (subtypes 1, 2, and 3) and archamoebid species and subtypes (Entamoeba dispar, Entamoeba hartmanni, Entamoeba coli RL1 and RL2, Endolimax nana, Iodamoeba bütschlii RL1) in 27 (75%) and 22 (61%) of the 36 stool samples, respectively. Meanwhile, the assay had limited sensitivity for flagellates as evidenced by the fact that no Giardia-specific reads were found in any of the five Giardia-positive samples included, and Dientamoeba-specific reads were observed only in 3/13 D. fragilis-positive samples. None of the samples were positive for Cryptosporidium by any of the methods. In conclusion, a large variety of intestinal eukaryotic protists were detected and differentiated at species and subtype level; however, limited sensitivity for common flagellates was observed.

Complete Genome Sequence of the Circular Extrachromosomal Element of Naegleria gruberi Strain EGB Ribosomal DNA

The circular extrachromosomal element of Naegleria gruberi strain EGB was linearized, molecularly cloned, and fully sequenced. The sequence comprises 14,007 bp and encodes the organism’s rRNA genes, two potential open reading frames, and numerous repeated sequence regions.

Identification of EhTIF-IA: The putative E. histolytica orthologue of the human ribosomal RNA transcription initiation factor-IA

Initiation of rDNA transcription requires the assembly of a specific multi-protein complex at the rDNA promoter containing the RNA Pol I with auxiliary factors. One of these factors is known as Rrn3P in yeast and Transcription Initiation Factor IA (TIF-IA) in mammals. Rrn3p/TIF-IA serves as a bridge between RNA Pol I and the pre-initiation complex at the promoter. It is phosphorylated at multiple sites and is involved in regulation of rDNA transcription in a growth-dependent manner. In the early branching parasitic protist Entamoeba histolytica, the rRNA genes are present exclusively on circular extra chromosomal plasmids. The protein factors involved in regulation of rDNA transcription in E. histolytica are not known. We have identified the E. histolytica equivalent of TIF-1A (EhTIF-IA) by homology search within the database and was further cloned and expressed. Immuno-localization studies showed that EhTIF-IA co-localized partially with fibrillarin in the peripherally localized nucleolus. EhTIF-IA was shown to interact with the RNA Pol I-specific subunit RPA12 both in vivo and in vitro. Mass spectroscopy data identified RNA Pol I-specific subunits and other nucleolar proteins to be the interacting partners of EhTIF-IA. Our study demonstrates for the first time a conserved putative RNA Pol I transcription factor TIF-IA in E. histolytica.

Laboratory methods of identification of Entamoeba histolytica and its differentiation from look-alike Entamoeba spp

Entamoeba histolytica, the causative agent of intestinal and extraintestinal amebiasis, is a common parasitic cause of significant morbidity and mortality in the developing countries. Hence, early detection and differentiation of pathogenic E. histolytica from nonpathogenic/commensal Entamoeba spp (Entamoeba dispar/Entamoeba moshkovskii/Entamoeba bangladeshi) plays a crucial role in clinical management of patients with amebiasis. Most diagnostic tests currently available do not reliably differentiate between the species of Entamoeba and are less sensitive, cumbersome to perform. Molecular-based methods are highly sensitive, easy to perform and differentiates the pathogenic Entamoeba from nonpathogenic species, serving the criteria for an ideal diagnostic test for amebiasis. Recently, microarray technology has been found to be a promising tool for the diagnostic and epidemiological evaluation of amebiasis.

Detection of the amoeba Entamoeba gingivalis in periodontal pockets

Periodontitis is a public health issue, being one of the most prevalent diseases worldwide. However, the aetiology of the disease is still unclear: genetics of patients cannot explain the dispersed or isolated localisation of gingival pockets, while bacteria-based models are insufficient to distinguish gingivitis and periodontitis. The possible role of parasites in the establishment of periodontitis has been poorly studied until now. The aim of this project was to study a potential link between colonisation of gingival crevices by the amoeba Entamoeba gingivalis and periodontitis. In eight different dental clinics in France, samples were taken in periodontal pockets (72) or healthy sites (33), and submitted to microscopic observation and molecular identification by PCR with a new set of primers designed to specifically detect E. gingivalis. This blind sample analysis showed the strong sensitivity of PCR compared with clinical diagnosis (58/72 = 81%), and microscopy (51/65 = 78%). The results of this work show that the parasites detected by microscopy mainly – if not exclusively – belong to the species E. gingivalis and that the presence of the parasite is correlated with periodontitis.

Development of loop-mediated isothermal amplification for rapid detection of Entamoeba histolytica

OBJECTIVE

To develop a loop-mediated isothermal amplification (LAMP) assay for the detection of Entamoeba histolytica E. histolytica, the causative agent of amebiasis.

METHODS

The LAMP primer set was designed from E. histolytica hemolysin gene HLY6. Genomic DNA of E. histolytica trophozoites strain HK9 was used to optimize the LAMP mixture and conditions. Amplification of DNA in the LAMP mixture was monitored through visual inspection for turbidity of the LAMP mix as well as addition of fluorescent dye.

RESULTS

Positive LAMP reactions turned turbid while negative ones remained clear. Upon addition of a fluorescent dye, all positive reactions turned green while the negative control remained orange under ambient light. After electrophoresis in 1.5% agarose gels, a ladder of multiple bands of different sizes can be observed in positive samples while no bands were detected in the negative control. The sensitivity of the assay was found to be 5 parasites per reaction which corresponds to approximately 15.8 ng/μ L DNA. The specificity of the assay was verified by the absence of amplified products when DNA from other gastrointestinal parasites such as the morphologically similar but non-pathogenic species, Entamoeba dispar 39, and other diarrhea-causing organisms such as Blastocystis hominis and Escherichia coli were used.

CONCLUSIONS

The LAMP assay we have developed enables the detection of E. histolytica with rapidity and ease, therefore rendering it is suitable for laboratory and field diagnosis of amebiasis.

The ribosomal DNA plasmids of entamoeba

In most organisms, the nuclear ribosomal RNA (rRNA) genes are highly repetitive and arranged as tandem repeats on one or more chromosomes. In Entamoeba, however, these genes are located almost exclusively on extrachromosomal circular DNA molecules with no clear evidence so far of a chromosomal copy. Such an uncommon location of rRNA genes may be a direct consequence of cellular physiology, as suggested by studies with Saccharomyces cerevisiae mutants in which the rDNA is extrachromosomal. In this review, Sudha Bhattacharya, Indrani Som and Alok Bhattacharya summarize current knowledge on the structural organization and replication of the Entamoeba rDNA plasmids. Other than the rRNAs encoded by these molecules, no protein-coding genes (including ribosomal protein genes) are found on any of them. They are unique among plasmids in that they do not initiate replication from a fixed origin but use multiple sites dispersed throughout the molecule. Further studies should establish the unique biochemical features of Entamoeba that lead to extrachromosomal rDNA.

PCR diagnosis of Entamoeba histolytica cysts in stool samples

Amebiasis is a protozoan disease caused by Entamoeba histolytica and a potential health threat in areas where sanitation and hygiene are inappropriate. Highly sensitive PCR methods for detection of E. histolytica in clinical and environmental samples are extremely useful to control amebiasis and to promote public health. The present study compared several primer sets for small subunit (SSU) rDNA and histone genes of E. histolytica cysts. A 246 bp of the SSU rDNA gene of pure cysts contained in phosphate-buffered saline (PBS) and in stool samples was successfully amplified by nested PCR, using the 1,147-246 bp primer set, of the primary PCR products which were pre-amplified using the 1,147 bp primer as the template. The detection limit of the nested PCR using the 1,147-246 primer set was 10 cysts in both groups (PBS and stool samples). The PCR to detect histone gene showed negative results. We propose that the nested PCR technique to detect SSU rDNA can be used as a highly sensitive genetic method to detect E. histolytica cysts in stool samples.

Regulation of gene expression in protozoa parasites

Infections with protozoa parasites are associated with high burdens of morbidity and mortality across the developing world. Despite extensive efforts to control the transmission of these parasites, the spread of populations resistant to drugs and the lack of effective vaccines against them contribute to their persistence as major public health problems. Parasites should perform a strict control on the expression of genes involved in their pathogenicity, differentiation, immune evasion, or drug resistance, and the comprehension of the mechanisms implicated in that control could help to develop novel therapeutic strategies. However, until now these mechanisms are poorly understood in protozoa. Recent investigations into gene expression in protozoa parasites suggest that they possess many of the canonical machineries employed by higher eukaryotes for the control of gene expression at transcriptional, posttranscriptional, and epigenetic levels, but they also contain exclusive mechanisms. Here, we review the current understanding about the regulation of gene expression in Plasmodium sp., Trypanosomatids, Entamoeba histolytica and Trichomonas vaginalis.

Rapid Diagnosis of Intestinal Parasitic Protozoa, with a Focus on Entamoeba histolytica

Entamoeba histolytica is an invasive intestinal pathogenic parasitic protozoan that causes amebiasis. It must be distinguished from Entamoeba dispar and E. moshkovskii, nonpathogenic commensal parasites of the human gut lumen that are morphologically identical to E. histolytica. Detection of specific E. histolytica antigens in stools is a fast, sensitive technique that should be considered as the method of choice. Stool real-time PCR is a highly sensitive and specific technique but its high cost make it unsuitable for use in endemic areas where there are economic constraints. Serology is an important component of the diagnosis of intestinal and especially extraintestinal amebiasis as it is a sensitive test that complements the detection of the parasite antigens or DNA. Circulating Gal/GalNac lectin antigens can be detected in the serum of patients with untreated amoebic liver abscess. On the horizon are multiplex real-time PCR assays which permit the identification of multiple enteropathogens with high sensitivity and specificity.

The nucleolus in Entamoeba histolytica and Entamoeba invadens is located at the nuclear periphery

The ribosomal RNA genes in the human parasite Entamoeba histolytica and its reptilian counterpart Entamoeba invadens are located on extrachromosomal circles. The expression of rRNA genes generally takes place in a specialized nuclear compartment-the nucleolus. In Entamoeba species the nuclear space that may be called the nucleolus has yet to be defined. Previous studies showed that the rDNA circles are located at the nuclear periphery. Here we have raised antibodies against the E. histolytica homologue of fibrillarin, a highly conserved protein known to be a marker for nucleolus. These antibodies cross-reacted preferentially with the nuclear periphery, forming a peripheral ring. There was complete colocalization of fibrillarin with the signal obtained by antibodies against E. histolytica RNA polymerase I (but not polymerase II and III), strongly suggesting that the nucleolus in E. histolytica is indeed located at the nuclear periphery. The dynamic nature of the nucleolus was evident when cells were subjected to a variety of growth stresses. Although the peripheral nucleolar structure was retained, stress was accompanied by significant cytoplasmic localization of RNA polymerase I, and to some extent fibrillarin. The nucleolus in E. invadens was also located at the nuclear periphery. When these cells were induced to encyst the nucleolar ring structure was lost, giving way to small, fragmented foci. This study gives the first clear insight into nucleolar structure in Entamoeba.

Molecular epidemiology of amebiasis

Entamoeba histolytica, the causative agent of human amebiasis, remains a significant cause of morbidity and mortality in developing countries and is responsible for up to 100,000 deaths worldwide each year. Entamoeba dispar, morphologically indistinguishable from E. histolytica, is more common in humans in many parts of the world. Similarly Entamoeba moshkovskii, which was long considered to be a free-living ameba, is also morphologically identical to E. histolytica and E. dispar, and is highly prevalent in some E. histolytica endemic countries. However, the only species to cause disease in humans is E. histolytica. Most old epidemiological data on E. histolytica are unusable as the techniques employed do not differentiate between the above three Entamoeba species. Molecular tools are now available not only to diagnose these species accurately but also to study intra-species genetic diversity. Recent studies suggest that only a minority of all E. histolytica infections progress to the development of clinical symptoms in the host and there exist population level differences between the E. histolytica strains isolated from the asymptomatic and symptomatic individuals. Nevertheless the underlying factors responsible for variable clinical outcome of infection by E. histolytica remain largely unknown. We anticipate that the recently completed E. histolytica genome sequence and new molecular techniques will rapidly advance our understanding of the epidemiology and pathogenicity of amebiasis.

Diagnosis of intestinal amoebiasis by using nested polymerase chain reaction-restriction fragment length polymorphism assay

BACKGROUND

Microscopy is unreliable to distinguish the pathogenic Entamoeba histolytica from the nonpathogenic Entamoeba dispar or Entamoeba moshkovskii in stool specimens.

METHODS

Nested polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was carried out to detect E. histolytica, E. dispar, and E. moshkovskii DNA in stool samples of 202 patients positive for E. histolytica, E. dispar, or E. moshkovskii by microscopy or culture and in 35 controls. The TechLab E. histolytica II enzyme-linked immunosorbent assay (ELISA) was performed to detect Gal/GalNAc lectin in 45 stool samples positive for E. histolytica, E. dispar, or E. moshkovskii by microscopy or culture. Rapid-indirect hemagglutination assay (IHA) was performed to detect serum antiamoebic antibodies in the 85 patients positive for E. histolytica, E. dispar, or E. moshkovskii in their stool specimens and in the 35 controls.

RESULTS

Nested PCR-RFLP was positive in 175 of 202 (86.6%) patient stool samples and was negative in all 35 negative control stool samples. ELISA was positive in 29 of 45 (64.4%) patient stool samples. The IHA test was positive in 19 of 85 (22.4%) patient serum samples and in one (2.8%) of the 35 control serum samples. Nested PCR-RFLP detected E. histolytica DNA in stool specimens of 12 (63.2%) of 19 seropositive patients, and in 31 (47%) of 66 seronegative patients. TechLab E. histolytica II ELISA detected E. histolytica antigen in stool specimens of six (54.5%) of 11 seropositive patients, and in 23 (67.6%) of 34 seronegative patients.

CONCLUSIONS

Nested PCR-RFLP was useful for the specific detection of E. histolytica, E. dispar, and E. moshkovskii in stool samples.

Laboratory diagnostic techniques for Entamoeba species

The genus Entamoeba contains many species, six of which (Entamoeba histolytica, Entamoeba dispar, Entamoeba moshkovskii, Entamoeba polecki, Entamoeba coli, and Entamoeba hartmanni) reside in the human intestinal lumen. Entamoeba histolytica is the causative agent of amebiasis and is considered a leading parasitic cause of death worldwide in humans. Although recent studies highlight the recovery of E. dispar and E. moshkovskii from patients with gastrointestinal symptoms, there is still no convincing evidence of a causal link between the presence of these two species and the symptoms of the host. New approaches to the identification of E. histolytica are based on detection of E. histolytica-specific antigen and DNA in stool and other clinical samples. Several molecular diagnostic tests, including conventional and real-time PCR, have been developed for the detection and differentiation of E. histolytica, E. dispar, and E. moshkovskii in clinical samples. The purpose of this review is to discuss different methods that exist for the identification of E. histolytica, E. dispar, and E. moshkovskii which are available to the clinical diagnostic laboratory. To address the need for a specific diagnostic test for amebiasis, a substantial amount of work has been carried out over the last decade in different parts of the world. The molecular diagnostic tests are increasingly being used for both clinical and research purposes. In order to minimize undue treatment of individuals infected with other species of Entamoeba such as E. dispar and E. moshkovskii, efforts have been made for specific diagnosis of E. histolytica infection and not to treat based simply on the microscopic examination of Entamoeba species in the stool. The incorporation of many new technologies into the diagnostic laboratory will lead to a better understanding of the public health problem and measures to control the disease.

The Entamoeba histolytica Ehcp112 gene has a distal and weak promoter

Ehcp112 encodes the Entamoeba histolytica EhCP112 cysteine protease that is part of the EhCPADH complex. By in silico analysis we identified putative transcription factor-binding sites along 837 bp upstream the Ehcp112 gene ATG codon. A TATA-like motif (TATATAAA) was located at -36 to -29 bp, a GAAC box (GAACC) was found at -10 to -14 bp and an Inr sequence (TTCAAC) at -8 to -2 bp. These tripartite promoter elements are in non-canonical positions, downstream the transcription initiation site (-280 bp). We cloned four Ehcp112 promoter fragments in pBSCAT-ACT plasmid to obtain pI (355 bp), pII (681 bp), pIII (833 bp), and pIV (554 bp) constructs. In transfected trophozoites, only pIII drove CAT activity with 44% efficiency in relation to actin promoter activity. Our results showed the presence of a distal and weak promoter in the Ehcp112 gene. The active DNA region is inside the open reading frame of the Ehrab B gene, suggesting that expression of both genes could be coordinately regulated.

Species- and strain-specific probes derived from repetitive DNA for distinguishing Entamoeba histolytica and Entamoeba dispar

Entamoeba histolytica and Entamoeba dispar are two morphologically indistinguishable species that are found in the human gut. Of the two, E. histolytica is considered to be pathogenic while E. dispar is nonpathogenic. To generate molecular probes to detect and distinguish between the two species, we utilized repeat sequences present in Entamoeba genome. We have developed probes and primers from rDNA episomes, and unidentified Entamoeba EST1 repeat for this purpose, and used them for dot blot hybridization and PCR amplification. To investigate the possible existence of invasive and noninvasive strains of E. histolytica, the ability to differentiate individual isolates is necessary. For this purpose, we have utilized a modification of the AFLP procedure called 'Transposon display,' which generates and displays large number of genomic bands associated with a transposon. We have used the abundant retrotransposon, EhSINE1, for this purpose,and demonstrated its potential as a marker to study strain variation in E. histolytica. This technique could suitably be employed in carrying out significant molecular epidemiological studies and large-scale typing of this parasite.

Entamoeba histolytica: rapid identification and differentiation of Indian isolates by riboprinting

Entamoeba histolytica infection still remains one of the major public health problem for developing countries like India. A rapid and accurate detection of this parasite is essential for prevention and control of amoebiasis. In this study, using the method of 'riboprinting' (PCR-RFLP of rRNA genes from amoeba) we have analysed 15 stool samples from symptomatic patients of amoebiasis. All 15 patients of clinical amoebiasis had E. histolytica in their stool and two of the samples also showed mixed infection of E. dispar. Apart from the known restriction enzyme sites within the amoeba SSU-rRNA genes, a new Sau3A site having a discriminatory value is identified in these E. histolytica isolates from India. Hence, it is possible to rapidly identify E. histolytica DNA and differentiating it from E. dispar using minute amounts of clinical stool samples, thus eliminating the laborious parasite culturing process. Thus, riboprinting is advantageous for clearcut identification of E. histolytica in order to decide an effective antiamoebic therapy.

Analysis of intergenic spacer transcripts suggests 'read-around' transcription of the extrachromosomal circular rDNA in Euglena gracilis

We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3'-end of the large subunit ribosomal RNA (rRNA) gene from the 5'-end of the small subunit (SSU) rRNA gene in the circular, extrachromosomal ribosomal DNA (rDNA) of Euglena gracilis. The IGS contains a 277 nt stretch of sequence that is related to a sequence found in ITS 1, an internal transcribed spacer between the SSU and 5.8S rRNA genes. Primer extension analysis of IGS transcripts identified three abundant reverse transcriptase stops that may be analogous to the transcription initiation site (TIS) and two processing sites (A' and A0) that are found in this region in other eukaryotes. Features that could influence processing at these sites include an imperfect palindrome near site A0 and a sequence near site A' that could potentially base pair with U3 small nucleolar RNA. Our identification of the TIS (verified by mung bean nuclease analysis) is considered tentative because we also detected low-abundance transcripts upstream of this site throughout the entire IGS. This result suggests the possibility of 'read-around' transcription, i.e. transcription that proceeds multiple times around the rDNA circle without termination.

Specific detection of Entamoeba histolytica DNA by hemolysin gene targeted PCR

Diagnostic differentiation of pathogenic Entamoeba histolytica from non-pathogenic Entamoeba dispar is of great clinical importance. We have developed and evaluated a new polymerase chain reaction (PCR) assay (haemo-PCR) based on the novel E. histolytica hemolysin gene HLY6. The specificity of this assay was confirmed by analyzing different Entamoeba species, faeces samples, human and bacterial DNA, and digestion of amplification products with appropriate restriction enzymes. The sensitivity was confirmed by serial dilutions of E. histolytica HM-1:IMSS DNA in the excess of human DNA. Totally, 45 clinical samples were analyzed by the haemo-PCR assay including amoebic liver abscess (ALA) fluids from 23 patients suspected for amoebiasis, four faeces samples containing E. histolytica and E. dispar, and positive and negative controls. The results were compared with those obtained with PCRs for cystein-rich surface protein (P30) and small subunit ribosomal RNA (ssu rRNA) genes. The haemo-PCR gave a positive result in 18 (89%) ALA fluids compared with 14 (77%) and five (28%) by PCR for p30, and ssu rRNA, respectively. PCR products were obtained only from specimens containing E. histolytica DNA. The haemo-PCR assay was therefore found to be a valuable diagnostic tool for identification of E. histolytica infections both in faeces and ALA samples.

Inter- and intra-strain variation in the 5.8S ribosomal RNA and internal transcribed spacer sequences of Entamoeba histolytica and comparison with Entamoeba dispar, Entamoeba moshkovskii and Entamoeba invadens

The ribosomal RNA genes in Entamoeba histolytica are located on circular DNA molecules in about 200 copies per genome equivalent. Nucleotide sequence analysis of the 5.8S rRNA gene and the flanking internal transcribed spacers was carried out to determine the degree of sequence divergence in the multiple rRNA gene copies of a given strain; amongst three different E. histolytica strains (HM-1:IMSS, Rahman and HK-9); and amongst four species of Entamoeba (Entamoeba histolytica, Entamoeba dispar, Entamoeba moshkovskii and Entamoeba invadens). The results show that all rRNA gene copies of a given strain are identical. Few nucleotide positions varied between strains of a species but the differences were very pronounced amongst species. In general, the internal transcribed spacer 2 sequence was more variable and may be useful for strain- and species-identification. The 5.8S rRNA gene and the internal transcribed spacer 2 of E. invadens were unusually small in size.

Lack of a chromosomal copy of the circular rDNA plasmid of Entamoeba histolytica

A number of small circular DNAs constitute a part of the genome of Entamoeba histolytica. Among them, the 24.5 kb circular DNA encoding rRNA (EhR1) is the most abundant. Pulsed field gel electrophoresis was used to determine if a chromosomal copy of EhR1 exists and what fraction of the total genome is circular. The results show that the chromosomes of E. histolytica are linear, and that no copy of EhR1 could be detected in any of the linear chromosomes.

Pantropic retroviral vectors mediate gene transfer and expression in Entamoeba histolytica

Transformation of Entamoeba histolytica has been previously reported, but the foreign genes have all been replicated episomally. Pantropic retroviral vectors based on the Moloney murine leukemia virus with the envelope glycoprotein of vesicular stomatitis virus (VSV-G) have an extremely broad host range and can be concentrated to high titer. To investigate whether these pseudotyped, pantropic vectors can mediate gene transfer and expression in E. histolytica, we constructed a retroviral vector, in which a hygromycin phosphotransferase is expressed from the E. histolytica actin promoter. Data confirm the infection, integration, and expression of a foreign gene mediated by the provirus. To our knowledge, this is the most evolutionarily distant example of successful integration and expression of a mammalian retrovirus. Pantropic retroviral vectors may thus facilitate genetic analysis in species lacking transformation systems.

Simple differential detection of Entamoeba histolytica and Entamoeba dispar in fresh stool specimens by sodium acetate-acetic acid-formalin concentration and PCR

Amoebiasis is caused by two distinct species, a pathogenic form (Entamoeba histolytica) and a nonpathogenic form (Entamoeba dispar), which are morphologically identical. Although the distinction between these two species is of great clinical importance, the methods developed for this purpose either are very time-consuming or involve laborious procedures for isolation of the DNA. We report here a simple PCR method starting with fresh stool specimen that allows for the sensitive and reliable distinction between E. histolytica and E. dispar. After initial concentration by the sodium acetate-acetic acid-formalin (SAF) method and digestion with proteinase K, a 0.88-kb sequence of the multicopy 16S rRNA gene served as a target for PCR amplification. The method starting with unpreserved specimens proved to be very sensitive and was not influenced by the quick exposure to SAF fixative during the initial concentration step. However, storage in SAF fixative prior to testing resulted in a decreased sensitivity within 2 days. The detection limit of the method was as low as one copy of the 16S rRNA gene. No cross-reactivity was observed with other common intestinal protozoa. Mixed infections involving both E. histolytica and E. dispar could easily be detected at a ratio of 1:10,000 by agarose gel electrophoresis or a DNA hybridization immunoassay.

Upstream regulatory elements controlling expression of the Entamoeba histolytica lectin

Entamoeba histolytica genomic organization and putative promoter elements appear to be distinct from both metazoan and better characterized protozoan organisms. The recent development of DNA-mediated transfection for E. histolytica enabled characterization of cis-acting promoter elements required for gene expression. A deletion and replacement analysis was conducted on the promoter of an E. histolytica gene encoding the heavy subunit of the N-acetyl-beta-D-galactosamine-specific adhesin (hgl5). Deletion of the DNA from -1000 bases to -272 bases upstream from the start of transcription of hgl5 did not decrease reporter gene expression. Subsequent nested deletions and 10-bp replacement mutagenesis identified four positive upstream regulatory elements between bases -219 to -200, -189 to -160, -69 to -60, and -49 to -40. A negative upstream regulatory element between bases -89 to -80 was conserved upstream of three other E. histolytica genes. Mutation of the previously unidentified 'GAAC' element conserved within the putative core promoter decreased reporter gene expression by 75%. Site directed mutagenesis of the putative TATA element decreased reporter gene expression by greater than 50%, while mutation of the putative initiator element resulted in a more modest decrease. This analysis suggests that E. histolytica promoters are unlike other protozoan promoters, with AT-rich upstream regulatory elements, a non-consensus TATA element, the "GAAC' element, and an unusual initiator element.

Replication initiates at multiple dispersed sites in the ribosomal DNA plasmid of the protozoan parasite Entamoeba histolytica

In the protozoan parasite Entamoeba histolytica (which causes amoebiasis in humans), the rRNA genes (rDNA) in the nucleus are carried on an extrachromosomal circular plasmid. For strain HM-1:IMSS, the size of the rDNA plasmid is 24.5 kb, and 200 copies per genome are present. Each circle contains two rRNA transcription units as inverted repeats separated by upstream and downstream spacers. We have studied the replication of this molecule by neutral/neutral two-dimensional gel electrophoresis and by electron microscopy. All restriction fragments analyzed by two-dimensional gel electrophoresis gave signals corresponding to simple Y's and bubbles. This showed that replication initiated in this plasmid at multiple, dispersed locations spread throughout the plasmid. On the basis of the intensity of the bubble arcs, initiations from the rRNA transcription units seemed to occur more frequently than those from intergenic spacers. Multiple, dispersed initiation sites were also seen in the rDNA plasmid of strain HK-9 when it was analyzed by two-dimensional gel electrophoresis. Electron microscopic visualization of replicating plasmid molecules in strain HM-1:IMISS showed multiple replication bubbles in the same molecule. The location of bubbles on the rDNA circle was mapped by digesting with PvuI or BsaHI, which linearize the molecule, and with SacII, which cuts the circle twice. The distance of the bubbles from one end of the molecule was measured by electron microscopy. The data corroborated those from two-dimensional gels and showed that replication bubbles were distributed throughout the molecule and that they appeared more frequently in rRNA transcription units. The same interpretation was drawn from electron microscopic analysis of the HK-9 plasmid. Direct demonstration of more than one bubble in the same molecule is clear evidence that replication of this plasmid initiates at multiple sites. Potential replication origins are distributed throughout the plasmid. Such a mechanism is not known to operate in any naturally occurring prokaryotic or eukaryotic plasmid.

Direct sequencing of the PCR amplified SSU rRNA gene of Entamoeba dispar and the design of primers for rapid differentiation from Entamoeba histolytica

Since 1993, strains of Entamoeba histolytica sensu lato have been assigned to 2 species on the basis of clinical, biochemical, immunological and genetic evidence: the pathogenic strains to E. histolytica sensu stricto, the non-pathogenic strains to Entamoeba dispar. Analysis of the gene encoding for the small subunit ribosomal RNA (SSU rDNA) supports the existence of 2 species. However, while 3 whole SSU rDNA sequences are available in the data bases for E. histolytica, only a partial sequence has been published for E. dispar. Here we report a SSU rDNA sequence for E. dispar. Compared to those of E. histolytica, this sequence shows 1.7% nucleotide substitutions. On the basis of our rDNA data, 2 primers were designed to produce polymerase chain reaction (PCR) amplification from both E. histolytica and E. dispar. Primer specificity for the 2 amoebae was assessed both theoretically against the data bases, and experimentally against a collection of eukaryotic and prokaryotic DNAs. The amplified stretch encompasses a polymorphic Dde I restriction site which allows, after cleavage of the fragment, E. histolytica and E. dispar to be distinguished. The reliability of this method of identification was assessed comparing the results with those based on classic isoenzyme analysis.

Recent advances in amebiasis

Advancements in our understanding of amebiasis have been rapid over the decade that I have followed this field. What was identified morphologically for years as Entamoeba histolytica has been redescribed with modern techniques as a complex of two species, the commensal parasite E. dispar and the pathogenic parasite E. histolytica that is the cause of colitis and liver abscess. Antigen detection tests are now available for the rapid detection in stool of the pathogenic species E. histolytica. New understandings of the importance of luminal as well as tissue-active antimebic medications in the treatment of invasive disease have been reached. The groundwork is being laid for an understanding of the protective immune responses to infection, and at the lab bench DNA transfection of the parasite has opened studies of pathogenesis to genetic analysis. While necessarily an incomplete sketch of the field, I have attempted here to highlight some recent and important developments of interest to clinicians and microbiologists.

Identification and analysis of the start site of ribosomal RNA transcription of Entamoeba histolytica

In this article we report the identification of the start site of ribosomal RNA transcription unit of the enteric parasite E. histolytica. We cloned the upstream region of the ribosomal RNA and we defined the 5' boundary of the transcription unit with nuclear run-on assays. We report that ribosomal transcription starts 2447 bp upstream the SSU ribosomal gene, at an adenosine residue. This data was supported both by S1 mapping and by primer extension analysis; that the mapped site was indeed the transcription start point was demonstrated by RNAse protection of the in vitro capped RNA. Our sequence data around the transcription start point shows two different tandem repeat clusters immediately downstream from the transcription start point.

Nucleotide sequence organisation and analysis of the nuclear ribosomal DNA circle of the protozoan parasite Entamoeba histolytica

We have sequenced the extrachromsomal ribosomal DNA (rDNA) circle of the human protozoan parasite Entamoeba histolytica HM-1:IMSS and present here the complete sequence organisation of the 24.5-kb molecule. Each circle contains two 5.9-kb rDNA transcription units organised as inverted repeats. The regions downstream (3543 bp) and upstream (9216 bp) of the rDNAs contain various families of short tandem repeats. Some of the upstream repeats share extensive sequence homology with the downstream repeats. In addition to the rDNAs themselves, the rDNA circle appears to code for only one other transcript which is 0.7 kb in size as seen in Northern blots. From DNA sequence analysis, no open reading frame could be assigned to the transcript. Extrachromosomal rDNA circles also exist in other E. histolytica strains. Restriction enzyme maps of rDNA circles were constructed from E. histolytica strains 200:NIH, HK-9 and Rahman; and Entamoeba moshkovskii strain Laredo. Striking differences were observed in the organisation of some of them, e.g. the HK-9, Rahman and Laredo circles contained only one rDNA unit and lacked the 0.7-kb transcript sequence. The short repeat sequences upstream and downstream of rDNAs were present in HK-9 and Rahman but absent in Laredo. Circles with one rDNA unit may be derived from those with two units by homologous recombination at direct repeat sequences located upstream and downstream of the two rDNAs.

Heterogeneity of the ribosomal DNA episome in strains and species of Entamoeba

Ribosomal DNA sequences in several species of the genus Entamoeba are highly repeated and display restriction fragment-length polymorphism (RFLP), which has been used to identify species and differentiate strains. However, the continuous variability of the non-transcribed repeat sequences in the ribosomal episome hinders an accurate typification. Looking for more reliable markers, we used DNA probes containing conserved sequences in the ribosomal episome--coding regions for the 16S and 5.8S rRNAs and transcribed spacers flanking the rDNA sequences, and the coding region for the 3' end of the 26S rRNA--to analyse hybridization patterns from five cloned pathogenic strains of Entamoeba histolytica, two strains of the also pathogenic Entamoeba invadens and the non-pathogenic Laredo strain of Entamoeba moshkovskii. Our results provide reliable bases for the differentiation of clones, strains and species of Entamoeba and the reconstruction of E. histolytica episomes. Differences in the number and length of rDNA-containing DNA fragments, previously observed by other investigators and confirmed by us, can be better defined by the present analysis.

Isolation and characterization of a species-specific multicopy DNA sequence from Entamoeba histolytica

A genomic library of Entamoeba histolytica (pathogenic strain HM-1:IMSS) was screened to detect repetitive DNA clones other than those from the highly abundant ribosomal DNA (rDNA). One such clone (HMc) had a 2.3 kb insert which hybridized with the main genome and not the rDNA circle. Southern hybridization of E. histolytica genomic DNA, digested with EcoR I and probed with HMc, showed multiple bands. The banding pattern was identical in all axenic pathogenic strains tested. Differences, however, existed when the banding pattern of a pathogenic strain was compared with that of a non-pathogenic strain. HMc was present in about 25-30 copies per genome in strain HM-1:IMSS. Nucleotide sequence analysis of HMc revealed a partial open reading frame which hybridized with a 1.35 kb poly A+ transcript in Northern blots. The deduced amino acid sequence did not, however, show significant homology with known proteins. The HMc sequence was found only in E. histolytica as it hybridized with 5 different axenic strains of E. histolytica but did not recognize other closely related species of Entamoeba. It has thus the potential to be used as a species-specific DNA probe.

Coding of hemolysins within the ribosomal RNA repeat on a plasmid in Entamoeba histolytica

The pathogenesis of amoebic dysentery is a result of cytolysis of the colonic mucosa by the parasitic protozoan Entamoeba histolytica. The cytolysis results in extensive local ulceration and allows the amoeba to penetrate and metastasize to distant sites. Factors involved in this process were defined with three clones that express hemolytic activities in Escherichia coli. These potential amoebic virulence determinants were also toxic to human colonic epithelial cells, the primary cellular targets in amoebal invasion of the large intestine. The coding sequences for the hemolysins were close to each other on a 2.6-kilobase segment of a 25-kilobase extrachromosomal DNA element. The structural genes for the hemolysins were within inverted repeats that encode ribosomal RNAs.

Unusual gene organization in the protozoan parasite Entamoeba histolytica

We have analyzed three independent genomic loci of the protozoan parasite Entamoeba histolytica that contain coding regions for the iron-containing superoxide dismutase, the pore-forming peptide, and the galactose-inhibitable lectin. All of the three structural genes were found to be closely linked unidirectionally to other coding sequences. The intergenic regions did not exceed 1,350 nucleotides. Nuclear run-on data demonstrated that at least the galactose-inhibitable lectin gene is transcribed in a monocistronic fashion. Comparison of the genomic sequences described here with several others reported previously for E. histolytica revealed a number of invariable peculiarities for the gene organization of this parasite: (i) Coding sequences are not interrupted by introns; (ii) 5' untranslated regions are rather short and transcription starts at the consensus sequences ATTCA or ATCA; (iii) an unusual TATA-motif is located about 30 nucleotides upstream of the start of transcription and comprises the sequence TATTTAAA, which reveals protein binding activity as determined by gel retardation assays; (iv) the conserved pentanucleotide motif TAA/TTT is found within the relatively short 3' untranslated regions and functions putatively as the transcription termination signal; and (v) a stretch of up to 12 pyrmidine residues is located at the end of transcribed sequences.

A variable DNA region of Entamoeba histolytica is expressed in several transcripts which differ in genetically related clones

A highly variable DNA region (EhVR1), isolated from Entamoeba histolytica clone A, strain HM1:IMSS, is transcribed into several transcripts, which differ in genetically related clones. EhVR1 (3.5 kb) is composed of two contiguous fragments; one of these 1.9 kb long, at the 3' end, identified similar transcripts in clones A, L6 and C2 (all derived from strain HM1:IMMS), the other of 1.6 kb, at the 5' end, detected 0.5, 0.6 and 0.7 kb transcripts only in clone A. Variability of the 1.6 kb fragment was found even within the same clone maintained under different conditions. EhVR1 was localized to 1.3 and 1.4 Mb linear chromosomes and also found in circular molecules. The sequence of the 1.6 kb fragment revealed the presence of a large number of different repeats, including inverted and palindromic repeats. A p145 sequence, previously detected in episomal DNA of the amoeba, was found at the 5' end of EhVR1. The presence of EhVR1 in linear and circular molecules, its high number of repeats, and its variability in genetically related clones suggest the existence of DNA regions that undergo dynamic non-reciprocal recombination between circular episomes and linear chromosomes, and may thus contribute to variability in the trophozoite genome.

Molecular karyotype of related clones of Entamoeba histolytica

The molecular karyotype of 3 clones derived from strain HM1:IMSS of Entamoeba histolytica was studied by transverse alternating field electrophoresis. 11-20 bands ranging between 0.3 and over 3 Mb were resolved. Hybridization with total DNA detected highly repetitive sequences in the slow-migrating molecules, while non-repetitive sequences were located in the intermediate and fast-migrating molecules. rDNA, tubulin, actin, cysteine proteases DNA fragments, and a variable DNA sequence (EhVR1) located the respective genes mainly in the 1.3-1.5-Mb region, although they differed in the three clones. Two-dimensional transverse alternating field electrophoresis showed that more than one high-molecular weight molecule may comigrate in a single DNA band. rDNA, and EhVR1 hybridized with slow-migrating bands in a characteristic ladder pattern. Most of the bands recognized by EhVR1 seems to be linear molecules, although exonuclease III-resistant bands also hybridized with EhVR1, suggesting the presence of circles.

Entamoeba histolytica as a model for the primitive eukaryotic cell

Entamoeba histolytica is a structurally simple eukaryote lacking mitochondria, peroxisomes and a well-developed Golgi apparatus, also in its biochemistry, it deviates substantially from the more complex eukoryotes. These features have alternatively been interpreted as archaic, ie. the ancestor of Entamoeba branched off before the primitive eukaryotic cell obtained proto-mitochondria, or as regressive, ie. Entamoeba has lost its mitochondria in the course of its adaptation to a parasitic life style. Tilly Bakker-Grunwald and Claudia Wöstmann favor the first interpretation and discuss in which respects E. histolytica may serve as a model for the primitive eukaryote.

The amoeba enigma

After more than 70 years of intermittent debate over the true relationship between the 'pathogenic' and 'non-pathogenic' forms of Entamoeba histolytica, the application of molecular biology has finally yielded an unambiguous answer: these are not interconvertible phenotypes of the same parasite, a kind of unicellular Jekyll and Hyde, but two quite distinct genetic entities that just happen to look the same. But given the overwhelming evidence now available from gene sequences, pointing to an evolutionary divergence some tens of millions of years ago, why is it that certain eminent workers in the field are still claiming that, at least in vitro, conversion between the two phenotypes can take place? In this article Bill Spice and John Ackers review recent developments in the molecular biology of E. histolytica and assess the continuing controversy over the status of this enigmatic parasite.

Entamoeba histolytica extrachromosomal circular ribosomal DNA: analysis of clonal variation in a hypervariable region

The ribosomal RNA genes of the protozoan parasite Entamoeba histolytica are highly repeated and display restriction fragment length polymorphism. Using a set of four DNA probes spanning the coding region and part of the flanking region of the E. histolytica ribosomal RNA genes, an analysis of the DNA bands generated by EcoRI digestion of Entamoeba DNA is presented. This analysis included five strains of E. histolytica, four strains of E. moshkovskii, and one strain each of E. invadens and E. terrapinae. No common bands were observed between E. histolytica and the other Entamoeba. Within E. histolytica, two bands were conserved in all strains while the others were polymorphic. Detailed analysis of DNA from independently isolated clones of the strain HM-1:IMSS of E. histolytica showed two bands to be highly polymorphic. Of these, the 4.4-kb band of clone 6 was further analyzed. Polymorphism in this band could even be demonstrated in cells of the same clone. Restriction enzyme analysis of this DNA band from two clones of HM-1:IMSS showed that the polymorphism may be due to variable numbers of DraI repeat units present in this DNA stretch.

Nucleotide sequence of a small subunit ribosomal RNA (16S-like rRNA) gene from Entamoeba histolytica: differentiation of pathogenic from nonpathogenic isolates

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