Expression and function of a family of transmembrane kinases from the protozoan parasite Entamoeba histolytica

Single-Cell RNA Sequencing Reveals that the Switching of the Transcriptional Profiles of Cysteine-Related Genes Alters the Virulence of Entamoeba histolytica

Studies on the trophozoite of Entamoeba histolytica suggested this organism could accumulate polyploid cells in its proliferative phase and differentiate its cell cycle from that of other eukaryotes. Therefore, a single-cell sequencing technique was used to study the switching of the RNA transcription profiles of single amoebic trophozoites.

Entamoeba histolytica is an intestinal protozoan that causes human amoebic colitis and extraintestinal abscesses. Virulence variation is observed in the pathogenicity of E. histolytica trophozoites, but the detailed mechanism remains unclear. Here, a single trophozoite was cultured alone, and the progeny of the trophozoites of each generation were subjected to single-cell RNA sequencing (scRNA-seq) to study the transcriptional profiles of trophozoites. The scRNA-seq analysis indicated the importance of sulfur metabolism and the proteasome pathway in pathogenicity, whereas the isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis did not identify the bulk trophozoites. The trophozoite improved the synthesis of cysteine under cysteine-deficient conditions but downregulated the expression of the intermediate subunit of the lectin of E. histolytica trophozoites and retained the expression of the heavy subunit of lectin, resulting in decreased amoebic phagocytosis and cytotoxicity. The variation in the transmembrane kinase gene family might be critical in regulating the proteasome pathway. Thus, the scRNA-seq technique provided an improved understanding of the biological characteristics and the mechanism of virulence variation of amoebic trophozoites.

IMPORTANCE Studies on the trophozoite of Entamoeba histolytica suggested this organism could accumulate polyploid cells in its proliferative phase and differentiate its cell cycle from that of other eukaryotes. Therefore, a single-cell sequencing technique was used to study the switching of the RNA transcription profiles of single amoebic trophozoites. We separated individual trophozoites from axenic cultured trophozoites, CHO cell-incubated trophozoites, and in vivo trophozoites. We found important changes in the sulfur and cysteine metabolism in pathogenicity. The trophozoites strategically regulated the expression of the cysteine-rich protein-encoding genes under cysteine-deficient conditions, thereby decreasing amoebic phagocytosis and cytotoxicity. The single-cell sequencing technique shows evident advantages in comparison with the isobaric tags for relative and absolute quantitation (iTRAQ) proteomic technology (bulk trophozoite level) and reveals the regulation strategy of trophozoites in the absence of exogenous cysteine. This regulation strategy may be the mechanism of virulence variation of amoebic trophozoites.

Signals and signal transduction pathways in Entamoeba histolytica during the life cycle and when interacting with bacteria or human cells

Entamoeba histolytica is the etiological agent of amebiasis in humans. This ameba parasite resides as a commensal in the intestine where it shares intestinal resources with the bacterial microbiome. In the intestinal ecosystem, the ameba encysts and eventually develops disease by invading the tissues. E. histolytica possesses cell surface receptors for the proper sensing of signals involved in encystation or sustaining parasite interaction with bacteria and human cells. Among those receptors are the Gal/GalNAc lectin, G protein-coupled receptors, and transmembrane kinases. In addition there are recently discovered, promising proteins, including orthologs of Toll-type receptors and β trefoil lectins. These proteins trigger a wide variety of signal transduction pathways; however, most of the players involved in the signaling pathways evoked in this parasite are unknown. This review provides an overview of amoebic receptors and their role in encystation, adherence to bacteria or human cells, as well as the reported intracellular signal transduction processes that they can trigger. This knowledge is essential for understanding the lifestyle of E. histolytica and its cytopathic effect on bacteria and human cells that are responsible for infection.

Endocytosis, signal transduction and proteolytic cleaving of human holotransferrin in Entamoeba histolytica

Amoebiasis is a parasitic infection of the human large intestine caused by Entamoeba histolytica; this disease mainly affects people from developing countries. To survive, this primitive protozoan has a high demand for iron, and it uses host iron proteins upon invasion. Transferrin (Tf) is a plasma iron-binding protein that transports and delivers iron to all cells. Iron-loaded Tf (holoTf) in humans can support the proliferation of amoebae in vitro by binding to an amoebic TfR (EhTfR), and amoebae endocytose it inside clathrin-coated vesicles. In this study, it was found that EhTfR phosphorylation is required for human holoTf endocytosis by E. histolytica. Once this complex is endocytosed, human holoTf could be degraded with a nutritional purpose by cysteine proteases. HoloTf endocytosis initiates the activation of the mitogen-activated protein kinases (MAPKs) and focal adhesion kinase (FAK) pathways, which induce cell proliferation with phosphoinositide 3-kinase (PI-3 K) and Ca²⁺ involvement. In the first minutes after holoTf is endocytosed, several proteins are phosphorylated including transketolase, enolase, L-myo-inositol-1-phosphate synthase and phosphoglucomutase, which control carbohydrate metabolism, and heat shock protein-70. The study of these proteins and their signal transduction pathways could be useful for developing future therapies.

Transferrin: Endocytosis and Cell Signaling in Parasitic Protozoa

Iron is the fourth most abundant element on Earth and the most abundant metal in the human body. This element is crucial for life because almost all organisms need iron for several biological activities. This is the case with pathogenic organisms, which are at the vanguard in the battle with the human host for iron. The latest regulates Fe concentration through several iron-containing proteins, such as transferrin. The transferrin receptor transports iron to each cell that needs it and maintains it away from pathogens. Parasites have developed several strategies to obtain iron as the expression of specific transferrin receptors localized on plasma membrane, internalized through endocytosis. Signal transduction pathways related to the activation of the receptor have functional importance in proliferation. The study of transferrin receptors and other proteins with action in the signaling networks is important because these proteins could be used as therapeutic targets due to their specificity or to differences with the human counterpart. In this work, we describe proteins that participate in signal transduction processes, especially those that involve transferrin endocytosis, and we compare these processes with those found in T. brucei, T. cruzi, Leishmania spp., and E. histolytica parasites.

Regulation of serum-responsive transmembrane kinase EhTMKB1-9 by an unsaturated lipid, oleic acid in protistan parasite Entamoeba histolytica

Transmembrane kinases of Entamoeba histolytica are known to play a wide range of roles from virulence, phagocytosis, and proliferation to stress response. Transmembrane kinase EhTMKB1-9 is thought to be involved in early proliferative response and it was originally identified as a serum inducible gene. Ability to stimulate EhTMKB1 expression of serum starved cells resides in unsaturated fatty acids associated with albumin fraction of serum and the mechanism of stimulation follows activation of EhTMKB1-9 promoter. Gel shift assay showed the presence of proteins that bind to the specific site of EhTMKB1-9 upstream region and the concentration of these protein(s) go down on serum starvation, but level of binding protein(s) go up on serum or fatty acid replenishment. This increase in concentration of binding molecule(s) is due to new synthesis rather than activation of existing molecule(s) as a protein synthesis inhibitor blocked enhanced level of gel shifted material on replenishment. The stimulating activity resides in the fatty acyl chain, but not in the head group. Moreover, the fatty acid initiates signaling through class I PI3 kinases that result in activation of EhTMKB1-9 expression. These results suggest a novel mechanism of gene regulation in E. histolytica, and unsaturated fatty acids as potential new signaling molecules.

Differentially expressed genes of virulent and nonvirulent Entamoeba histolytica strains identified by suppression subtractive hybridization

Entamoeba histolytica is a parasite which presents capacity to degrade tissues and therefore has a pathogenic behavior. As this behavior is not shown by all strains, there have been several studies investigating molecular basis of the cytotoxicity process. Using the suppression subtractive hybridization (SSH) technique, differential gene expressions of two E. histolytica strains, one virulent (EGG) and one nonvirulent (452), have been analyzed with the purpose of isolating genes which may be involved with amoebic virulence. Nine cDNA fragments presenting high homology with E. histolytica previously sequenced genes were subtracted. Of these, four genes were confirmed by RT-PCR. Two coding for hypothetical proteins, one for a cysteine-rich protein, expressed only in the virulent strain, EGG and another one, coding for grainin 2 protein, exclusive from 452 strain. This study provided new insight into the proteins differences in the virulent and nonvirulent E. histolytica strains. We believe that further studies with these proteins may prove association of them with tissue damage, providing new perceptions to improve treatment or diagnosis of the invasive disease.

The Entamoeba histolytica serum-inducible transmembrane kinase EhTMKB1-9 is involved in intestinal amebiasis

Entamoeba histolytica possesses a family of approximately 100 putative transmembrane kinases (TMKs), indicating that the parasite has an extensive means of environmental sensing. The TMKs have been divided into nine sub-groups based on the sequence composition of their intracellular kinase as well as extracellular cysteine-rich domains. EhTMKB1-9 has been recently shown to be expressed in proliferating trophozoites and induced by serum. Interference with EhTMKB1-9 by antisense RNA knockdown or expression of a truncated protein diminished proliferation, adhesion and cytotoxicity. Here we report the involvement of EhTMKB1-9 in phagocytosis and its virulence function in the formation of amebic colitis. Trophozoites induced to express higher levels of wild type EhTMKB1-9 showed increased capacity for endocytosis. In contrast, cells compromised for the EhTMKB1-9 expression through antisense inhibition showed significantly lower levels of phagocytosis and endocytosis under the experimental conditions. The role of EhTMKB1-9 as a virulence factor was studied using animal models of amebiasis. Trophozoites expressing high levels of mutant protein lacking the kinase domain showed a competitive disadvantage with regard to survival as well as invasive phenotype in the murine model of amebic colitis. The same parasites however, were not compromised in their ability to generate abscess in the gerbil model of invasive liver amebiasis. EhTMKB1-9 is the second member from the "B" group of EhTMKs which seems to be deployed by the parasite during intestinal infection. TMKs are attractive targets for drug development because of their requirement in virulence and proliferation.

Lipids induce expression of serum-responsive transmembrane kinase EhTMKB1-9 in an early branching eukaryote Entamoeba histolytica

Mechanisms underlying the initiation of proliferative response are known only for a few organisms, and are not understood for the medically important organisms including Entamoeba histolytica. The trans membrane kinase EhTMKB1-9 of E. histolytica is one of the early indicators of proliferation and its' expression is regulated by serum, one of the components necessary for cellular proliferation in vitro. In this study we show that bovine serum albumin (BSA) can induce EhTMKB1-9 expression in place of serum, and that both follow the same mechanism. Both serum and BSA use the same promoter element and the activation process is initiated through a PI3 kinase-mediated pathway. We further show that BSA activates EhTMKB1-9 due to the lipids associated with it and that unsaturated fatty acids are responsible for activation. These results suggest that lipid molecules are ligand(s) for initiation of a signaling system that stimulates EhTMKB1-9 expression.

Mechanisms of adherence, cytotoxicity and phagocytosis modulate the pathogenesis of Entamoeba histolytica

The unicellular parasite Entamoeba histolytica, the causative agent of the human disease amebiasis, has traditionally been distinguished from its nonpathogenic cousin Entamoeba dispar by its propensity for the ingestion of erythrocytes. This classic feature, along with the parasite’s ability to cause extensive host cell death, are critical mechanisms of pathogenesis during human infection. Recent advances have led to a greater understanding of the molecular components that allow E. histolytica to kill and phagocytose extracellular targets during human infection and include detailed studies of the role of the parasite’s cysteine proteinases and other effectors of cytotoxicity, as well as the mechanisms of ligand recognition, signaling and intracellular trafficking during phagocytosis.

A Sequential Model of Host Cell Killing and Phagocytosis by Entamoeba histolytica

The protozoan parasite Entamoeba histolytica is responsible for invasive intestinal and extraintestinal amebiasis. The virulence of Entamoeba histolytica is strongly correlated with the parasite's capacity to effectively kill and phagocytose host cells. The process by which host cells are killed and phagocytosed follows a sequential model of adherence, cell killing, initiation of phagocytosis, and engulfment. This paper presents recent advances in the cytolytic and phagocytic processes of Entamoeba histolytica in context of the sequential model.

Serum-dependent selective expression of EhTMKB1-9, a member of Entamoeba histolytica B1 family of transmembrane kinases

Entamoeba histolytica transmembrane kinases (EhTMKs) can be grouped into six distinct families on the basis of motifs and sequences. Analysis of the E. histolytica genome revealed the presence of 35 EhTMKB1 members on the basis of sequence identity (≥95%). Only six homologs were full length containing an extracellular domain, a transmembrane segment and an intracellular kinase domain. Reverse transcription followed by polymerase chain reaction (RT-PCR) of the kinase domain was used to generate a library of expressed sequences. Sequencing of randomly picked clones from this library revealed that about 95% of the clones were identical with a single member, EhTMKB1-9, in proliferating cells. On serum starvation, the relative number of EhTMKB1-9 derived sequences decreased with concomitant increase in the sequences derived from another member, EhTMKB1-18. The change in their relative expression was quantified by real time PCR. Northern analysis and RNase protection assay were used to study the temporal nature of EhTMKB1-9 expression after serum replenishment of starved cells. The results showed that the expression of EhTMKB1-9 was sinusoidal. Specific transcriptional induction of EhTMKB1-9 upon serum replenishment was further confirmed by reporter gene (luciferase) expression and the upstream sequence responsible for serum responsiveness was identified. EhTMKB1-9 is one of the first examples of an inducible gene in Entamoeba. The protein encoded by this member was functionally characterized. The recombinant kinase domain of EhTMKB1-9 displayed protein kinase activity. It is likely to have dual specificity as judged from its sensitivity to different kinase inhibitors. Immuno-localization showed EhTMKB1-9 to be a surface protein which decreased on serum starvation and got relocalized on serum replenishment. Cell lines expressing either EhTMKB1-9 without kinase domain, or EhTMKB1-9 antisense RNA, showed decreased cellular proliferation and target cell killing. Our results suggest that E. histolytica TMKs of B1 family are functional kinases likely to be involved in serum response and cellular proliferation.

The presence of a vast array of putative transmembrane kinase genes suggests an extensive network of signaling systems in E. histolytica, particularly the ability to perceive signals from the extracellular environment and transduce these intracellularly. However, it has been very difficult to work with these molecules due to the presence of a large number of homologs. It is also not clear if these molecules are indeed protein kinases, as no kinase activity has yet been shown associated with these molecules. In this report, we show that EhTMKB1-9 is a protein kinase and it is one of the early serum-induced genes. It is a predominant EhTMKB1 molecule that is expressed in proliferating cells and its expression is modulated by serum. Cells containing a reduced level of EhTMKB1-9 or high level of a mutant protein result in decreased proliferation, target cell killing and adherence. The results presented in this report suggest that EhTMKB1-9 is an important signaling molecule likely to be involved in E. histolytica proliferation and virulence. We have also identified a serum starvation induced response where expression of EhTMKB1-18 was found to be induced.

Members of the Entamoeba histolytica transmembrane kinase family play non-redundant roles in growth and phagocytosis

Entamoeba histolytica contains a large and novel family of transmembrane kinases (TMKs). The expression patterns of the E. histolytica TMKs in individual trophozoites and the roles of the TMKs for sensing and responding to extracellular cues were incompletely characterised. Here we provide evidence that single cells express multiple TMKs and that TMK39 and TMK54 likely serve non-redundant cellular functions. Laser-capture microdissection was used in conjunction with microarray analysis to demonstrate that single trophozoites express more than one TMK gene. Anti-peptide antibodies were raised against unique regions in the extracellular domains of TMK39, TMK54 and PaTMK, and TMK expression was analysed at the protein level. Flow cytometric assays revealed that populations of trophozoites homogeneously expressed TMK39, TMK54 and PaTMK, while confocal microscopy identified different patterns of cell surface expression for TMK39 and TMK54. The functions of TMK39 and TMK54 were probed by the inducible expression of dominant-negative mutants. While TMK39 co-localised with ingested beads and expression of truncated TMK39 interfered with trophozoite phagocytosis of apoptotic lymphocytes, expression of a truncated TMK54 inhibited growth of amoebae and altered the surface expression of the heavy subunit of the E. histolytica Gal/GalNAc lectin. Overall, our data indicates that multiple members of the novel E. histolytica TMK family are utilised for non-redundant functions by the parasite.

Using differential gene expression to study Entamoeba histolytica pathogenesis

The release of the Entamoeba histolytica genome has facilitated the development of techniques to survey rapidly and to relate gene expression with biology. The association and potential contribution of differential gene expression to the life cycle and the virulence of this protozoan parasite of humans are reviewed here.

New insights into Entamoeba histolytica pathogenesis

PURPOSE OF REVIEW

Entamoeba histolytica is an important global pathogen and a leading cause of parasitic death worldwide. This article summarizes significant research findings over the last year.

RECENT FINDINGS

Efforts have focused primarily on identification of novel virulence determinants in E. histolytica, transcriptional profiling during tissue invasion and stage conversion, and characterization of basic cell biological processes. Additionally, new techniques for gene silencing have been identified.

SUMMARY

A comprehensive examination of the parasite lifestyle on a whole genome level has been undertaken, allowing identification of new virulence genes and signaling pathways and processes relevant to amebic biology.

Analysis of the protein kinome of Entamoeba histolytica

Protein kinases play important roles in almost all major signaling and regulatory pathways of eukaryotic organisms. Members in the family of protein kinases make up a substantial fraction of eukaryotic proteome. Analysis of the protein kinase repertoire (kinome) would help in the better understanding of the regulatory processes. In this article, we report the identification and analysis of the repertoire of protein kinases in the intracellular parasite Entamoeba histolytica. Using a combination of various sensitive sequence search methods and manual analysis, we have identified a set of 307 protein kinases in E. histolytica genome. We have classified these protein kinases into different subfamilies originally defined by Hanks and Hunter and studied these kinases further in the context of noncatalytic domains that are tethered to catalytic kinase domain. Compared to other eukaryotic organisms, protein kinases from E. histolytica vary in terms of their domain organization and displays features that may have a bearing in the unusual biology of this organism. Some of the parasitic kinases show high sequence similarity in the catalytic domain region with calmodulin/calcium dependent protein kinase subfamily. However, they are unlikely to act like typical calcium/calmodulin dependent kinases as they lack noncatalytic domains characteristic of such kinases in other organisms. Such kinases form the largest subfamily of kinases in E. histolytica. Interestingly, a PKA/PKG-like subfamily member is tethered to pleckstrin homology domain. Although potential cyclins and cyclin-dependent kinases could be identified in the genome the likely absence of other cell cycle proteins suggests unusual nature of cell cycle in E. histolytica. Some of the unusual features recognized in our analysis include the absence of MEK as a part of the Mitogen Activated Kinase signaling pathway and identification of transmembrane region containing Src kinase-like kinases. Sequences which could not be classified into known subfamilies of protein kinases have unusual domain architectures. Many such unclassified protein kinases are tethered to domains which are Cysteine-rich and to domains known to be involved in protein-protein interactions. Our kinome analysis of E. histolytica suggests that the organism possesses a complex protein phosphorylation network that involves many unusual kinases.