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Small GTPases Jan 2022Rab GTPase is a paralog-rich gene family that controls the maintenance of the eukaryotic cell compartmentalization system. Diverse eukaryotes have varying numbers of Rab...
Rab GTPase is a paralog-rich gene family that controls the maintenance of the eukaryotic cell compartmentalization system. Diverse eukaryotes have varying numbers of Rab paralogs. Currently, little is known about the evolutionary pattern of Rab GTPase in most major eukaryotic 'supergroups'. Here, we present a comprehensive phylogenetic reconstruction of the Rab GTPase gene family in the eukaryotic 'supergroup' Amoebozoa, a diverse lineage represented by unicellular and multicellular organisms. We demonstrate that Amoebozoa conserved 20 of the 23 ancestral Rab GTPases predicted to be present in the last eukaryotic common ancestor and massively expanded several 'novel' in-paralogs. Due to these 'novel' in-paralogs, the Rab family composition dramatically varies between the members of Amoebozoa; as a consequence, 'supergroup'-based studies may significantly change our current understanding of the evolution and diversity of this gene family. The high diversity of the Rab GTPase gene family in Amoebozoa makes this 'supergroup' a key lineage to study and advance our knowledge of the evolution of Rab in Eukaryotes.
Topics: Phylogeny; rab GTP-Binding Proteins; Evolution, Molecular; Amoebozoa; Eukaryota
PubMed: 33779495
DOI: 10.1080/21541248.2021.1903794 -
Experimental Cell Research Sep 2022Interplay between models and experimental data advances discovery and understanding in biology, particularly when models generate predictions that allow well-designed...
Interplay between models and experimental data advances discovery and understanding in biology, particularly when models generate predictions that allow well-designed experiments to distinguish between alternative mechanisms. To illustrate how this feedback between models and experiments can lead to key insights into biological mechanisms, we explore three examples from cellular slime mold chemotaxis. These examples include studies that identified chemotaxis as the primary mechanism behind slime mold aggregation, discovered that cells likely measure chemoattractant gradients by sensing concentration differences across cell length, and tested the role of cell-associated chemoattractant degradation in shaping chemotactic fields. Although each study used a different model class appropriate to their hypotheses - qualitative, mathematical, or simulation-based - these examples all highlight the utility of modeling to formalize assumptions and generate testable predictions. A central element of this framework is the iterative use of models and experiments, specifically: matching experimental designs to the models, revising models based on mismatches with experimental data, and validating critical model assumptions and predictions with experiments. We advocate for continued use of this interplay between models and experiments to advance biological discovery.
Topics: Chemotactic Factors; Chemotaxis; Computer Simulation; Dictyosteliida; Dictyostelium; Models, Biological
PubMed: 35618013
DOI: 10.1016/j.yexcr.2022.113218 -
International Journal of Molecular... Sep 2019Sulfur metabolism is essential for all living organisms. Recently, unique features of the metabolic pathway for sulfated biomolecules have been described. is a genus... (Review)
Review
Sulfur metabolism is essential for all living organisms. Recently, unique features of the metabolic pathway for sulfated biomolecules have been described. is a genus in the phylum Amoebozoa and includes the causative agent for amoebiasis, a global public health problem. This review gives an overview of the general features of the synthesis and degradation of sulfated biomolecules, and then highlights the characteristics that are unique to . Future biological and pharmaceutical perspectives are also discussed.
Topics: Antiprotozoal Agents; Biological Evolution; Entamoeba; Entamoebiasis; Gene Transfer, Horizontal; Humans; Lipid Metabolism; Parasite Encystment; Protozoan Proteins; Sulfatases; Sulfotransferases; Sulfur
PubMed: 31546588
DOI: 10.3390/ijms20194679 -
Experimental Parasitology Nov 2014In this short overview of the genus Naegleria a brief historical sketch is given since the discovery of this amoeboflagellate in 1899 and the finding in 1970 that one... (Review)
Review
In this short overview of the genus Naegleria a brief historical sketch is given since the discovery of this amoeboflagellate in 1899 and the finding in 1970 that one species, Naegleria fowleri causes primary amoebic meningoencephalitis in man. Eight different types of this pathogen are known which have an uneven distribution over the world. Until now 47 different Naegleria spp. are described, of which two other species cause disease in experimental animals, and their geographical dispersal is indicated. The presence of group I introns in the SSU and in the LSU rDNA in the genus is discussed, as well as the possibility of sex or mating. It is also mentioned that the genome of N. fowleri should not be compared to that of Naegleria gruberi, to know why the former is pathogenic, but to the genome of its closest relative Naegleria lovaniensis.
Topics: Animals; Central Nervous System Protozoal Infections; Humans; Naegleria; Phylogeny
PubMed: 25108159
DOI: 10.1016/j.exppara.2014.07.011 -
Indian Journal of Medical Microbiology 2022Free-living amoebae (FLA) exist in various environmental sources and are the causative agents of many serious human diseases. We surveyed various natural and artificial...
PURPOSE
Free-living amoebae (FLA) exist in various environmental sources and are the causative agents of many serious human diseases. We surveyed various natural and artificial water bodies in areas of north India to detect the presence of FLA species.
MATERIALS AND METHODS
Surface water samples were collected from 29 water bodies and subjected to microscopy, non-nutrient agar (NNA) culture, and various polymerase chain reaction (PCR) assays for the detection of FLA.
RESULTS
FLA were found in 62.1% (18/29) of the natural and artificial water bodies by NNA culture. Based on PCR based detection, Acanthamoeba spp. was identified in 41.4% (12/29), Vannella spp./Vahlkampfia ovis in 17.2% (5/29) and Naegleria spp. in 20.7% (6/29) of the samples from different locations. PCR-sequencing of Naegleria positive samples identified them as Naegleria australiensis and Naegleria species.
CONCLUSIONS
The present study reports widespread occurrence of medically important FLA species in various natural and artificial water bodies, and highlights the need for regular molecular surveillance of FLA in the environment for better control and prevention of the diseases caused by FLA.
Topics: Acanthamoeba; Amoeba; Animals; Humans; Naegleria; Polymerase Chain Reaction; Sheep; Water
PubMed: 35660264
DOI: 10.1016/j.ijmmb.2022.05.002 -
BMC Ecology and Evolution Oct 2023Cyclic di-guanylate (c-di-GMP), synthesized by diguanylate cyclase, is a major second messenger in prokaryotes, where it triggers biofilm formation. The dictyostelid...
BACKGROUND
Cyclic di-guanylate (c-di-GMP), synthesized by diguanylate cyclase, is a major second messenger in prokaryotes, where it triggers biofilm formation. The dictyostelid social amoebas acquired diguanylate cyclase (dgcA) by horizontal gene transfer. Dictyostelium discoideum (Ddis) in taxon group 4 uses c-di-GMP as a secreted signal to induce differentiation of stalk cells, the ancestral somatic cell type that supports the propagating spores. We here investigated how this role for c-di-GMP evolved in Dictyostelia by exploring dgcA function in the group 2 species Polysphondylium pallidum (Ppal) and in Polysphondylium violaceum (Pvio), which resides in a small sister clade to group 4.
RESULTS
Similar to Ddis, dgcA is upregulated after aggregation in Ppal and Pvio and predominantly expressed in the anterior region and stalks of emerging fruiting bodies. DgcA null mutants in Ppal and Pvio made fruiting bodies with very long and thin stalks and only few spores and showed delayed aggregation and larger aggregates, respectively. Ddis dgcA- cells cannot form stalks at all, but showed no aggregation defects. The long, thin stalks of Ppal and Pvio dgcA- mutants were also observed in acaA- mutants in these species. AcaA encodes adenylate cyclase A, which mediates the effects of c-di-GMP on stalk induction in Ddis. Other factors that promote stalk formation in Ddis are DIF-1, produced by the polyketide synthase StlB, low ammonia, facilitated by the ammonia transporter AmtC, and high oxygen, detected by the oxygen sensor PhyA (prolyl 4-hydroxylase). We deleted the single stlB, amtC and phyA genes in Pvio wild-type and dgcA- cells. Neither of these interventions affected stalk formation in Pvio wild-type and not or very mildly exacerbated the long thin stalk phenotype of Pvio dgcA- cells.
CONCLUSIONS
The study reveals a novel role for c-di-GMP in aggregation, while the reduced spore number in Pvio and Ppal dgcA- is likely an indirect effect, due to depletion of the cell pool by the extended stalk formation. The results indicate that in addition to c-di-GMP, Dictyostelia ancestrally used an as yet unknown factor for induction of stalk formation. The activation of AcaA by c-di-GMP is likely conserved throughout Dictyostelia.
Topics: Dictyostelium; Ammonia; Phosphorus-Oxygen Lyases; Dictyosteliida; Oxygen
PubMed: 37803310
DOI: 10.1186/s12862-023-02169-z -
Frontiers in Cellular and Infection... 2021The human protozoan parasite can live in the human intestine for months or years without generating any symptoms in the host. For unknown reasons, amoebae can suddenly... (Review)
Review
The human protozoan parasite can live in the human intestine for months or years without generating any symptoms in the host. For unknown reasons, amoebae can suddenly destroy the intestinal mucosa and become invasive. This can lead to amoebic colitis or extraintestinal amoebiasis whereby the amoebae spread to other organs the blood vessels, most commonly the liver where abscesses develop. is the closest genetic relative of and is found in wild macaques. Another close relative is , which asyptomatically infects the human intestine. Although all three species are closely related, only and are able to penetrate their host's intestinal epithelium. Lineage-specific genes and gene families may hold the key to understanding differences in virulence among species. Here we discuss those genes found in that have relatives in only one or neither of its sister species, with particular focus on the peptidase, AIG, Ariel, and BspA families.
Topics: Amebiasis; Dysentery, Amebic; Entamoeba; Entamoeba histolytica; Entamoebiasis; Humans
PubMed: 33816346
DOI: 10.3389/fcimb.2021.641472 -
Current Opinion in Microbiology Aug 2014Parasites are often challenged by constant changes of the glucose concentration in their different hosts and/or within the different biotopes in the same host. During... (Review)
Review
Parasites are often challenged by constant changes of the glucose concentration in their different hosts and/or within the different biotopes in the same host. During its life cycle, Entamoeba histolytica, the causative protozoan parasite of human amoebiasis, is exposed to both a glucose-poor environment in the colon and a glucose-rich environment in the liver. High-throughput 'omics' technologies are now widely used to characterize the cell's global response to various stresses and these technologies can survey E. histolytica's global response to fluctuations in glucose concentration in its environment. In this review, we discuss the phenotypic and metabolic responses of E. histolytica to glucose challenges, and compare these responses to those of other protozoan parasites.
Topics: Cell Survival; Entamoeba histolytica; Gene Expression Profiling; Gene Regulatory Networks; Glucose; Humans; Stress, Physiological
PubMed: 25016247
DOI: 10.1016/j.mib.2014.06.005 -
Protist Oct 2022Endolimax nana is a common endobiont of the human intestine, but members of the genus have also been reported in non-human hosts and in non-intestinal organs. Limited...
Endolimax nana is a common endobiont of the human intestine, but members of the genus have also been reported in non-human hosts and in non-intestinal organs. Limited information is available regarding the genetic diversity of Endolimax, which is necessary to delineate species, host specificity and potential differences in clinical impact on the host. Here, we used cloning of PCR products followed by Sanger sequencing and next-generation PacBio Sequencing to obtain Endolimax-related nuclear ribosomal gene sequences and undertook a phylogenetic analysis to gain additional insight into the taxonomy of Endolimax and related organisms. The new sequences confirmed that E. nana forms a discrete clade within the Archamoebae and is related to Endolimax piscium and Iodamoeba. However, we identified substantial sequence divergence within E. nana and evidence for two distinct clades, which we propose to name E. nana ribosomal lineage 1 and E. nana ribosomal lineage 2. Both of the sequencing approaches applied in the study helped us to improve our understanding of genetic diversity across Endolimax, and it is likely that wider application of next-generation sequencing technologies will facilitate the generation of Endolimax-related DNA sequence data and help complete our understanding of its phylogenetic position and intrageneric diversity.
Topics: Endolimax; Phylogeny; Archamoebae; Sequence Analysis, DNA; Intestines
PubMed: 36152390
DOI: 10.1016/j.protis.2022.125908 -
Parasitology Research Mar 2024Balamuthia mandrillaris is the causative agent of granulomatous amoebic encephalitis, a rare and often fatal infection affecting the central nervous system. The amoeba...
Balamuthia mandrillaris is the causative agent of granulomatous amoebic encephalitis, a rare and often fatal infection affecting the central nervous system. The amoeba is isolated from diverse environmental sources and can cause severe infections in both immunocompromised and immunocompetent individuals. Given the limited understanding of B. mandrillaris, our research aimed to explore its protein profile, identifying potential immunogens crucial for early granulomatous amoebic encephalitis diagnosis. Cultures of B. mandrillaris and other amoebas were grown under axenic conditions, and total amoebic extracts were obtained. Proteomic analyses, including two-dimensional electrophoresis and mass spectrometry, were performed. A 50-kDa band showed a robust recognition of antibodies from immunized BALB/c mice; peptides contained in this band were matched with elongation factor-1 alpha, which emerged as a putative key immunogen. Besides, lectin blotting revealed the presence of glycoproteins in B. mandrillaris, and confocal microscopy demonstrated the focal distribution of the 50-kDa band throughout trophozoites. Cumulatively, these observations suggest the participation of the 50-kDa band in adhesion and recognition mechanisms. Thus, these collective findings demonstrate some protein characteristics of B. mandrillaris, opening avenues for understanding its pathogenicity and developing diagnostic and therapeutic strategies.
Topics: Animals; Mice; Balamuthia mandrillaris; Proteomics; Amebiasis; Amoeba; Infectious Encephalitis
PubMed: 38536506
DOI: 10.1007/s00436-024-08193-2