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Genes May 2022Transposable elements (TEs) are mobile genetic elements found in the majority of eukaryotic genomes. Genomic studies of protozoan parasites from the phylum Apicomplexa...
Transposable elements (TEs) are mobile genetic elements found in the majority of eukaryotic genomes. Genomic studies of protozoan parasites from the phylum Apicomplexa have only reported a handful of TEs in some species and a complete absence in others. Here, we studied sixty-four Apicomplexa genomes available in public databases, using a 'de novo' approach to build candidate TE models and multiple strategies from known TE sequence databases, pattern recognition of TEs, and protein domain databases, to identify possible TEs. We offer an insight into the distribution and the type of TEs that are present in these genomes, aiming to shed some light on the process of gains and losses of TEs in this phylum. We found that TEs comprise a very small portion in these genomes compared to other organisms, and in many cases, there are no apparent traces of TEs. We were able to build and classify 151 models from the TE consensus sequences obtained with RepeatModeler, 96 LTR TEs with LTRpred, and 44 LINE TEs with MGEScan. We found LTR Gypsy-like TEs in Eimeria, Gregarines, Haemoproteus, and Plasmodium genera. Additionally, we described LINE-like TEs in some species from the genera Babesia and Theileria. Finally, we confirmed the absence of TEs in the genus Cryptosporidium. Interestingly, Apicomplexa seem to be devoid of Class II transposons.
Topics: Animals; Apicomplexa; Cryptosporidiosis; Cryptosporidium; DNA Transposable Elements; Evolution, Molecular; Parasites
PubMed: 35627271
DOI: 10.3390/genes13050887 -
Revista Brasileira de Parasitologia... 2011The genus Hepatozoon includes hundreds of species that infect birds, reptiles, amphibians and mammals, in all continents with tropical and subtropical climates. Two... (Review)
Review
The genus Hepatozoon includes hundreds of species that infect birds, reptiles, amphibians and mammals, in all continents with tropical and subtropical climates. Two species have been described in domestic dogs: H. canis, reported in Europe, Asia, Africa, South America and the United States; and H. americanum, which so far has only been diagnosed in the United States. In Brazil, the only species found infecting dogs is H. canis. The objective of this review was to detail some aspects of canine hepatozoonosis, caused by H. canis, and the main points of its biology, transmission, pathogenicity, symptoms, epidemiology and diagnostic methods, with emphasis on research developed in Brazil.
Topics: Animals; Apicomplexa; Brazil; Dog Diseases; Dogs; Protozoan Infections, Animal
PubMed: 21961746
DOI: 10.1590/s1984-29612011000300002 -
Trends in Parasitology Oct 2020Recent breakthroughs in high-throughput technologies, transcriptomics, and advances in our understanding of gene regulatory networks have enhanced our perspective on the... (Review)
Review
Recent breakthroughs in high-throughput technologies, transcriptomics, and advances in our understanding of gene regulatory networks have enhanced our perspective on the complex interplay between parasite and host. Noncoding RNA molecules have been implicated in critical roles covering a broad range of biological processes in the Apicomplexa. Processes that are affected range from parasite development to host-parasite interactions and include interactions with epigenetic machinery and other regulatory factors. Here we review recent progress involving noncoding RNAs and their functions in the Apicomplexa, with a focus on three parasites: Plasmodium, Toxoplasma, and Cryptosporidium. We discuss the limitations and challenges of current methods applied to apicomplexan noncoding RNA study and discuss future directions in this exciting field.
Topics: Apicomplexa; Epigenesis, Genetic; Host-Parasite Interactions; RNA, Untranslated; Research
PubMed: 32828659
DOI: 10.1016/j.pt.2020.07.006 -
International Journal For Parasitology Nov 2012The alveolate superphylum includes many free-living and parasitic organisms, which are united by the presence of alveolar sacs lying proximal to the plasma membrane,... (Review)
Review
The alveolate superphylum includes many free-living and parasitic organisms, which are united by the presence of alveolar sacs lying proximal to the plasma membrane, providing cell structure. All species comprising the apicomplexan group of alveolates are parasites and have adapted to the unique requirements of the parasitic lifestyle. Here the evolution of apicomplexan secretory organelles that are involved in the critical process of egress from one cell and invasion of another is explored. The variations within the Apicomplexa and how these relate to species-specific biology will be discussed. In addition, recent studies have identified specific calcium-sensitive molecules that coordinate the various events and regulate the release of these secretory organelles within apicomplexan parasites. Some aspects of this machinery are conserved outside the Apicomplexa, and are beginning to elucidate the conserved nature of the machinery. Briefly, the relationship of this secretion machinery within the Apicomplexa will be discussed, compared with free-living and predatory alveolates, and how these might have evolved from a common ancestor.
Topics: Animals; Apicomplexa; Biological Evolution; Gene Expression Regulation; Organelles; Protozoan Infections
PubMed: 23068912
DOI: 10.1016/j.ijpara.2012.09.009 -
Trends in Parasitology Dec 2020Parasitic protozoa of the phylum Apicomplexa cause a range of human and animal diseases. Their complex life cycles - often heteroxenous with sexual and asexual phases in... (Review)
Review
Parasitic protozoa of the phylum Apicomplexa cause a range of human and animal diseases. Their complex life cycles - often heteroxenous with sexual and asexual phases in different hosts - rely on elaborate cytoskeletal structures to enable morphogenesis and motility, organize cell division, and withstand diverse environmental forces. This review primarily focuses on studies using Toxoplasma gondii and Plasmodium spp. as the best studied apicomplexans; however, many cytoskeletal adaptations are broadly conserved and predate the emergence of the parasitic phylum. After decades cataloguing the constituents of such structures, a dynamic picture is emerging of the assembly and maintenance of apicomplexan cytoskeletons, illuminating how they template and orient critical processes during infection. These observations impact our view of eukaryotic diversity and offer future challenges for cell biology.
Topics: Adaptation, Physiological; Animals; Apicomplexa; Cytoskeleton; Humans; Life Cycle Stages; Plasmodium; Toxoplasma
PubMed: 33011071
DOI: 10.1016/j.pt.2020.09.001 -
PLoS Pathogens Dec 2021The Apicomplexa phylum comprises thousands of distinct intracellular parasite species, including coccidians, haemosporidians, piroplasms, and cryptosporidia. These... (Review)
Review
The Apicomplexa phylum comprises thousands of distinct intracellular parasite species, including coccidians, haemosporidians, piroplasms, and cryptosporidia. These parasites are characterized by complex and divergent life cycles occupying a variety of host niches. Consequently, they exhibit distinct adaptations to the differences in nutritional availabilities, either relying on biosynthetic pathways or by salvaging metabolites from their host. Pantothenate (Pan, vitamin B5) is the precursor for the synthesis of an essential cofactor, coenzyme A (CoA), but among the apicomplexans, only the coccidian subgroup has the ability to synthesize Pan. While the pathway to synthesize CoA from Pan is largely conserved across all branches of life, there are differences in the redundancy of enzymes and possible alternative pathways to generate CoA from Pan. Impeding the scavenge of Pan and synthesis of Pan and CoA have been long recognized as potential targets for antimicrobial drug development, but in order to fully exploit these critical pathways, it is important to understand such differences. Recently, a potent class of pantothenamides (PanAms), Pan analogs, which target CoA-utilizing enzymes, has entered antimalarial preclinical development. The potential of PanAms to target multiple downstream pathways make them a promising compound class as broad antiparasitic drugs against other apicomplexans. In this review, we summarize the recent advances in understanding the Pan and CoA biosynthesis pathways, and the suitability of these pathways as drug targets in Apicomplexa, with a particular focus on the cyst-forming coccidian, Toxoplasma gondii, and the haemosporidian, Plasmodium falciparum.
Topics: Animals; Antiparasitic Agents; Apicomplexa; Coenzyme A; Humans; Pantothenic Acid; Protozoan Infections
PubMed: 34969059
DOI: 10.1371/journal.ppat.1010124 -
Current Topics in Medicinal Chemistry 2017Phosphoinositides (PIs) and their derivatives are essential cellular components that form the building blocks for cell membranes and regulate numerous cell functions.... (Review)
Review
BACKGROUND
Phosphoinositides (PIs) and their derivatives are essential cellular components that form the building blocks for cell membranes and regulate numerous cell functions. Specifically, the ability to generate myo-inositol 1,4,5-trisphosphate (InsP3) via phospholipase C (PLC) dependent hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) to InsP3 and diacylglycerol (DAG) initiates intracellular calcium signaling events representing a fundamental signaling mechanism dependent on PIs. InsP3 produced by PI turnover as a second messenger causes intracellular calcium release, especially from endoplasmic reticulum, by binding to the InsP3 receptor (InsP3R). Various PIs and the enzymes, such as phosphatidylinositol synthase and phosphatidylinositol 4-kinase, necessary for their turnover have been characterized in Apicomplexa, a large phylum of mostly commensal organisms that also includes several clinically relevant parasites. However, InsP3Rs have not been identified in genomes of apicomplexans, despite evidence that these parasites produce InsP3 that mediates intracellular Ca2+ signaling.
CONCLUSION
Evidence to supporting IP3-dependent signaling cascades in apicomplexans suggests that they may harbor a primitive or non-canonical InsP3R. Understanding these pathways may be informative about early branching eukaryotes, where such signaling pathways also diverge from animal systems, thus identifying potential novel and essential targets for therapeutic intervention.
Topics: Animals; Apicomplexa; Inositol 1,4,5-Trisphosphate; Second Messenger Systems; Signal Transduction
PubMed: 28137231
DOI: 10.2174/1568026617666170130121042 -
Molecular Microbiology Oct 2017The balance between phosphorylation and de-phosphorylation, which is delicately regulated by protein kinases and phosphatases, is critical for nearly all biological... (Review)
Review
The balance between phosphorylation and de-phosphorylation, which is delicately regulated by protein kinases and phosphatases, is critical for nearly all biological processes. The Apicomplexa are a large phylum which contains various parasitic protists, including human pathogens, such as Plasmodium, Toxoplasma, Cryptosporidium and Babesia species. The diverse life cycles of these parasites are highly complex and, not surprisingly, many of their key steps are exquisitely regulated by phosphorylation. Interestingly, many of the kinases and phosphatases, as well as the substrates involved in these events are unique to the parasites and therefore phosphorylation constitutes a viable target for antiparasitic intervention. Most progress on this realm has come from studies in Toxoplasma and Plasmodium of their respective kinomes and phosphoproteomes. Nonetheless, given their likely importance, phosphatases have recently become the focus of research within the apicomplexan parasites. In this review, we concentrate on serine/threonine phosphatases in apicomplexan parasites, with the focus on comprehensively identifying and naming protein phosphatases in available apicomplexan genomes, and summarizing the progress of their functional analyses in recent years.
Topics: Animals; Apicomplexa; Conserved Sequence; Genome; Humans; Parasites; Phosphoprotein Phosphatases; Phosphorylation; Phosphotransferases; Phylogeny; Plasmodium; Toxoplasma
PubMed: 28556455
DOI: 10.1111/mmi.13715 -
Frontiers in Cellular and Infection... 2017The next-generation gene editing based on CRISPR (clustered regularly interspaced short palindromic repeats) has been successfully implemented in a wide range of... (Review)
Review
The next-generation gene editing based on CRISPR (clustered regularly interspaced short palindromic repeats) has been successfully implemented in a wide range of organisms including some protozoan parasites. However, application of such a versatile game-changing technology in molecular parasitology remains fairly underexplored. Here, we briefly introduce in human and mouse research and usher new directions to drive the parasitology research in the years to come. In precise, we outline contemporary ways to embolden existing apicomplexan and kinetoplastid parasite models by commissioning front-line gene-tailoring methods, and illustrate how we can break the enduring gridlock of gene manipulation in non-model parasitic protists to tackle intriguing questions that remain long unresolved otherwise. We show how a judicious solicitation of the CRISPR technology can eventually balance out the two facets of pathogen-host interplay.
Topics: Animals; Apicomplexa; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Editing; Humans; Kinetoplastida; Phylogeny; Protozoan Infections
PubMed: 28730142
DOI: 10.3389/fcimb.2017.00292 -
BMC Genomics May 2022Genome architecture describes how genes and other features are arranged in genomes. These arrangements reflect the evolutionary pressures on genomes and underlie...
Genome architecture describes how genes and other features are arranged in genomes. These arrangements reflect the evolutionary pressures on genomes and underlie biological processes such as chromosomal segregation and the regulation of gene expression. We present a new tool called Genome Decomposition Analysis (GDA) that characterises genome architectures and acts as an accessible approach for discovering hidden features of a genome assembly. With the imminent deluge of high-quality genome assemblies from projects such as the Darwin Tree of Life and the Earth BioGenome Project, GDA has been designed to facilitate their exploration and the discovery of novel genome biology. We highlight the effectiveness of our approach in characterising the genome architectures of single-celled eukaryotic parasites from the phylum Apicomplexa and show that it scales well to large genomes.
Topics: Animals; Apicomplexa; Biological Evolution; Eukaryota; Genome; Parasites
PubMed: 35610562
DOI: 10.1186/s12864-022-08616-3