The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites

A 'One Health' perspective of Africa-wide distribution and prevalence of Giardia species in humans, animals and waterbodies: a systematic review and meta-analysis

Giardiasis, caused by Giardia duodenalis, is a leading cause of diarrhoea in resource-poor countries. To gain a better insight into the epidemiology of Giardia in Africa, we undertook a robust study to comprehend the distribution and prevalence of Giardia infection in humans, animals and their dispersal in the environment. Our protocol was registered with PROSPERO (registration number CRD42022317653). Deep literature search from 5 electronic databases, namely, AJOL, Google scholar, PubMed, ScienceDirect and Springer Link was performed using relevant keywords. Meta-analysis was performed using a random-effects model and heterogeneity among studies was evaluated using Cochran's Q and the I2-statistic. More than 500 eligible studies published from 1 January 1980 until 22 March 2022 were retrieved. In humans, exactly 48 124 Giardia spp. infection cases were registered from the 494 014 stool samples examined resulting in a pooled prevalence estimate (PPE) of 8.8% using microscopy. Whereas copro-antigen tests and molecular diagnostic methods generated PPE of 14.3 and 19.5%, respectively, with HIV+ subjects and those with diarrhoeatic stool having infection rates of 5.0 and 12.3%, respectively. The PPE of Giardia spp. infection in animals using molecular methods was 15.6%, which was most prevalent in pigs (25.2%) with Nigeria registering the highest prevalence at 20.1%. The PPE of Giardia spp. contamination from waterbodies was 11.9% from a total of 7950 samples which were detected using microscopy, with Tunisia documenting the highest infection rate of 37.3%. This meta-analysis highlights the necessity of ‘One Health’ approach for consolidated epidemiological studies and control of giardiasis in the African continent.

Functional Differentiation of Cyclins and Cyclin-Dependent Kinases in Giardia lamblia

Cyclin-dependent kinases (CDKs) are serine/threonine kinases that control the eukaryotic cell cycle. Limited information is available on Giardia lamblia CDKs (GlCDKs), GlCDK1 and GlCDK2. After treatment with the CDK inhibitor flavopiridol-HCl (FH), division of Giardia trophozoites was transiently arrested at the G1/S phase and finally at the G2/M phase. The percentage of cells arrested during prophase or cytokinesis increased, whereas DNA synthesis was not affected by FH treatment. Morpholino-mediated depletion of GlCDK1 caused arrest at the G2/M phase, while GlCDK2 depletion resulted in an increase in the number of cells arrested at the G1/S phase and cells defective in mitosis and cytokinesis. Coimmunoprecipitation experiments with GlCDKs and the nine putative G. lamblia cyclins (Glcyclins) identified Glcyclins 3977/14488/17505 and 22394/6584 as cognate partners of GlCDK1 and GlCDK2, respectively. Morpholino-based knockdown of Glcyclin 3977 or 22394/6584 arrested cells in the G2/M phase or G1/S phase, respectively. Interestingly, GlCDK1- and Glcyclin 3977-depleted Giardia showed significant flagellar extension. Altogether, our results suggest that GlCDK1/Glcyclin 3977 plays an important role in the later stages of cell cycle control and in flagellar biogenesis. In contrast, GlCDK2 along with Glcyclin 22394 and 6584 functions from the early stages of the Giardia cell cycle. IMPORTANCE Giardia lamblia CDKs (GlCDKs) and their cognate cyclins have not yet been studied. In this study, the functional roles of GlCDK1 and GlCDK2 were distinguished using morpholino-mediated knockdown and coimmunoprecipitation. GlCDK1 with Glcyclin 3977 plays a role in flagellum formation as well as cell cycle control of G. lamblia, whereas GlCDK2 with Glcyclin 22394/6584 is involved in cell cycle control.

Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia

During pre-mRNA processing, the poly(A) signal is recognized by a protein complex that ensures precise cleavage and polyadenylation of the nascent transcript. The location of this cleavage event establishes the length and sequence of the 3' UTR of an mRNA, thus determining much of its post-transcriptional fate. Using long-read sequencing, we characterize the polyadenylation signal and related sequences surrounding Giardia lamblia cleavage sites for over 2600 genes. We find that G. lamblia uses an AGURAA poly(A) signal, which differs from the mammalian AAUAAA. We also describe how G. lamblia lacks common auxiliary elements found in other eukaryotes, along with the proteins that recognize them. Further, we identify 133 genes with evidence of alternative polyadenylation. These results suggest that despite pared-down cleavage and polyadenylation machinery, 3' end formation still appears to be an important regulatory step for gene expression in G. lamblia.

Dual RNA Sequencing Reveals Key Events When Different Giardia Life Cycle Stages Interact With Human Intestinal Epithelial Cells In Vitro

Giardia intestinalis is a protozoan parasite causing diarrheal disease, giardiasis, after extracellular infection of humans and other mammals’ intestinal epithelial cells (IECs) of the upper small intestine. The parasite has two main life cycle stages: replicative trophozoites and transmissive cysts. Differentiating parasites (encysting cells) and trophozoites have recently been shown to be present in the same regions of the upper small intestine, whereas most mature cysts are found further down in the intestinal system. To learn more about host-parasite interactions during Giardia infections, we used an in vitro model of the parasite’s interaction with host IECs (differentiated Caco-2 cells) and Giardia WB trophozoites, early encysting cells (7 h), and cysts. Dual RNA sequencing (Dual RNAseq) was used to identify differentially expressed genes (DEGs) in both Giardia and the IECs, which might relate to establishing infection and disease induction. In the human cells, the largest gene expression changes were found in immune and MAPK signaling, transcriptional regulation, apoptosis, cholesterol metabolism and oxidative stress. The different life cycle stages of Giardia induced a core of similar DEGs but at different levels and there are many life cycle stage-specific DEGs. The metabolic protein PCK1, the transcription factors HES7, HEY1 and JUN, the peptide hormone CCK and the mucins MUC2 and MUC5A are up-regulated in the IECs by trophozoites but not cysts. Cysts specifically induce the chemokines CCL4L2, CCL5 and CXCL5, the signaling protein TRKA and the anti-bacterial protein WFDC12. The parasite, in turn, up-regulated a large number of hypothetical genes, high cysteine membrane proteins (HCMPs) and oxidative stress response genes. Early encysting cells have unique DEGs compared to trophozoites (e.g. several uniquely up-regulated HCMPs) and interaction of these cells with IECs affected the encystation process. Our data show that different life cycle stages of Giardia induce different gene expression responses in the host cells and that the IECs in turn differentially affect the gene expression in trophozoites and early encysting cells. This life cycle stage-specific host-parasite cross-talk is an important aspect to consider during further studies of Giardia’s molecular pathogenesis.

A hybrid sequencing and assembly strategy for generating culture free Giardia genomes

Giardia duodenalis is a pathogenic intestinal protozoan parasite of humans and many other animals. Giardia duodenalis is found throughout the world, and infection is known to have adverse health consequences for human and other mammalian hosts. Yet, many aspects of the biology of this ubiquitous parasite remain unresolved. Whole genome sequencing and comparative genomics can provide insight into the biology of G. duodenalis by helping to reveal traits that are shared by all G. duodenalis assemblages or unique to an individual assemblage or strain. However, these types of analyses are currently hindered by the lack of available G. duodenalis genomes, due, in part, to the difficulty in obtaining the genetic material needed to perform whole genome sequencing. In this study, a novel approach using a multistep cleaning procedure coupled with a hybrid sequencing and assembly strategy was assessed for use in producing high quality G. duodenalis genomes directly from cysts obtained from feces of two naturally infected hosts, a cat and dog infected with assemblage A and D, respectively. Cysts were cleaned and concentrated using cesium chloride gradient centrifugation followed by immunomagnetic separation. Whole genome sequencing was performed using both Illumina MiSeq and Oxford Nanopore MinION platforms. A hybrid assembly strategy was found to produce higher quality genomes than assemblies from either platform alone. The hybrid G. duodenalis genomes obtained from fecal isolates (cysts) in this study compare favorably for quality and completeness against reference genomes of G. duodenalis from cultured isolates. The whole genome assembly for assemblage D is the most contiguous genome available for this assemblage and is an important reference genome for future comparative studies. The data presented here support a hybrid sequencing and assembly strategy as a suitable method to produce whole genome sequences from DNA obtained from G. duodenalis cysts which can be used to produce novel reference genomes necessary to perform comparative genomics studies of this parasite.

•

Assemblage A and D genomes were generated directly from cysts isolated from feces.

•

Genomes were sequenced using Illumina and Oxford Nanopore sequencing platforms.

•

A hybrid sequencing/assembly strategy was used to generate G. duodenalis genomes.

•

A hybrid strategy yields reference quality genomes from fecal isolates.

•

These methods have generated the most contiguous Assemblage D genome to date.

High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis

Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3′UTR regions and characterise the Kozak sequence in the 5′UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.

A Detailed Gene Expression Map of Giardia Encystation

Giardia intestinalis is an intestinal protozoan parasite that causes diarrheal infections worldwide. A key process to sustain its chain of transmission is the formation of infectious cysts in the encystation process. We combined deep RNAseq of a broad range of encystation timepoints to produce a high-resolution gene expression map of Giardia encystation. This detailed transcriptomic map of encystation confirmed a gradual change of gene expression along the time course of encystation, showing the most significant gene expression changes during late encystation. Few genes are differentially expressed early in encystation, but the major cyst wall proteins CWP-1 and -2 are highly up-regulated already after 3.5 h encystation. Several transcription factors are sequentially up-regulated throughout the process, but many up-regulated genes at 7, 10, and 14 h post-induction of encystation have binding sites in the upstream regions for the Myb2 transcription factor, suggesting that Myb2 is a master regulator of encystation. We observed major changes in gene expression of several meiotic-related genes from 10.5 h of encystation to the cyst stage, and at 17.5 h encystation, there are changes in many different metabolic pathways and protein synthesis. Late encystation, 21 h to cysts, show extensive gene expression changes, most of all in VSP and HCMP genes, which are involved in antigenic variation, and genes involved in chromatin modifications. This high-resolution gene expression map of Giardia encystation will be an important tool in further studies of this important differentiation process.

Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata

BACKGROUND

Comparing a parasitic lineage to its free-living relatives is a powerful way to understand how that evolutionary transition to parasitism occurred. Giardia intestinalis (Fornicata) is a leading cause of gastrointestinal disease world-wide and is famous for its unusual complement of cellular compartments, such as having peripheral vacuoles instead of typical endosomal compartments. Endocytosis plays an important role in Giardia's pathogenesis. Endosomal sorting complexes required for transport (ESCRT) are membrane-deforming proteins associated with the late endosome/multivesicular body (MVB). MVBs are ill-defined in G. intestinalis, and roles for identified ESCRT-related proteins are not fully understood in the context of its unique endocytic system. Furthermore, components thought to be required for full ESCRT functionality have not yet been documented in this species.

RESULTS

We used genomic and transcriptomic data from several Fornicata species to clarify the evolutionary genome streamlining observed in Giardia, as well as to detect any divergent orthologs of the Fornicata ESCRT subunits. We observed differences in the ESCRT machinery complement between Giardia strains. Microscopy-based investigations of key components of ESCRT machinery such as GiVPS36 and GiVPS25 link them to peripheral vacuoles, highlighting these organelles as simplified MVB equivalents. Unexpectedly, we show ESCRT components associated with the endoplasmic reticulum and, for the first time, mitosomes. Finally, we identified the rare ESCRT component CHMP7 in several fornicate representatives, including Giardia and show that contrary to current understanding, CHMP7 evolved from a gene fusion of VPS25 and SNF7 domains, prior to the last eukaryotic common ancestor, over 1.5 billion years ago.

CONCLUSIONS

Our findings show that ESCRT machinery in G. intestinalis is far more varied and complete than previously thought, associates to multiple cellular locations, and presents changes in ESCRT complement which pre-date adoption of a parasitic lifestyle.

Real-Time PCR for Molecular Detection of Zoonotic and Non-Zoonotic Giardia spp. in Wild Rodents

Giardiasis in humans is a gastrointestinal disease transmitted by the potentially zoonotic Giardia duodenalis genotypes (assemblages) A and B. Small wild rodents such as mice and voles are discussed as potential reservoirs for G. duodenalis but are predominantly populated by the two rodent species Giardia microti and Giardia muris. Currently, the detection of zoonotic and non-zoonotic Giardia species and genotypes in these animals relies on cumbersome PCR and sequencing approaches of genetic marker genes. This hampers the risk assessment of potential zoonotic Giardia transmissions by these animals. Here, we provide a workflow based on newly developed real-time PCR schemes targeting the small ribosomal RNA multi-copy gene locus to distinguish G. muris, G. microti and G. duodenalis infections. For the identification of potentially zoonotic G. duodenalis assemblage types A and B, an established protocol targeting the single-copy gene 4E1-HP was used. The assays were specific for the distinct Giardia species or genotypes and revealed an analytical sensitivity of approximately one or below genome equivalent for the multi-copy gene and of about 10 genome equivalents for the single-copy gene. Retesting a biobank of small rodent samples confirmed the specificity. It further identified the underlying Giardia species in four out of 11 samples that could not be typed before by PCR and sequencing. The newly developed workflow has the potential to facilitate the detection of potentially zoonotic and non-zoonotic Giardia species in wild rodents.

Retortamonads from vertebrate hosts share features of anaerobic metabolism and pre-adaptations to parasitism with diplomonads

Although the mitochondria of extant eukaryotes share a single origin, functionally these organelles diversified to a great extent, reflecting lifestyles of the organisms that host them. In anaerobic protists of the group Metamonada, mitochondria are present in reduced forms (also termed hydrogenosomes or mitosomes) and a complete loss of mitochondrion in Monocercomonoides exilis (Metamonada:Preaxostyla) has also been reported. Within metamonads, retortamonads from the gastrointestinal tract of vertebrates form a sister group to parasitic diplomonads (e.g. Giardia and Spironucleus) and have also been hypothesized to completely lack mitochondria. We obtained transcriptomic data from Retortamonas dobelli and R. caviae and searched for enzymes of the core metabolism as well as mitochondrion- and parasitism-related proteins. Our results indicate that retortamonads have a streamlined metabolism lacking pathways for metabolites they are probably capable of obtaining from prey bacteria or their environment, reminiscent of the biochemical arrangement in other metamonads. Retortamonads were surprisingly found do encode homologs of components of Giardia's remarkable ventral disk, as well as homologs of regulatory NEK kinases and secreted lytic enzymes known for involvement in host colonization by Giardia. These can be considered pre-adaptations of these intestinal microorganisms to parasitism. Furthermore, we found traces of the mitochondrial metabolism represented by iron‑sulfur cluster assembly subunits, subunits of mitochondrial translocation and chaperone machinery and, importantly, [FeFe]‑hydrogenases and hydrogenase maturases (HydE, HydF and HydG). Altogether, our results strongly suggest that a remnant mitochondrion is still present.

Metabolic Reconstruction Elucidates the Lifestyle of the Last Diplomonadida Common Ancestor

Diplomonads are a group of microbial eukaryotes found in oxygen-poor environments. There are both parasitic (e.g., Giardia intestinalis) and free-living (e.g., Trepomonas) members in the group.

The identification of ancestral traits is essential to understanding the evolution of any group. In the case of parasitic groups, this helps us understand the adaptation to this lifestyle and a particular host. Most diplomonads are parasites, but there are free-living members of the group nested among the host-associated diplomonads. Furthermore, most of the close relatives within Fornicata are free-living organisms. This leaves the lifestyle of the ancestor unclear. Here, we present metabolic maps of four different diplomonad species. We identified 853 metabolic reactions and 147 pathways present in at least one of the analyzed diplomonads. Our study suggests that diplomonads represent a metabolically diverse group in which differences correlate with different environments (e.g., the detoxification of arsenic). Using a parsimonious analysis, we also provide a description of the putative metabolism of the last Diplomonadida common ancestor. Our results show that the acquisition and loss of reactions have shaped metabolism since this common ancestor. There is a net loss of reaction in all branches leading to parasitic diplomonads, suggesting an ongoing reduction in the metabolic capacity. Important traits present in host-associated diplomonads (e.g., virulence factors and the synthesis of UDP-N-acetyl-d-galactosamine) are shared with free-living relatives. The last Diplomonadida common ancestor most likely already had acquired important enzymes for the salvage of nucleotides and had a reduced capacity to synthesize nucleotides, lipids, and amino acids de novo, suggesting that it was an obligate host-associated organism.

IMPORTANCE Diplomonads are a group of microbial eukaryotes found in oxygen-poor environments. There are both parasitic (e.g., Giardia intestinalis) and free-living (e.g., Trepomonas) members in the group. Diplomonads are well known for their anaerobic metabolism, which has been studied for many years. Here, we reconstructed whole metabolic networks of four extant diplomonad species as well as their ancestors, using a bioinformatics approach. We show that the metabolism within the group is under constant change throughout evolutionary time, in response to the environments that the different lineages explore. Both gene losses and gains are responsible for the adaptation processes. Interestingly, it appears that the last Diplomonadida common ancestor had a metabolism that is more similar to extant parasitic than free-living diplomonads. This suggests that the host-associated lifestyle of parasitic diplomonads, such as the human parasite G. intestinalis, is an old evolutionary adaptation.

Eukaryote-conserved histone post-translational modification landscape in Giardia duodenalis revealed by mass spectrometry

Diarrheal disease caused by Giardia duodenalis is highly prevalent, causing over 200 million cases globally each year. The processes that drive parasite virulence, host immune evasion and transmission involve coordinated gene expression and have been linked to epigenetic regulation. Epigenetic regulatory systems are eukaryote-conserved, including in deep branching excavates such as Giardia, with several studies already implicating histone post-translational modifications in regulation of its pathogenesis and life cycle. However, further insights into Giardia chromatin dynamics have been hindered by a lack of site-specific knowledge of histone modifications. Using mass spectrometry, we have provided the first known molecular map of histone methylation, acetylation and phosphorylation modifications in Giardia core histones. We have identified over 50 previously unreported histone modifications including sites with established roles in epigenetic regulation, and co-occurring modifications indicative of post-translational modification crosstalk. These demonstrate conserved histone modifications in Giardia which are equivalent to many other eukaryotes, and suggest that similar epigenetic mechanisms are in place in this parasite. Further, we used sequence, domain and structural homology to annotate putative histone enzyme networks in Giardia, highlighting representative chromatin modifiers which appear sufficient for identified sites, particularly those from H3 and H4 variants. This study is to our knowledge the first and most comprehensive, complete and accurate view of Giardia histone post-translational modifications to date, and a substantial step towards understanding their associations in parasite development and virulence.