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Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Karolinska Inst, Dept Cell & Mol Biol, SE-17177 Stockholm, Sweden. KISP, Sci Life Lab, S-17165 Solna, Sweden..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
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2015 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 16, article id 697Article in journal (Refereed) Published
Abstract [en]

Background: The diarrhea-causing protozoan Giardia intestinalis makes up a species complex of eight different assemblages (A-H), where assemblage A and B infect humans. Comparative whole-genome analyses of three of these assemblages have shown that there is significant divergence at the inter-assemblage level, however little is currently known regarding variation at the intra-assemblage level. We have performed whole genome sequencing of two sub-assemblage AII isolates, recently axenized from symptomatic human patients, to study the biological and genetic diversity within assemblage A isolates. Results: Several biological differences between the new and earlier characterized assemblage A isolates were identified, including a difference in growth medium preference. The two AII isolates were of different sub-assemblage types (AII-1 [AS175] and AII-2 [AS98]) and showed size differences in the smallest chromosomes. The amount of genetic diversity was characterized in relation to the genome of the Giardia reference isolate WB, an assemblage AI isolate. Our analyses indicate that the divergence between AI and AII is approximately 1 %, represented by similar to 100,000 single nucleotide polymorphisms (SNP) distributed over the chromosomes with enrichment in variable genomic regions containing surface antigens. The level of allelic sequence heterozygosity (ASH) in the two AII isolates was found to be 0.25-0.35 %, which is 25-30 fold higher than in the WB isolate and 10 fold higher than the assemblage AII isolate DH (0.037 %). 35 protein-encoding genes, not found in the WB genome, were identified in the two AII genomes. The large gene families of variant-specific surface proteins (VSPs) and high cysteine membrane proteins (HCMPs) showed isolate-specific divergences of the gene repertoires. Certain genes, often in small gene families with 2 to 8 members, localize to the variable regions of the genomes and show high sequence diversity between the assemblage A isolates. One of the families, Bactericidal/ Permeability Increasing-like protein (BPIL), with eight members was characterized further and the proteins were shown to localize to the ER in trophozoites. Conclusions: Giardia genomes are modular with highly conserved core regions mixed up by variable regions containing high levels of ASH, SNPs and variable surface antigens. There are significant genomic variations in assemblage A isolates, in terms of chromosome size, gene content, surface protein repertoire and gene polymorphisms and these differences mainly localize to the variable regions of the genomes. The large genetic differences within one assemblage of G. intestinalis strengthen the argument that the assemblages represent different Giardia species.

Place, publisher, year, edition, pages
2015. Vol. 16, article id 697
National Category
Genetics Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-264039DOI: 10.1186/s12864-015-1893-6ISI: 000361093400009PubMedID: 26370391OAI: oai:DiVA.org:uu-264039DiVA, id: diva2:859235
Funder
Swedish Research Council FormasSwedish Research CouncilAvailable from: 2015-10-06 Created: 2015-10-05 Last updated: 2019-04-19Bibliographically approved
In thesis
1. Studies of Giardia-host interactions: role of cysteine-rich surface proteins.
Open this publication in new window or tab >>Studies of Giardia-host interactions: role of cysteine-rich surface proteins.
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Giardia intestinalis is a eukaryotic parasite that colonizes the small intestine of humans and animals causing the diarrheal disease known as giardiasis. This parasite is not invasive and does not internalize into host cells but it rather attaches to the brush border surface of the small intestine disrupting the epithelial barrier. Giardia causes around 280 million symptomatic infections in humans every year, while it can also cause chronic and asymptomatic infections. Giardiasis is a multifactorial disease but only few factors that directly contribute in the pathogenesis and virulence of the disease have been identified. G. intestinalis has eight genetic groups, but only two of them (A and B) are known to infect humans.

In this thesis, whole genome sequencing was performed for two human assemblage A isolates (AS175 and AS98) and were compared to assemblage A isolate WB genome (Paper I). Genome-wide variations were identified among the three isolates including isolate-specific coding sequences and high level of nucleotide diversity of multi-gene families such as VSPs and HCMPs.

We further used an in vitro model for parasite interaction with host intestinal epithelial cells (IECs) to study the interplay between Giardia and the human host. We have identified the major Giardia excretory-secretory products (ESPs) released by two Giardia isolates (WB and GS) when they interact with the Caco-2 IECs (Paper II). Wide changes in the transcriptome (Paper III) and the proteome (Paper IV) of the parasite (WB isolate) and the host IECs have been studied giving us a further understanding of the parasite-host interactions. An understudied gene family (HCMPs) was studied and further characterized during interactions in both RNA and protein level (Paper III, IV).

In conclusion, the thesis has provided a further understanding of Giardia-host interactions in vitro and the molecular mechanisms involved.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 85
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1816
Keywords
Giardia, intestinal parasite, parasite infection, host-parasite interaction, virulence factors, HCMPs, cysteine-rich proteins, secretome, proteome
National Category
Cell Biology
Identifiers
urn:nbn:se:uu:diva-382071 (URN)978-91-513-0670-4 (ISBN)
Public defence
2019-06-14, A1:111a, Husargatan 3, Uppsala, 09:15 (English)
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Supervisors
Available from: 2019-05-24 Created: 2019-04-19 Last updated: 2019-06-18

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