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A Detailed Gene Expression Map of Giardia Encystation. Genes (Basel) 2021; 12:genes12121932. [PMID: 34946882 PMCID: PMC8700996 DOI: 10.3390/genes12121932] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022] Open
Abstract
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.
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Heller M, Braga S, Müller N, Müller J. Transfection With Plasmid Causing Stable Expression of a Foreign Gene Affects General Proteome Pattern in Giardia lamblia Trophozoites. Front Cell Infect Microbiol 2020; 10:602756. [PMID: 33392107 PMCID: PMC7775365 DOI: 10.3389/fcimb.2020.602756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
Giardia lamblia is an important causative agent of persistent diarrhea in humans, domestic animals, and cattle. Basic research is usually performed with the strain WBC6 and includes genetic manipulations such as transfections. Here, we investigate how transfection with a plasmid causing stable expression of a foreign gene affects the whole proteome pattern. Using shotgun mass spectrometry, we compare the proteomes of untransfected trophozoites to trophozoites transfected with Escherichia coli glucuronidase A (GusA). Besides GusA, which is detected in the transfected trophozoites only, the proteomes of untransfected and transfected trophozoites differ by 132 differentially expressed proteins. In particular, transfection induces antigenic variation. Since transfection causing stable expression affects the proteome pattern, transfection experiments should take into account this effect. Due to a unique peptide panel, GusA is an example for a suitable internal standard for experiments involving transfected cells. Data are available via ProteomeXchange with identifier PXD022565.
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Affiliation(s)
- Manfred Heller
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Sophie Braga
- Proteomics & Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Norbert Müller
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Joachim Müller
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, Institute of Parasitology, University of Bern, Bern, Switzerland
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PeptideWitch-A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data. Proteomes 2020; 8:proteomes8030021. [PMID: 32825686 PMCID: PMC7564585 DOI: 10.3390/proteomes8030021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022] Open
Abstract
PeptideWitch is a python-based web module that introduces several key graphical and technical improvements to the Scrappy software platform, which is designed for label-free quantitative shotgun proteomics analysis using normalised spectral abundance factors. The program inputs are low stringency protein identification lists output from peptide-to-spectrum matching search engines for ‘control’ and ‘treated’ samples. Through a combination of spectral count summation and inner joins, PeptideWitch processes low stringency data, and outputs high stringency data that are suitable for downstream quantitation. Data quality metrics are generated, and a series of statistical analyses and graphical representations are presented, aimed at defining and presenting the difference between the two sample proteomes.
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Kim J, Park SJ. Role of gamma-giardin in ventral disc formation of Giardia lamblia. Parasit Vectors 2019; 12:227. [PMID: 31088539 PMCID: PMC6515615 DOI: 10.1186/s13071-019-3478-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022] Open
Abstract
Background Giardia lamblia, a protozoan pathogen causing diarrheal outbreaks, has characteristic cytoskeletal structures including eight flagella, a median body and a ventral disc. Gamma-giardin is a unique component protein of the cytoskeleton of this protozoan. Results Through comparative proteomic analysis between different stages of the cell cycle, G. lamblia γ-giardin (Glγ-giardin) was identified as an upregulated protein in the G2-phase. Increased Glγ-giardin expression in G2 was confirmed by western blot and real-time polymerase chain reaction analyses. Knockdown of this protein using a morpholino affected the formation of ventral discs, especially the microribbons of the discs, but exerted little effect on the binding ability of G. lamblia. The number of cells with four nuclei was increased in Glγ-giardin-knockdown cells. Expression of Glγ-giardin was decreased during encystation, in contrast with the G2-phase. Conclusions Knockdown experiments demonstrated that Glγ-giardin is a component of the trilaminar structure of the ventral disc. Expression of Glγ-giardin is induced in the G2-phase prior to active cell division, whereas its expression decreases during encystation, a dormant stage of G. lamblia. Electronic supplementary material The online version of this article (10.1186/s13071-019-3478-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juri Kim
- Department of Environmental Medical Biology and Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Soon-Jung Park
- Department of Environmental Medical Biology and Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul, South Korea.
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Ortega-Pierres M, Jex AR, Ansell BR, Svärd SG. Recent advances in the genomic and molecular biology of Giardia. Acta Trop 2018; 184:67-72. [PMID: 28888474 DOI: 10.1016/j.actatropica.2017.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/05/2017] [Indexed: 01/01/2023]
Abstract
Giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. Robust tools for analyzing gene function in this parasite have been developed and a range of genetic tools are now available. These together with public databases have provided insights on the function of different genes in Giardia. In this review we provide a current perspective on different molecular aspects of Giardia related to genomics, regulation of encystation, trophozoite transcriptional responses to physiological and xenobiotic (drug-induced) stress, and mechanisms of drug resistance. We also examine recent insights that have contributed to gain knowledge in the study of VSPs, antigenic variation, epigenetics, DNA repair and in the direct manipulation of gene function in Giardia, with a particular focus on the inducible Cre/loxP system.
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Cacciò SM, Lalle M, Svärd SG. Host specificity in the Giardia duodenalis species complex. INFECTION GENETICS AND EVOLUTION 2017; 66:335-345. [PMID: 29225147 DOI: 10.1016/j.meegid.2017.12.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 12/15/2022]
Abstract
Giardia duodenalis is a unicellular flagellated parasite that infects the gastrointestinal tract of a wide range of mammalian species, including humans. Investigations of protein and DNA polymorphisms revealed that G. duodenalis should be considered as a species complex, whose members, despite being morphologically indistinguishable, can be classified into eight groups, or Assemblages, separated by large genetic distances. Assemblages display various degree of host specificity, with Assemblages A and B occurring in humans and many other hosts, Assemblage C and D in canids, Assemblage E in hoofed animals, Assemblage F in cats, Assemblage G in rodents, and Assemblage H in pinnipeds. The factors determining host specificity are only partially understood, and clearly involve both the host and the parasite. Here, we review the results of in vitro and in vivo experiments, and clinical observations to highlight relevant biological and genetic differences between Assemblages, with a focus on human infection.
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Affiliation(s)
- Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Marco Lalle
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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Prokaryotic Expression of α-13 Giardin Gene and Its Intracellular Localization in Giardia lamblia. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1603264. [PMID: 28286754 PMCID: PMC5329650 DOI: 10.1155/2017/1603264] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/18/2017] [Indexed: 12/02/2022]
Abstract
To study prokaryotic expression and subcellular localization of α-13 giardin in Giardia lamblia trophozoites, α-13 giardin gene was amplified and cloned into prokaryotic expression vector pET-28a(+). The positive recombinant plasmid was transformed into E. coli BL21(DE3) for expression by using IPTG and autoinduction expression system (ZYM-5052). The target protein was validated by SDS-PAGE and Western blotting and purified by Ni-NTA Resin. Rabbits were immunized with purified fusion proteins for preparation of polyclonal antibody; then the intracellular location of α-13 giardin was determined by fluorescence immunoassay. The results showed that the length of α-13 giardin gene was 1038 bp, encoding a polypeptide of 345 amino acids. The expressed product was a fusion protein with about 40 kDa largely present in soluble form. The target protein accounted for 21.0% of total proteins after being induced with IPTG, while it accounted for 28.8% with ZYM-5052. The anti-α13-giardin polyclonal antibody possessed good antigenic specificity as well as excellent binding activity with recombinant α-13 giardin. Immunofluorescence assays revealed that α-13 giardin was localized in the cytoplasm of G. lamblia trophozoite, suggesting that it is a cytoplasm-associated protein. The present study may lay a foundation for further functional research on α-13 giardin of G. lamblia.
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Coelho CH, Costa AO, Silva ACC, Pucci MM, Serufo AV, Busatti HGNO, Durigan M, Perales J, Chapeaurouge A, da Silva e Silva DA, Gomes MA, Toledo JS, Singer SM, Silva-Pereira RA, Fernandes AP. Genotyping and Descriptive Proteomics of a Potential Zoonotic Canine Strain of Giardia duodenalis, Infective to Mice. PLoS One 2016; 11:e0164946. [PMID: 27760188 PMCID: PMC5070761 DOI: 10.1371/journal.pone.0164946] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 10/04/2016] [Indexed: 01/20/2023] Open
Abstract
The zoonotic potential of giardiasis, as proposed by WHO since the late 70's, has been largely confirmed in this century. The genetic assemblages A and B of Giardia duodenalis are frequently isolated from human and canine hosts. Most of the assemblage A strains are not infective to adult mice, which can limit the range of studies regarding to biology of G. duodenalis, including virulence factors and the interaction with host immune system. This study aimed to determine the infectivity in mice of an assemblage A Giardia duodenalis strain (BHFC1) isolated from a dog and to classify the strain in sub-assemblages (AI, AII, AIII) through the phylogenetic analysis of beta-giardin (bg), triose phosphate isomerase (tpi) and glutamate dehydrogenase (gdh) genes. In addition, the proteomic profile of soluble and insoluble protein fractions of trophozoites was analyzed by 2D-electrophoresis. Accordingly, trophozoites of BHFC1 were highly infective to Swiss mice. The phylogenetic analysis of tpi and gdh revealed that BHFC1 clustered to sub-assemblage AI. The proteomic map of soluble and insoluble protein fractions led to the identification of 187 proteins of G. duodenalis, 27 of them corresponding to hypothetical proteins. Considering both soluble and soluble fractions, the vast majority of the identified proteins (n = 82) were classified as metabolic proteins, mainly associated with carbon and lipid metabolism, including 53 proteins with catalytic activity. Some of the identified proteins correspond to antigens while others can be correlated with virulence. Besides a significant complementation to the proteomic data of G. duodenalis, these data provide an important source of information for future studies on various aspects of the biology of this parasite, such as virulence factors and host and pathogen interactions.
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Affiliation(s)
- Camila Henriques Coelho
- Departamento de Analises Clinicas e Toxicológicas – Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Adriana Oliveira Costa
- Departamento de Analises Clinicas e Toxicológicas – Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Carolina Carvalho Silva
- Departamento de Analises Clinicas e Toxicológicas – Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maíra Mazzoni Pucci
- Centro de Pesquisas René Rachou - FIOCRUZ/MG, Belo Horizonte, Minas Gerais, Brazil
| | - Angela Vieira Serufo
- Departamento de Analises Clinicas e Toxicológicas – Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Maurício Durigan
- Centro de Biologia Molecular e Engenharia Genética (CBMEG-UNICAMP), Campinas, Brazil
| | - Jonas Perales
- Laboratório de Toxinologia, Instituto Oswaldo Cruz- FIOCRUZ/RJ, Rio de Janeiro, Brazil
| | - Alex Chapeaurouge
- Laboratório de Toxinologia, Instituto Oswaldo Cruz- FIOCRUZ/RJ, Rio de Janeiro, Brazil
| | | | - Maria Aparecida Gomes
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Juliano Simões Toledo
- Departamento de Analises Clinicas e Toxicológicas – Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Steven M. Singer
- Biology Department – Georgetown University, Washington, United States of America
| | | | - Ana Paula Fernandes
- Departamento de Analises Clinicas e Toxicológicas – Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- * E-mail:
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Einarsson E, Ma'ayeh S, Svärd SG. An up-date on Giardia and giardiasis. Curr Opin Microbiol 2016; 34:47-52. [PMID: 27501461 DOI: 10.1016/j.mib.2016.07.019] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/27/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022]
Abstract
Giardia intestinalis is a non-invasive protozoan parasite infecting the upper small intestine causing acute, watery diarrhea or giardiasis in 280 million people annually. Asymptomatic infections are equally common and recent data have suggested that infections even can be protective against other diarrheal diseases. Most symptomatic infections resolve spontaneously but infections can lead to chronic disease and treatment failures are becoming more common world-wide. Giardia infections can also result in irritable bowel syndrome (IBS) and food allergies after resolution. Until recently not much was known about the mechanism of giardiasis or the cause of post-giardiasis syndromes and treatment failures, but here we will describe the recent progress in these areas.
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Affiliation(s)
- Elin Einarsson
- Department of Cell and Molecular Biology, BMC, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Showgy Ma'ayeh
- Department of Cell and Molecular Biology, BMC, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, BMC, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden.
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Emery SJ, Lacey E, Haynes PA. Quantitative proteomics in Giardia duodenalis —Achievements and challenges. Mol Biochem Parasitol 2016; 208:96-112. [DOI: 10.1016/j.molbiopara.2016.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 12/31/2022]
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Einarsson E, Troell K, Hoeppner MP, Grabherr M, Ribacke U, Svärd SG. Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis. PLoS Negl Trop Dis 2016; 10:e0004571. [PMID: 27015092 PMCID: PMC4807828 DOI: 10.1371/journal.pntd.0004571] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/03/2016] [Indexed: 12/29/2022] Open
Abstract
Differentiation into infectious cysts through the process of encystation is crucial for transmission and survival of the intestinal protozoan parasite Giardia intestinalis. Hitherto the majority of studies have focused on the early events, leaving late encystation poorly defined. In order to further study encystation, focusing on the later events, we developed a new encystation protocol that generates a higher yield of mature cysts compared to standard methods. Transcriptome changes during the entire differentiation from trophozoites to cysts were thereafter studied using RNA sequencing (RNA-seq). A high level of periodicity was observed for up- and down-regulated genes, both at the level of the entire transcriptome and putative regulators. This suggests the trajectory of differentiation to be coordinated through developmentally linked gene regulatory activities. Our study identifies a core of 13 genes that are consistently up-regulated during initial encystation. Of these, two constitute previously uncharacterized proteins that we were able to localize to a new type of encystation-specific vesicles. Interestingly, the largest transcriptional changes were seen in the late phase of encystation with the majority of the highly up-regulated genes encoding hypothetical proteins. Several of these were epitope-tagged and localized to further characterize these previously unknown genetic components of encystation and possibly excystation. Finally, we also detected a switch of variant specific surface proteins (VSPs) in the late phase of encystation. This occurred at the same time as nuclear division and DNA replication, suggesting a potential link between the processes. The intestinal protozoan parasite Giardia intestinalis and many other medically important protozoan parasites must encyst and form infective cysts in order to transmit to new hosts. Encystation efficiency is in that way connected to efficiency of transmission. We have developed new in vitro differentiation protocols and made the first RNA-seq based gene expression study of the complete Giardia encystation process. Our data provides a road map of Giardia encystation and a starting point from where it is possible to further explore important processes occurring during encystation. Information about this vital process for survival in the environment of this and other cyst forming parasites can be used in the development of new types of interventions.
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Affiliation(s)
- Elin Einarsson
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - Karin Troell
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - Marc P. Hoeppner
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology, Kiel, Germany
| | - Manfred Grabherr
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ulf Ribacke
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - Staffan G. Svärd
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
- * E-mail:
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Emery SJ, Mirzaei M, Vuong D, Pascovici D, Chick JM, Lacey E, Haynes PA. Induction of virulence factors in Giardia duodenalis independent of host attachment. Sci Rep 2016; 6:20765. [PMID: 26867958 PMCID: PMC4751611 DOI: 10.1038/srep20765] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023] Open
Abstract
Giardia duodenalis is responsible for the majority of parasitic gastroenteritis in humans worldwide. Host-parasite interaction models in vitro provide insights into disease and virulence and help us to understand pathogenesis. Using HT-29 intestinal epithelial cells (IEC) as a model we have demonstrated that initial sensitisation by host secretions reduces proclivity for trophozoite attachment, while inducing virulence factors. Host soluble factors triggered up-regulation of membrane and secreted proteins, including Tenascins, Cathepsin-B precursor, cystatin, and numerous Variant-specific Surface Proteins (VSPs). By comparison, host-cell attached trophozoites up-regulated intracellular pathways for ubiquitination, reactive oxygen species (ROS) detoxification and production of pyridoxal phosphate (PLP). We reason that these results demonstrate early pathogenesis in Giardia involves two independent host-parasite interactions. Motile trophozoites respond to soluble secreted signals, which deter attachment and induce expression of virulence factors. Trophozoites attached to host cells, in contrast, respond by up-regulating intracellular pathways involved in clearance of ROS, thus anticipating the host defence response.
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Affiliation(s)
- Samantha J Emery
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Pty, Ltd, Smithfield, NSW 2165, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW, 2109, Australia
| | - Joel M Chick
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ernest Lacey
- Microbial Screening Technologies, Pty, Ltd, Smithfield, NSW 2165, Australia
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Ankarklev J, Franzén O, Peirasmaki D, Jerlström-Hultqvist J, Lebbad M, Andersson J, Andersson B, Svärd SG. Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates. BMC Genomics 2015; 16:697. [PMID: 26370391 PMCID: PMC4570179 DOI: 10.1186/s12864-015-1893-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/01/2015] [Indexed: 12/31/2022] Open
Abstract
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 ~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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1893-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johan Ankarklev
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
| | - Oscar Franzén
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, SE-171 77, Stockholm, Sweden. .,Science for Life Laboratory, KISP, Tomtebodavägen 23A, 171 65, Solna, Sweden.
| | - Dimitra Peirasmaki
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
| | - Marianne Lebbad
- Department of Microbiology, Public Health Agency of Sweden, SE-171 82, Solna, Sweden.
| | - Jan Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, SE-171 77, Stockholm, Sweden. .,Science for Life Laboratory, KISP, Tomtebodavägen 23A, 171 65, Solna, Sweden.
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Science for Life Laboratory, BMC, Uppsala University, Box 596, SE-751 24, Uppsala, Sweden.
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