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Sato S, Dacher M, Kurumizaka H. Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses. EPIGENOMES 2022; 6:epigenomes6030022. [PMID: 35997368 PMCID: PMC9396995 DOI: 10.3390/epigenomes6030022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
In eukaryotes, genomic DNA is bound with histone proteins and packaged into chromatin. The nucleosome, a fundamental unit of chromatin, regulates the accessibility of DNA to enzymes involved in gene regulation. During the past few years, structural analyses of chromatin architectures have been limited to evolutionarily related organisms. The amino acid sequences of histone proteins are highly conserved from humans to yeasts, but are divergent in the deeply branching protozoan groups, including human parasites that are directly related to human health. Certain large DNA viruses, as well as archaeal organisms, contain distant homologs of eukaryotic histone proteins. The divergent sequences give rise to unique and distinct nucleosome architectures, although the fundamental principles of histone folding and DNA contact are highly conserved. In this article, we review the structures and biophysical properties of nucleosomes containing histones from the human parasites Giardia lamblia and Leishmania major, and histone-like proteins from the Marseilleviridae amoeba virus family. The presented data confirm the sharing of the overall DNA compaction system among evolutionally distant species and clarify the deviations from the species-specific nature of the nucleosome.
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Oliveira RVF, de Souza W, Vögerl K, Bracher F, Benchimol M, Gadelha APR. In vitro effects of the 4-[(10H-phenothiazin-10-yl)methyl]-N-hydroxybenzamide on Giardia intestinalis trophozoites. Acta Trop 2022; 232:106484. [PMID: 35483428 DOI: 10.1016/j.actatropica.2022.106484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/01/2022]
Abstract
Giardiasis is an intestinal disease caused by the parasite protozoan Giardia intestinalis. For more than five decades, the treatment of this disease has been based on compounds such as nitroimidazoles and benzimidazoles. The parasite's adverse effects and therapeutic failure are largely recognized. Therefore, it is necessary to develop new forms of chemotherapy treatment against giardiasis. Lysine deacetylases (KDACs), which remove an acetyl group from lysine residues in histone and non-histone proteins as tubulin, are found in the Giardia genome and can become an interesting option for giardiasis treatment. In the present study, we evaluated the effects of 4-[(10H-phenothiazin-10-yl)methyl]-N-hydroxybenzamide, a new class I/II KDAC inhibitor, on G. intestinalis growth, cytoskeleton, and ultrastructure organization. This compound decreased parasite proliferation and viability and displayed an IC50 value of 179 nM. Scanning electron microscopy revealed the presence of protrusions on the cell surface after treatment. In addition, the vacuoles containing concentric membranous lamella and glycogen granules were observed in treated trophozoites. The cell membrane appeared deformed just above these vacuoles. Alterations on the microtubular cytoskeleton of the parasite were not observed after drug exposure. The number of diving cells with incomplete cytokinesis increased after treatment, indicating that the compound can interfere in the late steps of cell division. Our results indicate that 4-[(10H-phenothiazin-10-yl)methyl]-N-hydroxybenzamide should be explored to develop new therapeutic compounds for treating giardiasis.
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Wang Q, Fan L, Su X, Ying J, Xu L, Li C, Wang Y, Liu L. Genome-wide characterization of Histone gene family and expression profiling during microspore development in radish (Raphanus sativus L.). Gene 2022; 815:146180. [PMID: 34990794 DOI: 10.1016/j.gene.2021.146180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/31/2021] [Accepted: 12/06/2021] [Indexed: 11/04/2022]
Abstract
Histone, a predominant protein component of chromatin, participates in DNA packaging and transcriptional regulation. However, the available information of Histone gene family is limited in radish. In this study, a total of 42 Histone gene family members were identified from the radish genome. Sequence alignment and phylogenetic analyses classified the Histone family into three groups (H2A, H2B and H3). Motif analysis showed that the functions of some motifs shared by H3 subfamily genes were related to chromosome regulation and cell development activities, such as motif 5 containing Cks1 and PPR region. Analysis of intron/exon structure indicated that RsCENH3 (RsHistone 18) has the characteristics of variant Histone. Furthermore, several motifs, including the LTR, G-box and TC-elements, were found in the promoters of RsHistone genes, which involved in cell development or various abiotic stresses responses. Transcriptome analysis indicated that the RsHistone genes exhibited higher expression level in floral buds than in roots and leaves. Subcellular localization showed that the RsCENH3 was localized on the nucleus, and it was highly expressed in the floral bud of 3.0-4.0 mm in radish. These findings would provide valuable information for characterization and potential utilization of Histone genes, and facilitate the efficient induction of double haploid plants in radish.
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Affiliation(s)
- Qijiao Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiaojun Su
- Institute of Vegetable Sciences, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, People's Republic of China
| | - Jiali Ying
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Cui Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China; College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, People's Republic of China.
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4
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Sato S, Takizawa Y, Hoshikawa F, Dacher M, Tanaka H, Tachiwana H, Kujirai T, Iikura Y, Ho CH, Adachi N, Patwal I, Flaus A, Kurumizaka H. Cryo-EM structure of the nucleosome core particle containing Giardia lamblia histones. Nucleic Acids Res 2021; 49:8934-8946. [PMID: 34352093 PMCID: PMC8421212 DOI: 10.1093/nar/gkab644] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/05/2021] [Accepted: 07/21/2021] [Indexed: 12/16/2022] Open
Abstract
Giardia lamblia is a pathogenic unicellular eukaryotic parasite that causes giardiasis. Its genome encodes the canonical histones H2A, H2B, H3, and H4, which share low amino acid sequence identity with their human orthologues. We determined the structure of the G. lamblia nucleosome core particle (NCP) at 3.6 Å resolution by cryo-electron microscopy. G. lamblia histones form a characteristic NCP, in which the visible 125 base-pair region of the DNA is wrapped in a left-handed supercoil. The acidic patch on the G. lamblia octamer is deeper, due to an insertion extending the H2B α1 helix and L1 loop, and thus cannot bind the LANA acidic patch binding peptide. The DNA and histone regions near the DNA entry-exit sites could not be assigned, suggesting that these regions are asymmetrically flexible in the G. lamblia NCP. Characterization by thermal unfolding in solution revealed that both the H2A–H2B and DNA association with the G. lamblia H3–H4 were weaker than those for human H3–H4. These results demonstrate the uniformity of the histone octamer as the organizing platform for eukaryotic chromatin, but also illustrate the unrecognized capability for large scale sequence variations that enable the adaptability of histone octamer surfaces and confer internal stability.
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Affiliation(s)
- Shoko Sato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Fumika Hoshikawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mariko Dacher
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroki Tanaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiroaki Tachiwana
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukari Iikura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Cheng-Han Ho
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Indu Patwal
- Center for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland Galway, H91 TK33, Ireland
| | - Andrew Flaus
- Center for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland Galway, H91 TK33, Ireland
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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5
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Lagunas-Rangel FA, Yee J, Bermúdez-Cruz RM. An update on cell division of Giardia duodenalis trophozoites. Microbiol Res 2021; 250:126807. [PMID: 34130067 DOI: 10.1016/j.micres.2021.126807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022]
Abstract
Giardia duodenalis is a flagellated protozoan that is responsible for many cases of diarrheal disease worldwide and is characterized by its great divergence from the model organisms commonly used in studies of basic cellular processes. The life cycle of Giardia involves an infectious cyst form and a proliferative and mobile trophozoite form. Each Giardia trophozoite has two nuclei and a complex microtubule cytoskeleton that consists of eight flagellar axonemes, basal bodies, the adhesive disc, the funis and the median body. Since the success of Giardia infecting other organisms depends on its ability to divide and proliferate efficiently, Giardia must coordinate its cell division to ensure the duplication and partitioning of both nuclei and the multiple cytoskeletal structures. The purpose of this review is to summarize current knowledge about cell division and its regulation in this protist.
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Affiliation(s)
- Francisco Alejandro Lagunas-Rangel
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico; Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Janet Yee
- Department of Biology, Biochemistry and Molecular Biology Program, Trent University, Peterborough, ON, Canada
| | - Rosa María Bermúdez-Cruz
- Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico.
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6
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Eukaryote-conserved histone post-translational modification landscape in Giardia duodenalis revealed by mass spectrometry. Int J Parasitol 2020; 51:225-239. [PMID: 33275945 DOI: 10.1016/j.ijpara.2020.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/01/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022]
Abstract
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.
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7
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Lagunas-Rangel FA, Bermúdez-Cruz RM. Epigenetics in the early divergent eukaryotic Giardia duodenalis: An update. Biochimie 2019; 156:123-128. [DOI: 10.1016/j.biochi.2018.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/12/2018] [Indexed: 11/29/2022]
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8
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Lillico R, Zhou T, Khorshid Ahmad T, Stesco N, Gozda K, Truong J, Kong J, Lakowski TM, Namaka M. Increased Post-Translational Lysine Acetylation of Myelin Basic Protein Is Associated with Peak Neurological Disability in a Mouse Experimental Autoimmune Encephalomyelitis Model of Multiple Sclerosis. J Proteome Res 2018; 17:55-62. [PMID: 29111742 DOI: 10.1021/acs.jproteome.7b00270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Citrullination of arginine residues is a post-translational modification (PTM) found on myelin basic protein (MBP), which neutralizes MBPs positive charge, and is implicated in myelin damage and multiple sclerosis (MS). Here we identify lysine acetylation as another neutralizing PTM to MBP that may be involved in myelin damage. We quantify changes in lysine and arginine PTMs on MBP derived from mice induced with an experimental autoimmune encephalomyelitis (EAE) model of MS using liquid chromatography tandem mass spectrometry. The changes in PTMs are correlated to changes in neurological disability scoring (NDS), as a marker of myelin damage. We found that lysine acetylation increased by 2-fold on MBP during peak NDS post-EAE induction. We also found that mono- and dimethyl-lysine, as well as asymmetric dimethyl-arginine residues on MBP were elevated at peak EAE disability. These findings suggest that the acetylation and methylation of lysine on MBP are PTMs associated with the neurological disability produced by EAE. Since histone deacetylase (HDAC) inhibitors have been previously shown to improve neurological disability, we also show that treatment with trichostatin A (a HDAC inhibitor) improves the NDS of EAE mice but does not change MBP acetylation.
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Affiliation(s)
- Ryan Lillico
- The Rady Faculty of Health Sciences, College of Pharmacy, Pharmaceutical Analysis Laboratory, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Ting Zhou
- The Rady Faculty of Health Sciences, College of Pharmacy, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Tina Khorshid Ahmad
- The Rady Faculty of Health Sciences, College of Pharmacy, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Nicholas Stesco
- The Rady Faculty of Health Sciences, College of Pharmacy, Pharmaceutical Analysis Laboratory, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Kiana Gozda
- The Rady Faculty of Health Sciences, College of Pharmacy, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Jessica Truong
- The Rady Faculty of Health Sciences, College of Pharmacy, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Jiming Kong
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Ted M Lakowski
- The Rady Faculty of Health Sciences, College of Pharmacy, Pharmaceutical Analysis Laboratory, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
| | - Michael Namaka
- The Rady Faculty of Health Sciences, College of Pharmacy, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
- Joint Laboratory of Biological Psychiatry Between Shantou University Medical College and College of Medicine, University of Manitoba , Winnipeg, Manitoba R3T 2N2, Canada
- Department of Rehabilitation Medicine, Health Sciences Centre (HSC) , Winnipeg, Manitoba R3A 1R9, Canada
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9
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Carranza PG, Gargantini PR, Prucca CG, Torri A, Saura A, Svärd S, Lujan HD. Specific histone modifications play critical roles in the control of encystation and antigenic variation in the early-branching eukaryote Giardia lamblia. Int J Biochem Cell Biol 2016; 81:32-43. [PMID: 27771437 DOI: 10.1016/j.biocel.2016.10.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/29/2016] [Accepted: 10/17/2016] [Indexed: 12/16/2022]
Abstract
During evolution, parasitic microorganisms have faced the challenges of adapting to different environments to colonize a variety of hosts. Giardia lamblia, a common cause of intestinal disease, has developed fascinating strategies to adapt both outside and inside its host's intestine, such as trophozoite differentiation into cyst and the switching of its major surface antigens. How gene expression is regulated during these adaptive processes remains undefined. Giardia lacks some typical eukaryotic features, like canonical transcription factors, linker histone H1, and complex promoter regions; suggesting that post-transcriptional and translational control of gene expression is essential for parasite survival. However, epigenetic factors may also play critical roles at the transcriptional level. Here, we describe the most common post-translational histone modifications; characterize enzymes involved in these reactions, and analyze their association with the Giardia's differentiation processes. We present evidence that NAD+-dependent and NAD+-independent histone deacetylases regulate encystation; however, a unique NAD+-independent histone deacetylase modulate antigenic switching. The rates of acetylation of H4K8 and H4K16 are critical for encystation, whereas a decrease in acetylation of H4K8 and methylation of H3K9 occur preferentially during antigenic variation. These results show the complexity of the mechanisms regulating gene expression in this minimalistic protozoan parasite.
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Affiliation(s)
- Pedro G Carranza
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Católica de Córdoba, Argentina
| | - Pablo R Gargantini
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Católica de Córdoba, Argentina; Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - César G Prucca
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Católica de Córdoba, Argentina
| | - Alessandro Torri
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Católica de Córdoba, Argentina
| | - Alicia Saura
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Católica de Córdoba, Argentina; Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Hugo D Lujan
- Laboratorio de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Católica de Córdoba, Argentina; Centro de Investigación y Desarrollo en Inmunología y Enfermedades Infecciosas (CIDIE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina.
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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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Structural organization of very small chromosomes: study on a single-celled evolutionary distant eukaryote Giardia intestinalis. Chromosoma 2014; 124:81-94. [DOI: 10.1007/s00412-014-0486-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/05/2014] [Accepted: 08/18/2014] [Indexed: 12/30/2022]
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12
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Abstract
Structural proteomics aims to understand the structural basis of protein interactions and functions. A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects -- to obtain 3D structures for each protein. To achieve this ambitious goal, the slow and costly structure determination experiments are supplemented with theoretical approaches. The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques.
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Affiliation(s)
- András Fiser
- Department of Biochemistry, Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA.
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13
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Faso C, Bischof S, Hehl AB. The proteome landscape of Giardia lamblia encystation. PLoS One 2013; 8:e83207. [PMID: 24391747 PMCID: PMC3877021 DOI: 10.1371/journal.pone.0083207] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/09/2013] [Indexed: 11/18/2022] Open
Abstract
Giardia lamblia is an intestinal protozoan parasite required to survive in the environment in order to be transmitted to a new host. To ensure parasite survival, flagellated trophozoites colonizing the small intestine differentiate into non-motile environmentally-resistant cysts which are then shed in the environment. This cell differentiation process called encystation is characterized by significant morphological remodeling which includes secretion of large amounts of cyst wall material. Although much is known about the transcriptional regulation of encystation and the synthesis and trafficking of cyst wall material, the investigation of global changes in protein content and abundance during G. lamblia encystation is still unaddressed. In this study, we report on the quantitative analysis of the G. lamblia proteome during encystation using tandem mass spectrometry. Quantification of more than 1000 proteins revealed major changes in protein abundance in early, mid and late encystation, notably in constitutive secretory protein trafficking. Early stages of encystation were marked by a striking decrease of endoplasmic reticulum-targeted variant-specific surface proteins and significant increases in cytoskeleton regulatory components, NEK protein kinases and proteins involved in protein folding and glycolysis. This was in stark contrast to cells in the later stages of encystation which presented a surprisingly similar proteome composition to non-encysting trophozoites. Altogether these data constitute the first quantitative atlas of the Giardia proteome covering the whole process of encystation and point towards an important role for post-transcriptional control of gene expression in Giardia differentiation. Furthermore, our data provide a valuable resource for the community-based annotation effort of the G. lamblia genome, where almost 70% of all predicted gene models remains “hypothetical”.
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Affiliation(s)
- Carmen Faso
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
- * E-mail: (ABH); (CF)
| | | | - Adrian B. Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
- * E-mail: (ABH); (CF)
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14
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Abstract
Functional characterization of a protein is often facilitated by its 3D structure. However, the fraction of experimentally known 3D models is currently less than 1% due to the inherently time-consuming and complicated nature of structure determination techniques. Computational approaches are employed to bridge the gap between the number of known sequences and that of 3D models. Template-based protein structure modeling techniques rely on the study of principles that dictate the 3D structure of natural proteins from the theory of evolution viewpoint. Strategies for template-based structure modeling will be discussed with a focus on comparative modeling, by reviewing techniques available for all the major steps involved in the comparative modeling pipeline.
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Affiliation(s)
- Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
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15
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Hofstetrová K, Uzlíková M, Tůmová P, Troell K, Svärd SG, Nohýnková E. Giardia intestinalis: aphidicolin influence on the trophozoite cell cycle. Exp Parasitol 2009; 124:159-66. [PMID: 19735659 DOI: 10.1016/j.exppara.2009.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 08/25/2009] [Accepted: 09/02/2009] [Indexed: 10/20/2022]
Abstract
This study is a thorough examination of the effects of the DNA polymerase inhibitor aphidicolin on the nuclear cycle and cell cycle progression characteristics, as well as their reversibility, in Giardia intestinalis. Giardia trophozoites are arrested in the G1/S-junction after aphidicolin treatment according to their DNA content. However, cell growth continues and trophozoites arrested with aphidicolin resemble cells in the G2 phase and trophozoites in ageing cultures. Extensive treatment with aphidicolin causes side effects and we detected positive signals for phosphorylated histone H2A, which, in mammalian cells, is involved in a signalling pathway triggered as a reaction to double stranded DNA breaks. These results suggest that aphidicolin causes dissociation of the nuclear and cytoplasmic cycles, a phenomenon that has also been described for other inhibitors in mammalian cell lines. Thus, if aphidicolin is used for synchronization of Giardia trophozoites, this fact must be accounted for, and treatment with aphidicolin must be minimal.
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Affiliation(s)
- Klára Hofstetrová
- 3rd Department of Infectious and Tropical Diseases, First Faculty of Medicine, Charles University in Prague and University Hospital Bulovka, Czech Republic
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16
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Chen K, Meng Q, Ma L, Liu Q, Tang P, Chiu C, Hu S, Yu J. A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic Acids Res 2008; 36:6228-36. [PMID: 18829715 PMCID: PMC2577358 DOI: 10.1093/nar/gkn626] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
There have been two types of well-characterized DNA sequence periodicities; both are found to be associated with important molecular mechanisms. One is a 3-nt periodicity corresponding to codon triplets, the other is a 10.5-nt periodicity related to the structure of DNA helixes. In the process of analyzing the genome and transcriptome of Trichomonas vaginalis, we observed a 120.9-nt periodicity along DNA sequences. Different from the 3- and 10.5-nt periodicities, this novel periodicity originates near the 5′-end of transcripts, extends along the direction of transcription, and weakens gradually along transcripts. As a result, codon usage as well as amino acid composition is constrained by this periodicity. Similar periodicities were also identified in other organisms, but with variable length associated with the length of nucleosome units. We validated this association experimentally in T. vaginalis, and demonstrated that the periodicity manifests nucleotide variations between linker-DNA and wrapping-DNA along nucleosome array. We conclude that this novel DNA sequence periodicity is a signature of nucleosome organization suggesting that nucleosomes are well-positioned with regularity, especially near the 5′-end of transcripts.
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Affiliation(s)
- Kaifu Chen
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Graduate University of Chinese Academy of Sciences, Beijing, China
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17
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Li C, Song L, Zhao J, Zou H, Su J, Zhang H. Genomic organization, nucleotide sequence analysis of the core histone genes cluster in Chlamys farreri and molecular evolution assessment of the H2A and H2B. ACTA ACUST UNITED AC 2007; 17:440-51. [PMID: 17381045 DOI: 10.1080/10425170600752593] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This work represents the nucleotide sequence of the core histone gene cluster from scallop Chlamys farreri. The tandemly repeated unit of 5671 bp containing a copy of the four core histone genes H4, H2B, H2A and H3 was amplified and identified by the techniques of homology cloning and genomic DNA walking. All the histone genes in the cluster had the structures in their 3' flanking region which related to the evolution of histone gene expression patterns throughout the cell cycle, including two different termination signals, the hairpin structure and at least one AATAAA polyadenylation signal. In their 5' region, the transcription initiation sites with a conserved sequence of 5'-PyATTCPu-3' known as the CAP site were present in all genes except to H2B, generally 37-45 bp upstream of the start code. Canonical TATA and CAAT boxes were identified only in certain histone genes. In the case of the promoters of H2B and H2A genes, there was a 5'-GATCC-3' element, which had been found to be essential to start transcription at the appropriate site. After this element, in the promoter of H2B, there was another sequence, 5'-GGATCGAAACGTTC-3', which was similar to the consensus sequence of 5'-GGAATAAACGTATTC-3' corresponding to the H2B-specific promoter element. The presence of enhancer sequences (5'-TGATATATG-3') was identified from the H4 and H3 genes, matching perfectly with the consensus sequence defined for histone genes. There were several slightly more complex repetitive DNA in the intergene regions. The presence of the series of conserved sequences and reiterated sequences was consistent with the view that mollusc histone gene cluster arose by duplicating of an ancestral precursor histone gene, the birth-and-death evolution model with strong purifying selection enabled the histone cluster less variation and more conserved function. Meanwhile, the H2A and the H2B were demonstrated to be potential good marks for phylogenetic analysis. All the results will be contributed to the characterization of repeating histone gene families in molluscs.
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Affiliation(s)
- Chenghua Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China.
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18
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Yee J, Tang A, Lau WL, Ritter H, Delport D, Page M, Adam RD, Müller M, Wu G. Core histone genes of Giardia intestinalis: genomic organization, promoter structure, and expression. BMC Mol Biol 2007; 8:26. [PMID: 17425802 PMCID: PMC1872034 DOI: 10.1186/1471-2199-8-26] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Accepted: 04/10/2007] [Indexed: 11/19/2022] Open
Abstract
Background Giardia intestinalis is a protist found in freshwaters worldwide, and is the most common cause of parasitic diarrhea in humans. The phylogenetic position of this parasite is still much debated. Histones are small, highly conserved proteins that associate tightly with DNA to form chromatin within the nucleus. There are two classes of core histone genes in higher eukaryotes: DNA replication-independent histones and DNA replication-dependent ones. Results We identified two copies each of the core histone H2a, H2b and H3 genes, and three copies of the H4 gene, at separate locations on chromosomes 3, 4 and 5 within the genome of Giardia intestinalis, but no gene encoding a H1 linker histone could be recognized. The copies of each gene share extensive DNA sequence identities throughout their coding and 5' noncoding regions, which suggests these copies have arisen from relatively recent gene duplications or gene conversions. The transcription start sites are at triplet A sequences 1–27 nucleotides upstream of the translation start codon for each gene. We determined that a 50 bp region upstream from the start of the histone H4 coding region is the minimal promoter, and a highly conserved 15 bp sequence called the histone motif (him) is essential for its activity. The Giardia core histone genes are constitutively expressed at approximately equivalent levels and their mRNAs are polyadenylated. Competition gel-shift experiments suggest that a factor within the protein complex that binds him may also be a part of the protein complexes that bind other promoter elements described previously in Giardia. Conclusion In contrast to other eukaryotes, the Giardia genome has only a single class of core histone genes that encode replication-independent histones. Our inability to locate a gene encoding the linker histone H1 leads us to speculate that the H1 protein may not be required for the compaction of Giardia's small and gene-rich genome.
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Affiliation(s)
- Janet Yee
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Anita Tang
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Wei-Ling Lau
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Heather Ritter
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Dewald Delport
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Melissa Page
- Departments of Biology and Chemistry, Biochemistry Program, Trent University, Peterborough, Ontario, K9J 7B8, Canada
| | - Rodney D Adam
- Departments of Immunobiology and Medicine, University of Arizona College of Medicine, Tucson, AZ 85724, USA
| | - Miklós Müller
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
- Collegium Budapest, H 1012 Budapest, Hungary
| | - Gang Wu
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
- Haskins Laboratories and Department of Chemistry and Physical Sciences, Pace University, 41 Park Row, New York, NY 10038, USA
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19
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Hwang UW. Prokaryotic and eukaryotic features observed on the secondary structures of Giardia SSU rRNAs and its phylogenetic implications. Parasitol Res 2007; 100:1159-63. [PMID: 17279392 DOI: 10.1007/s00436-007-0471-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
Phylogenetic position of a diplomonad protist Giardia, a principle cause of diarrhea, among eukaryotes has been vigorously debated so far. Through the comparisons of primary and secondary structures of SSU rRNAs of G. intestinalis, G. microti, G. ardeae, and G. muris, I found two major indel regions (a 6-nt indel and a 22-26-nt indel), which correspond to the helix 10 of the V2 region and helices E23-8 to E23-9 of the V4 region, respectively. As generally shown in eukaryotes, G. intestinalis and G. microti have commonly a relatively longer helix 10 (a 7-bp stem and a 4-nt loop), and also the eukaryote-specific helices E23-6 to E23-9. On the other hand, G. muris and G. ardeae have a shorter helix 10: a 2-bp stem and a 6-nt loop in G. ardeae and a 3-bp stem and a 6-nt loop in G. muris. In the V4, they have a single long helix (like the P23-1 helix in prokaryotes) instead of the helices E23-6 to E23-9. Among the four Giardia species, co-appearance of prokaryote- and eukaryote-typical features might be significant evidence to suggest that Giardia (Archezoa) is a living fossil showing an "intermediate stage" during the evolution from prokaryotes to eukaryotes.
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Affiliation(s)
- Ui Wook Hwang
- Department of Biology, Teachers College, Kyungpook National University, Daegu 702-701, South Korea.
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20
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Song X, Gjoneska E, Ren Q, Taverna SD, Allis CD, Gorovsky MA. Phosphorylation of the SQ H2A.X motif is required for proper meiosis and mitosis in Tetrahymena thermophila. Mol Cell Biol 2007; 27:2648-60. [PMID: 17242195 PMCID: PMC1899910 DOI: 10.1128/mcb.01910-06] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Phosphorylation of the C terminus SQ motif that defines H2A.X variants is required for efficient DNA double-strand break (DSB) repair in diverse organisms but has not been studied in ciliated protozoa. Tetrahymena H2A.X is one of two similarly expressed major H2As, thereby differing both from mammals, where H2A.X is a quantitatively minor component, and from Saccharomyces cerevisiae where it is the only type of major H2A. Tetrahymena H2A.X is phosphorylated in the SQ motif in both the mitotic micronucleus and the amitotic macronucleus in response to DSBs induced by chemical agents and in the micronucleus during prophase of meiosis, which occurs in the absence of a synaptonemal complex. H2A.X is phosphorylated when programmed DNA rearrangements occur in developing macronuclei, as for immunoglobulin gene rearrangements in mammals, but not during the DNA fragmentation that accompanies breakdown of the parental macronucleus during conjugation, correcting the previous interpretation that this process is apoptosis-like. Using strains containing a mutated (S134A) SQ motif, we demonstrate that phosphorylation of this motif is important for Tetrahymena cells to recover from exogenous DNA damage and is required for normal micronuclear meiosis and mitosis and, to a lesser extent, for normal amitotic macronuclear division; its absence, while not lethal, leads to the accumulation of DSBs in both micro- and macronuclei. These results demonstrate multiple roles of H2A.X phosphorylation in maintaining genomic integrity in different phases of the Tetrahymena life cycle.
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Affiliation(s)
- Xiaoyuan Song
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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21
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Dawson SC, Sagolla MS, Cande WZ. The cenH3 histone variant defines centromeres in Giardia intestinalis. Chromosoma 2006; 116:175-84. [PMID: 17180675 DOI: 10.1007/s00412-006-0091-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Revised: 10/20/2006] [Accepted: 11/09/2006] [Indexed: 11/26/2022]
Abstract
Histone H3 variants play critical roles in the functional specialization of chromatin by epigenetically marking centromeric chromatin and transcriptionally active or silent genes. Specifically, the cenH3 histone variant acts as the primary epigenetic determinant of the site of kinetochore assembly at centromeres. Although the function of histone variants is well studied in plants, animals, and fungi, there is little knowledge of the evolutionary conservation of histone variants and their function in most protists. We find that Giardia intestinalis--a diplomonad parasite with two equivalent nuclei--has two phylogenetically distinct histone H3 variants with N-terminal extensions and nonconserved promoters. To determine their role in chromatin dynamics, conventional H3 and the two H3 variants were GFP-tagged, and their subcellular location was monitored during interphase and mitosis. We demonstrate that one cenH3-like variant has a conserved function in epigenetically marking centromeres. The other H3 variant (H3B) has a punctate distribution on chromosomes, but does not colocalize with active transcriptional regions as indicated by H3K4 methylation. We suggest that H3B could instead mark noncentromeric heterochromatin. Giardia is a member of the Diplomonads and represents an ancient divergence from metazoans and fungi. We confirm the ancient role of histone H3 variants in modulating chromatin architecture, and suggest that monocentric chromosomes represent an ancestral chromosome morphology.
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Affiliation(s)
- S C Dawson
- Section of Microbiology, 255 Briggs Hall, One Shields Avenue, UC-Davis, Davis, CA 95616, USA.
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22
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Best AA, Morrison HG, McArthur AG, Sogin ML, Olsen GJ. Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia. Genome Res 2004; 14:1537-47. [PMID: 15289474 PMCID: PMC509262 DOI: 10.1101/gr.2256604] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Giardia lamblia genome sequencing project affords us a unique opportunity to conduct comparative analyses of core cellular systems between early and late-diverging eukaryotes on a genome-wide scale. We report a survey to identify canonical transcription components in Giardia, focusing on RNA polymerase (RNAP) subunits and transcription-initiation factors. Our survey revealed that Giardia contains homologs to 21 of the 28 polypeptides comprising eukaryal RNAPI, RNAPII, and RNAPIII; six of the seven RNAP subunits without giardial homologs are polymerase specific. Components of only four of the 12 general transcription initiation factors have giardial homologs. Surprisingly, giardial TATA-binding protein (TBP) is highly divergent with respect to archaeal and higher eukaryotic TBPs, and a giardial homolog of transcription factor IIB was not identified. We conclude that Giardia represents a transition during the evolution of eukaryal transcription systems, exhibiting a relatively complete set of RNAP subunits and a rudimentary basal initiation apparatus for each transcription system. Most class-specific RNAP subunits and basal initiation factors appear to have evolved after the divergence of Giardia from the main eukaryotic line of descent. Consequently, Giardia is predicted to be unique in many aspects of transcription initiation with respect to paradigms derived from studies in crown eukaryotes.
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Affiliation(s)
- Aaron A Best
- Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemical and Life Sciences Laboratory, Urbana, Illinois 61801, USA
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23
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Katz LA, Bornstein JG, Lasek-Nesselquist E, Muse SV. Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes. Mol Biol Evol 2003; 21:555-62. [PMID: 14694079 DOI: 10.1093/molbev/msh048] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The accumulation of divergent histone H4 amino acid sequences within and between ciliate lineages challenges traditional views of the evolution of this essential eukaryotic protein. We analyzed histone H4 sequences from 13 species of ciliates and compared these data with sequences from well-sampled eukaryotic clades. Ciliate histone H4s differ from one another at as many as 46% of their amino acids, in contrast with the highly conserved character of this protein in most other eukaryotes. Equally striking, we find paralogs of histone H4 within ciliate genomes that differ by up to 25% of their amino acids, whereas paralogs in other eukaryotes share identical or nearly identical amino acid sequences. Moreover, the most divergent H4 proteins within ciliates are found in the lineages with highly processed macronuclear genomes. Our analyses demonstrate that the dual nature of ciliate genomes-the presence of a "germline" micronucleus and a "somatic" macronucleus within each cell-allowed the dramatic variation in ciliate histone genes by altering functional constraints or enabling adaptive evolution of the histone H4 protein, or both.
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Affiliation(s)
- Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA.
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24
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Abstract
PURPOSE OF REVIEW Giardia intestinalis (syn. duodenalis or lamblia) is one of the most common intestinal parasites in the world, with an estimated 2.8 x 10(6) infections per year in humans, and it contributes to diarrhea and nutritional deficiencies in children in developing regions. The wide prevalence of Giardia and its unique place in evolutionary biology have led to ongoing research. RECENT FINDINGS Research into the basic biology of Giardia has highlighted some of its unique properties as an 'early-branching' eukaryote. Although Giardia do not contain mitochondria, they have developed pathways to perform some mitochondrial functions. Investigations into encystation and excystation have identified new gene products that are important in cyst wall formation, and signal transduction events that occur during excystation. The ability to transfect Giardia stably will lead to an improved understanding of its development and metabolism. Molecular typing of G. intestinalis isolates indicates that most animal parasites are not associated with human infection. Insights into immunology have helped define the role of IL-6 in the early control of murine giardiasis, and the contributions of IgA in controlling infection. Further studies of giardiasis in poorly nourished children in developing regions supports an important contributing role of Giardia in stunting and cognitive impairment. Finally, new diagnostic assays using antigen detection are being evaluated and a new agent, nitazoxanide, has been approved in the USA for the treatment of giardiasis and cryptosporidiosis in children. SUMMARY Research into the biology of Giardia should increase knowledge about protist differentiation and will complement studies in other biological systems. Continued study of the role of Giardia in chronic diarrhea and malnutrition in developing regions will help focus strategies to improve childhood growth and nutrition.
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Affiliation(s)
- Syed A Ali
- Division of Infectious Diseases, University of Connecticut School of Medicine, Farmington, Connecticut, USA
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25
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Marti‐Renom MA, Madhusudhan M, Eswar N, Pieper U, Shen M, Sali A, Fiser A, Mirkovic N, John B, Stuart A. Modeling Protein Structure from its Sequence. ACTA ACUST UNITED AC 2003. [DOI: 10.1002/0471250953.bi0501s03] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marc A. Marti‐Renom
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and The California Institute for Quantitative Biomedical Research University of California at San Francisco San Francisco California
| | - M.S. Madhusudhan
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and The California Institute for Quantitative Biomedical Research University of California at San Francisco San Francisco California
| | - Narayanan Eswar
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and The California Institute for Quantitative Biomedical Research University of California at San Francisco San Francisco California
| | - Ursula Pieper
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and The California Institute for Quantitative Biomedical Research University of California at San Francisco San Francisco California
| | - Min‐yi Shen
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and The California Institute for Quantitative Biomedical Research University of California at San Francisco San Francisco California
| | - Andrej Sali
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry and The California Institute for Quantitative Biomedical Research University of California at San Francisco San Francisco California
| | - Andras Fiser
- Department of Biochemistry and Seaver Foundation Center for Bioinformatics Albert Einstein College of Medicine Bronx New York
| | - Nebojsa Mirkovic
- Laboratory of Molecular Biophysics The Rockefeller University New York New York
| | - Bino John
- Laboratory of Molecular Biophysics The Rockefeller University New York New York
| | - Ashley Stuart
- Laboratory of Molecular Biophysics The Rockefeller University New York New York
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26
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Affiliation(s)
- András Fiser
- Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, Bronz, New York 10461, USA
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27
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Morrison HG, Zamora G, Campbell RK, Sogin ML. Inferring protein function from genomic sequence: Giardia lamblia expresses a phosphatidylinositol kinase-related kinase similar to yeast and mammalian TOR. Comp Biochem Physiol B Biochem Mol Biol 2002; 133:477-91. [PMID: 12470813 DOI: 10.1016/s1096-4959(02)00218-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Functional assays of genes have historically led to insights about the activities of a protein or protein cascade. However, the rapid expansion of genomic and proteomic information for a variety of diverse taxa is an alternative and powerful means of predicting function by comparing the enzymes and metabolic pathways used by different organisms. As part of the Giardia lamblia genome sequencing project, we routinely survey the complement of predicted proteins and compare those found in this putatively early diverging eukaryote with those of prokaryotes and more recently evolved eukaryotic lineages. Such comparisons reveal the minimal composition of conserved metabolic pathways, suggest which proteins may have been acquired by lateral transfer, and, by their absence, hint at functions lost in the transition from a free-living to a parasitic lifestyle. Here, we describe the use of bioinformatic approaches to investigate the complement and conservation of proteins in Giardia involved in the regulation of translation. We compare an FK506 binding protein homologue and phosphatidylinositol kinase-related kinase present in Giardia to those found in other eukaryotes for which complete genomic sequence data are available. Our investigation of the Giardia genome suggests that PIK-related kinases are of ancient origin and are highly conserved.
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Affiliation(s)
- Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543-1015, USA.
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28
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Piontkivska H, Rooney AP, Nei M. Purifying selection and birth-and-death evolution in the histone H4 gene family. Mol Biol Evol 2002; 19:689-97. [PMID: 11961102 DOI: 10.1093/oxfordjournals.molbev.a004127] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Histones are small basic proteins encoded by a multigene family and are responsible for the nucleosomal organization of chromatin in eukaryotes. Because of the high degree of protein sequence conservation, it is generally believed that histone genes are subject to concerted evolution. However, purifying selection can also generate a high degree of sequence homogeneity. In this study, we examined the long-term evolution of histone H4 genes to determine whether concerted evolution or purifying selection was the major factor for maintaining sequence homogeneity. We analyzed the proportion (p(S)) of synonymous nucleotide differences between the H4 genes from 59 species of fungi, plants, animals, and protists and found that p(S) is generally very high and often close to the saturation level (p(S) ranging from 0.3 to 0.6) even though protein sequences are virtually identical for all H4 genes. A small proportion of genes showed a low level of p(S) values, but this appeared to be caused by recent gene duplication. Our findings suggest that the members of this gene family evolve according to the birth-and-death model of evolution under strong purifying selection. Using histone-like genes in archaebacteria as outgroups, we also showed that H1, H2A, H2B, H3, and H4 histone genes in eukaryotes form separate clusters and that these classes of genes diverged nearly at the same time, before the eukaryotic kingdoms diverged.
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Affiliation(s)
- Helen Piontkivska
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, 328 Mueller Lab, University Park, PA 16802, USA.
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Triana O, Galanti N, Olea N, Hellman U, Wernstedt C, Lujan H, Medina C, Toro GC. Chromatin and histones from Giardia lamblia: a new puzzle in primitive eukaryotes. J Cell Biochem 2001; 82:573-82. [PMID: 11500935 DOI: 10.1002/jcb.1159] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The three deepest eukaryote lineages in small subunit ribosomal RNA phylogenies are the amitochondriate Microsporidia, Metamonada, and Parabasalia. They are followed by either the Euglenozoa (e.g., Euglena and Trypanosoma) or the Percolozoa as the first mitochondria-containing eukaryotes. Considering the great divergence of histone proteins in protozoa we have extended our studies of histones from Trypanosomes (Trypanosoma cruzi, Crithidia fasciculata and Leishmania mexicana) to the Metamonada Giardia lamblia, since Giardia is thought to be one of the most primitive eukaryotes. In the present work, the structure of G. lamblia chromatin and the histone content of the soluble chromatin were investigated and compared with that of higher eukaryotes, represented by calf thymus. The chromatin is present as nucleosome filaments which resemble the calf thymus array in that they show a more regular arrangement than those described for Trypanosoma. SDS-polyacrylamide gel electrophoresis and protein characterization revealed that the four core histones described in Giardia are in the same range of divergence with the histones from other lower eukaryotes. In addition, G. lamblia presented an H1 histone with electrophoretic mobility resembling the H1 of higher eukaryotes, in spite of the fact that H1 has a different molecular mass in calf thymus. Giardia also presents a basic protein which was identified as an HU-like DNA-binding protein usually present in eubacteria, indicating a chimaeric composition for the DNA-binding protein set in this species. Finally, the phylogenetic analysis of selected core histone protein sequences place Giardia divergence before Trypanosoma, despite the fact that Trypanosoma branch shows an acceleration in the evolutionary rate pointing to an unusual evolutionary behavior in this lineage.
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Affiliation(s)
- O Triana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 7, Chile
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Abstract
Giardia lamblia is a common cause of diarrhea in humans and other mammals throughout the world. It can be distinguished from other Giardia species by light or electron microscopy. The two major genotypes of G. lamblia that infect humans are so different genetically and biologically that they may warrant separate species or subspecies designations. Trophozoites have nuclei and a well-developed cytoskeleton but lack mitochondria, peroxisomes, and the components of oxidative phosphorylation. They have an endomembrane system with at least some characteristics of the Golgi complex and encoplasmic reticulum, which becomes more extensive in encysting organisms. The primitive nature of the organelles and metabolism, as well as small-subunit rRNA phylogeny, has led to the proposal that Giardia spp. are among the most primitive eukaryotes. G. lamblia probably has a ploidy of 4 and a genome size of approximately 10 to 12 Mb divided among five chromosomes. Most genes have short 5' and 3' untranslated regions and promoter regions that are near the initiation codon. Trophozoites exhibit antigenic variation of an extensive repertoire of cysteine-rich variant-specific surface proteins. Expression is allele specific, and changes in expression from one vsp gene to another have not been associated with sequence alterations or gene rearrangements. The Giardia genome project promises to greatly increase our understanding of this interesting and enigmatic organism.
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Affiliation(s)
- R D Adam
- Department of Medicine, University of Arizona College of Medicine, 1501N. Campbell, Tucson, AZ 85724-5049, USA.
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Shirakura T, Maki Y, Yoshida H, Arisue N, Wada A, Sánchez LB, Nakamura F, Müller M, Hashimoto T. Characterization of the ribosomal proteins of the amitochondriate protist, Giardia lamblia. Mol Biochem Parasitol 2001; 112:153-6. [PMID: 11166398 DOI: 10.1016/s0166-6851(00)00356-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- T Shirakura
- The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106-8569, Japan
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