1
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Smith SS. The bisulfite reaction with cytosine and genomic DNA structure. Anal Biochem 2024; 691:115532. [PMID: 38609028 DOI: 10.1016/j.ab.2024.115532] [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: 12/09/2023] [Revised: 02/19/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
The bisulfite reaction with native DNA has been extensively employed in the detection of non-B DNA structures that can form spontaneously in DNA. These sequences are dynamic in that they can adopt both normal Watson-Crick paired B-DNA or unusual structures like the Triplex, G-Quadruplex, i-motif and Cruciform or Hairpin. Considerable evidence now suggests that these dynamic sequences play roles in both epigenetics and mutagenesis. The bisulfite reaction with native DNA offers a key approach to their detection. In this application whole cells, isolated nuclei or isolated DNA are treated with bisulfite under non-denaturing conditions in order to detect bisulfite accessible regions DNA that are associated with these structures. Here I review the stereochemistry of the bisulfite reaction, the electronic structure of its DNA cytosine substrates and its application in the detection of unusual structures in native DNA.
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Affiliation(s)
- Steven S Smith
- Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA.
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2
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Li H, Liu H, Zhu D, Dou C, Gang B, Zhang M, Wan Z. Biological function molecular pathways and druggability of DNMT2/TRDMT1. Pharmacol Res 2024; 205:107222. [PMID: 38782147 DOI: 10.1016/j.phrs.2024.107222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
5-methylcytosine (m5C) is among the most common epigenetic modification in DNA and RNA molecules, and plays an important role in the animal development and disease pathogenesis. Interestingly, unlike other m5C DNA methyltransferases (DNMTs), DNMT2/TRDMT1 has the double-substrate specificity and adopts a DNMT-similar catalytic mechanism to methylate RNA. Moreover, it is widely involved in a variety of physiological regulatory processes, such as the gene expression, precise protein synthesis, immune response, and disease occurrence. Thus, comprehending the epigenetic mechanism and function of DNMT2/TRDMT1 will probably provide new strategies to treat some refractory diseases. Here, we discuss recent studies on the spatiotemporal expression pattern and post-translational modifications of DNMT2/TRDMT1, and summarize the research advances in substrate characteristics, catalytic recognition mechanism, DNMT2/TRDMT1-related genes or proteins, pharmacological application, and inhibitor development. This review will shed light on the pharmacological design by targeting DNMT2/TRDMT1 to treat parasitic, viral and oncologic diseases.
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Affiliation(s)
- Huari Li
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China; College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei Province 430070, PR China.
| | - Huiru Liu
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Daiyun Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, Hubei Province 430070, PR China; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Chengli Dou
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Baocai Gang
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Mengjie Zhang
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
| | - Ziyu Wan
- Department of Biochemistry and Molecular Biology, College of Laboratory Medicine, Anhui Province Key Laboratory of Cancer Translational Medicine, and The First Affiliated Hospital of Bengbu Medical University, Bengbu Medical University, No.2600 Donghai Avenue, Bengbu, Anhui Province 233030, PR China
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3
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Edelbroek B, Kjellin J, Jerlström-Hultqvist J, Koskiniemi S, Söderbom F. Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis. Sci Data 2024; 11:678. [PMID: 38909042 PMCID: PMC11193728 DOI: 10.1038/s41597-024-03513-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni- to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Jonas Kjellin
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden.
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4
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Edelbroek B, Kjellin J, Biryukova I, Liao Z, Lundberg T, Noegel A, Eichinger L, Friedländer M, Söderbom F. Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity. Nucleic Acids Res 2024; 52:3121-3136. [PMID: 38375870 PMCID: PMC11014262 DOI: 10.1093/nar/gkae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024] Open
Abstract
MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Zhen Liao
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Torgny Lundberg
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Angelika A Noegel
- Centre for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Ludwig Eichinger
- Centre for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Marc R Friedländer
- Science for Life Laboratory, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
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5
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Wadhwa N, Kapoor S, Kapoor M. Arabidopsis T-DNA mutants affected in TRDMT1/DNMT2 show differential protein synthesis and compromised stress tolerance. FEBS J 2024; 291:92-113. [PMID: 37584564 DOI: 10.1111/febs.16935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 07/18/2023] [Accepted: 08/14/2023] [Indexed: 08/17/2023]
Abstract
TRDMT1/DNMT2 belongs to the conserved family of nucleic acid methyltransferases. Unlike the animal systems, studies on TRDMT1/DNMT2 in land plants have been limited. We show that TRDMT1/DNMT2 is strongly conserved in the green lineage. Studies in mosses have previously shown that TRDMT1/DNMT2 plays a crucial role in modulating molecular networks involved in stress perception and signalling and in transcription/stability of specific tRNAs under stress. To gain deeper insight into its biological roles in a flowering plant, we examined more closely the previously reported Arabidopsis SALK_136635C line deficient in TRDMT1/DNMT2 function [Goll MG et al. (2006) Science 311, 395-398]. RNAs derived from Arabidopsis Dnmt2-deficient plants lacked m5 C38 in tRNAAsp . In this study, by transient expression assays we show that Arabidopsis TRDMT1/DNMT2 is distributed in the nucleus, cytoplasm and RNA-processing bodies, suggesting a role for TRDMT1/DNMT2 in RNA metabolic processes possibly by shuttling between cellular compartments. Bright-field and high-resolution SEM and qPCR analysis reveal roles of TRDMT1/DNMT2 in proper growth and developmental progression. Quantitative proteome analysis by LC-MS/MS coupled with qPCR shows AtTRDMT1/AtDNMT2 function to be crucial for protein synthesis and cellular homeostasis via housekeeping roles and proteins with poly-Asp stretches and RNA pol II activity on selected genes are affected in attrdmt1/atdnmt2. This shift in metabolic pathways primes the mutant plants to become increasingly sensitive to oxidative and osmotic stress. Taken together, our study sheds light on the mechanistic role of TRDMT1/DNMT2 in a flowering plant.
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Affiliation(s)
- Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Sanjay Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
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6
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Drewell RA, Cormier TC, Steenwyk JL, Denis JS, Tabima J, Dresch J, Larochelle D. The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing. NAR Genom Bioinform 2023; 5:lqad035. [PMID: 37081864 PMCID: PMC10111430 DOI: 10.1093/nargab/lqad035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/13/2023] [Accepted: 03/30/2023] [Indexed: 04/22/2023] Open
Abstract
DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall very low number of sites with any detectable level of DNA methylation, occurring at significant levels in only 303-3432 cytosines out of the ∼7.5 million total cytosines in the genome depending on the replicate. Furthermore, a knockout of the DNMA enzyme leads to no overall decrease in DNA methylation. Of the identified sites, significant methylation is only detected at 11 sites in all four of the methylomes analyzed. Targeted bisulfite PCR sequencing and computational analysis demonstrate that the methylation profile does not change during development and that these 11 cytosines are most likely false positives generated by protection from bisulfite conversion due to their location in hairpin-forming palindromic DNA sequences. Our data therefore provide evidence that there is no significant DNA methylation in Dictyostelium before fruiting body formation and identify a reproducible experimental artifact from bisulfite sequencing.
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Affiliation(s)
- Robert A Drewell
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Tayla C Cormier
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Jacob L Steenwyk
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James St Denis
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Javier F Tabima
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Jacqueline M Dresch
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Denis A Larochelle
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
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7
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Singh D, Yadav R, Kaushik S, Wadhwa N, Kapoor S, Kapoor M. Transcriptome Analysis of ppdnmt2 and Identification of Superoxide Dismutase as a Novel Interactor of DNMT2 in the Moss Physcomitrella patens. FRONTIERS IN PLANT SCIENCE 2020; 11:1185. [PMID: 32849734 PMCID: PMC7419982 DOI: 10.3389/fpls.2020.01185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/21/2020] [Indexed: 05/07/2023]
Abstract
DNMT2 is a DNA/tRNA cytosine methyltransferase that is highly conserved in structure and function in eukaryotes. In plants however, limited information is available on the function of this methyltransferase. We have previously reported that in the moss Physcomitrella patens, DNMT2 plays a crucial role in stress recovery and tRNAAsp transcription/stability under salt stress. To further investigate the role of PpDNMT2 at genome level, in this study we have performed RNA sequencing of ppdnmt2. Transcriptome analysis reveals a number of genes and pathways to function differentially and suggests a close link between PpDNMT2 function and osmotic and ionic stress tolerance. We propose PpDNMT2 to play a pivotal role in regulating salt tolerance by affecting molecular networks involved in stress perception and signal transduction that underlie maintenance of ion homeostasis in cells. We also examined interactome of PpDNMT2 using affinity purification (AP) coupled to mass spectrometry (AP-MS). Quantitative proteomic analysis reveals several chloroplast proteins involved in light reactions and carbon assimilation and proteins involved in stress response and some not implicated in stress to co-immunoprecipitate with PpDNMT2. Comparison between transcriptome and interactome datasets has revealed novel association between PpDNMT2 activity and the antioxidant enzyme Superoxide dismutase (SOD), protein turnover mediated by the Ubiquitin-proteasome system and epigenetic gene regulation. PpDNMT2 possibly exists in complex with CuZn-SODs in vivo and the two proteins also directly interact in the yeast nucleus as observed by yeast two-hybrid assay. Taken together, the work presented in this study sheds light on diverse roles of PpDNMT2 in maintaining molecular and physiological homeostasis in P. patens. This is a first report describing transcriptome and interactome of DNMT2 in any land plant.
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Affiliation(s)
- Darshika Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Radha Yadav
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Shubham Kaushik
- Vproteomics, Valerian Chem Private Limited Green Park Mains, New Delhi, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
- *Correspondence: Meenu Kapoor,
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8
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Naiyer S, Bhattacharya A, Bhattacharya S. Advances in Entamoeba histolytica Biology Through Transcriptomic Analysis. Front Microbiol 2019; 10:1921. [PMID: 31481949 PMCID: PMC6710346 DOI: 10.3389/fmicb.2019.01921] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/05/2019] [Indexed: 12/13/2022] Open
Abstract
A large number of transcriptome-level studies in Entamoeba histolytica, the protozoan parasite that causes amoebiasis, have investigated gene expression patterns to help understand the pathology and biology of the organism. They have compared virulent and avirulent strains in lab culture and after tissue invasion, cells grown under different stress conditions, response to anti-amoebic drug treatments, and gene expression changes during the process of encystation. These studies have revealed interesting molecules/pathways that will help increase our mechanistic understanding of differentially expressed genes during growth perturbations and tissue invasion. Some of the important insights obtained from transcriptome studies include the observations that regulation of carbohydrate metabolism may be an important determinant for tissue invasion, while the novel up-regulated genes during encystation include phospholipase D, and meiotic genes, suggesting the possibility of meiosis during the process. Classification of genes according to expression levels showed that amongst the highly transcribed genes in cultured E. histolytica trophozoites were some virulence factors, raising the question of the role of these factors in normal parasite growth. Promoter motifs associated with differential gene expression and regulation were identified. Some of these motifs associated with high gene expression were located downstream of start codon, and were required for efficient transcription. The listing of E. histolytica genes according to transcript expression levels will help us determine the scale of post-transcriptional regulation, and the possible roles of predicted promoter motifs. The small RNA transcriptome is a valuable resource for detailed structural and functional analysis of these molecules and their regulatory roles. These studies provide new drug targets and enhance our understanding of gene regulation in E. histolytica.
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Affiliation(s)
- Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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9
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Abstract
Maintenance of genome stability requires control over the expression of transposable elements (TEs), whose activity can have substantial deleterious effects on the host. Chemical modification of DNA is a commonly used strategy to achieve this, and it has long been argued that the emergence of 5-methylcytosine (5mC) in many species was driven by the requirement to silence TEs. Potential roles in TE regulation have also been suggested for other DNA modifications, such as N6-methyladenine and oxidation derivatives of 5mC, although the underlying mechanistic relationships are poorly understood. Here, we discuss current evidence implicating DNA modifications and DNA-modifying enzymes in TE regulation across different species.
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Affiliation(s)
- Özgen Deniz
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK
| | - Jennifer M Frost
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK
| | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK.
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10
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Rambo IM, Marsh A, Biddle JF. Cytosine Methylation Within Marine Sediment Microbial Communities: Potential Epigenetic Adaptation to the Environment. Front Microbiol 2019; 10:1291. [PMID: 31244806 PMCID: PMC6579885 DOI: 10.3389/fmicb.2019.01291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/23/2019] [Indexed: 02/01/2023] Open
Abstract
Marine sediments harbor a vast amount of Earth's microbial biomass, yet little is understood regarding how cells subsist in this low-energy, presumably slow-growth environment. Cells in marine sediments may require additional methods for genetic regulation, such as epigenetic modification via DNA methylation. We investigated this potential phenomenon within a shallow estuary sediment core spanning 100 years of age. Here, we provide evidence of dynamic community m5-cytosine methylation within estuarine sediment metagenomes. The methylation states of individual CpG sites were reconstructed and quantified across three depths within the sediment core. A total of 6,254 CpG sites were aligned for direct comparison of methylation states between samples, and 4,235 of these sites mapped to taxa and genes. Our results demonstrate the presence of differential methylation within environmental CpG sites across an age gradient of sediment. We show that epigenetic modification can be detected via Illumina sequencing within complex environmental communities. The change in methylation state of environmentally relevant genes across depths may indicate a dynamic role of DNA methylation in regulation of biogeochemical processes.
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Affiliation(s)
| | | | - Jennifer F. Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
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11
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Pinzón N, Bertrand S, Subirana L, Busseau I, Escrivá H, Seitz H. Functional lability of RNA-dependent RNA polymerases in animals. PLoS Genet 2019; 15:e1007915. [PMID: 30779744 PMCID: PMC6396948 DOI: 10.1371/journal.pgen.1007915] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 03/01/2019] [Accepted: 12/24/2018] [Indexed: 11/18/2022] Open
Abstract
RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in animals than previously thought, even in insects, where they had been assumed not to exist. RdRP genes were present in the ancestors of numerous clades, and they were subsequently lost at a high frequency. In order to probe the function of RdRPs in a deuterostome (the cephalochordate Branchiostoma lanceolatum), we performed high-throughput analyses of small RNAs from various Branchiostoma developmental stages. Our results show that Branchiostoma RdRPs do not appear to participate in RNAi: we did not detect any candidate small RNA population exhibiting classical siRNA length or sequence features. Our results show that RdRPs have been independently lost in dozens of animal clades, and even in a clade where they have been conserved (cephalochordates) their function in RNAi amplification is not preserved. Such a dramatic functional variability reveals an unexpected plasticity in RNA silencing pathways. RNA interference (RNAi) is a conserved gene regulation system in eukaryotes. In non-animal eukaryotes, it necessitates RNA-dependent RNA polymerases (“RdRPs”). Among animals, only nematodes appear to require RdRPs for RNAi. Yet additional animal clades have RdRPs and it is assumed that they participate in RNAi. Here, we find that RdRPs are much more common in animals than previously thought, but their genes were independently lost in many lineages. Focusing on a species with RdRP genes (a cephalochordate), we found that it does not use them for RNAi. While RNAi is the only known function for eukaryotic RdRPs, our results suggest additional roles. Eukaryotic RdRPs thus have a complex evolutionary history in animals, with frequent independent losses and apparent functional diversification.
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Affiliation(s)
- Natalia Pinzón
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Isabelle Busseau
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
| | - Hector Escrivá
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hervé Seitz
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
- * E-mail:
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12
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Liao Z, Kjellin J, Hoeppner MP, Grabherr M, Söderbom F. Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum. RNA Biol 2018; 15:937-954. [PMID: 29966484 PMCID: PMC6161686 DOI: 10.1080/15476286.2018.1481697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.
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Affiliation(s)
- Zhen Liao
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
| | - Jonas Kjellin
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
| | - Marc P Hoeppner
- b Department of Medical Biochemistry and Microbiology , Uppsala University , Uppsala , Sweden.,c Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology , Kiel , Germany
| | - Manfred Grabherr
- b Department of Medical Biochemistry and Microbiology , Uppsala University , Uppsala , Sweden
| | - Fredrik Söderbom
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
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Vieira GC, D'Ávila MF, Zanini R, Deprá M, da Silva Valente VL. Evolution of DNMT2 in drosophilids: Evidence for positive and purifying selection and insights into new protein (pathways) interactions. Genet Mol Biol 2018; 41:215-234. [PMID: 29668012 PMCID: PMC5913717 DOI: 10.1590/1678-4685-gmb-2017-0056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/18/2017] [Indexed: 12/03/2022] Open
Abstract
The DNA methyltransferase 2 (DNMT2) protein is the most conserved member of the
DNA methyltransferase family. Nevertheless, its substrate specificity is still
controversial and elusive. The genomic role and determinants of DNA methylation
are poorly understood in invertebrates, and several mechanisms and associations
are suggested. In Drosophila, the only known DNMT gene is
Dnmt2. Here we present our findings from a wide search for
Dnmt2 homologs in 68 species of Drosophilidae. We
investigated its molecular evolution, and in our phylogenetic analyses the main
clades of Drosophilidae species were recovered. We tested whether the
Dnmt2 has evolved neutrally or under positive selection
along the subgenera Drosophila and Sophophora
and investigated positive selection in relation to several physicochemical
properties. Despite of a major selective constraint on Dnmt2,
we detected six sites under positive selection. Regarding the DNMT2 protein, 12
sites under positive-destabilizing selection were found, which suggests a
selection that favors structural and functional shifts in the protein. The
search for new potential protein partners with DNMT2 revealed 15 proteins with
high evolutionary rate covariation (ERC), indicating a plurality of DNMT2
functions in different pathways. These events might represent signs of molecular
adaptation, with molecular peculiarities arising from the diversity of
evolutionary histories experienced by drosophilids.
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Affiliation(s)
- Gilberto Cavalheiro Vieira
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Marícia Fantinel D'Ávila
- Departamento de Zoologia e Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Palmeira das Missões, RS, Brazil
| | - Rebeca Zanini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Maríndia Deprá
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Vera Lúcia da Silva Valente
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Departamento de Zoologia e Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Palmeira das Missões, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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14
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Shirk PD, Furlong RB, Dolan A, Werren JH. Functional characterization of the transcriptional regulatory elements of three highly expressed constitutive genes in the jewel wasp, Nasonia vitripennis. INSECT MOLECULAR BIOLOGY 2017; 26:743-751. [PMID: 28753244 DOI: 10.1111/imb.12333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The jewel wasp, Nasonia vitripennis Ashmead (Hymenoptera: Pteromalidae), is an easily reared parasitoid that is providing an ever increasingly malleable model for examining the biology and genetics of Hymenoptera. Utilizing genomic and transcriptome resources, 5' upstream transcriptional regulatory sequences (TREs) from three highly expressed genes were identified and cloned. Criteria for TRE selection included the presence of an adjacent gene 5' of the translation initiation site. One gene was methylated whereas the other two were nonmethylated. Each TRE, heat-shock protein 70 (hsp70), activator of 90 kDa hsp ATPase protein 1 (hsp90A), and lipid storage droplet surface-binding protein 1 (lsdp) was linked with enhanced green fluorescent protein (EGFP) coding sequence and cloned into both pDP9e somatic and piggyBac germline transformation vectors. EGFP expression patterns under control of each TRE were compared with patterns of DsRed fluorescence produced from the transformation vector cassette. Functional activity of each TRE was observed in cultured Spodoptera frugiperda 9 (Sf9) cells and Drosophila melanogaster as well as in N. vitripennis embryos demonstrating that all three sequences had functional transcriptional regulatory activity in three different insect orders. Identification and functional characterization of these three TREs will provide critical and necessary resources for further genetic analyses of N. vitripennis, Hymenoptera and other insects.
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Affiliation(s)
- P D Shirk
- USDA-ARS Center for Medical Agricultural and Veterinary Entomology, Gainesville, FL, USA
| | - R B Furlong
- USDA-ARS Center for Medical Agricultural and Veterinary Entomology, Gainesville, FL, USA
| | - A Dolan
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - J H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
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15
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Malicki M, Iliopoulou M, Hammann C. Retrotransposon Domestication and Control in Dictyostelium discoideum. Front Microbiol 2017; 8:1869. [PMID: 29051748 PMCID: PMC5633606 DOI: 10.3389/fmicb.2017.01869] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/13/2017] [Indexed: 01/22/2023] Open
Abstract
Transposable elements, identified in all eukaryotes, are mobile genetic units that can change their genomic position. Transposons usually employ an excision and reintegration mechanism, by which they change position, but not copy number. In contrast, retrotransposons amplify via RNA intermediates, increasing their genomic copy number. Hence, they represent a particular threat to the structural and informational integrity of the invaded genome. The social amoeba Dictyostelium discoideum, model organism of the evolutionary Amoebozoa supergroup, features a haploid, gene-dense genome that offers limited space for damage-free transposition. Several of its contemporary retrotransposons display intrinsic integration preferences, for example by inserting next to transfer RNA genes or other retroelements. Likely, any retrotransposons that invaded the genome of the amoeba in a non-directed manner were lost during evolution, as this would result in decreased fitness of the organism. Thus, the positional preference of the Dictyostelium retroelements might represent a domestication of the selfish elements. Likewise, the reduced danger of such domesticated transposable elements led to their accumulation, and they represent about 10% of the current genome of D. discoideum. To prevent the uncontrolled spreading of retrotransposons, the amoeba employs control mechanisms including RNA interference and heterochromatization. Here, we review TRE5-A, DIRS-1 and Skipper-1, as representatives of the three retrotransposon classes in D. discoideum, which make up 5.7% of the Dictyostelium genome. We compile open questions with respect to their mobility and cellular regulation, and suggest strategies, how these questions might be addressed experimentally.
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Affiliation(s)
- Marek Malicki
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Maro Iliopoulou
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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16
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Vieira GC, Vieira GF, Sinigaglia M, da Silva Valente VL. Linking epigenetic function to electrostatics: The DNMT2 structural model example. PLoS One 2017; 12:e0178643. [PMID: 28575027 PMCID: PMC5456315 DOI: 10.1371/journal.pone.0178643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 11/25/2022] Open
Abstract
The amino acid sequence of DNMT2 is very similar to the catalytic domains of bacterial and eukaryotic proteins. However, there is great variability in the region of recognition of the target sequence. While bacterial DNMT2 acts as a DNA methyltransferase, previous studies have indicated low DNA methylation activity in eukaryotic DNMT2, with preference by tRNA methylation. Drosophilids are known as DNMT2-only species and the DNA methylation phenomenon is a not elucidated case yet, as well as the ontogenetic and physiologic importance of DNMT2 for this species group. In addition, more recently study showed that methylation in the genome in Drosophila melanogaster is independent in relation to DNMT2. Despite these findings, Drosophilidae family has more than 4,200 species with great ecological diversity and historical evolution, thus we, therefore, aimed to examine the drosophilids DNMT2 in order to verify its conservation at the physicochemical and structural levels in a functional context. We examined the twenty-six DNMT2 models generated by molecular modelling and five crystallographic structures deposited in the Protein Data Bank (PDB) using different approaches. Our results showed that despite sequence and structural similarity between species close related, we found outstanding differences when they are analyzed in the context of surface distribution of electrostatic properties. The differences found in the electrostatic potentials may be linked with different affinities and processivity of DNMT2 for its different substrates (DNA, RNA or tRNA) and even for interactions with other proteins involved in the epigenetic mechanisms.
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Affiliation(s)
- Gilberto Cavalheiro Vieira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- * E-mail:
| | - Gustavo Fioravanti Vieira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marialva Sinigaglia
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Instituto do Câncer Infantil, Porto Alegre, RS, Brazil
| | - Vera Lúcia da Silva Valente
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Programa de Pós Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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17
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Geyer KK, Niazi UH, Duval D, Cosseau C, Tomlinson C, Chalmers IW, Swain MT, Cutress DJ, Bickham-Wright U, Munshi SE, Grunau C, Yoshino TP, Hoffmann KF. The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni. PLoS Negl Trop Dis 2017; 11:e0005246. [PMID: 28510608 PMCID: PMC5433704 DOI: 10.1371/journal.pntd.0005246] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/10/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. METHODOLOGY/PRINCIPLE FINDINGS Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions. Firstly, methyl-CpG binding domain protein (Bgmbd2/3) and DNA methyltransferase 1 (Bgdnmt1) genes are transcriptionally enriched in gonadal compared to somatic tissues with 5-azacytidine (5-AzaC) treatment significantly inhibiting oviposition. Secondly, elevated levels of 5-methyl cytosine (5mC), DNA methyltransferase activity and 5mC binding in pigmented hybrid- compared to inbred (NMRI)- B. glabrata populations indicate a role for the snail's DNA methylation machinery in maintaining hybrid vigour or heterosis. Thirdly, locus-specific detection of 5mC by bisulfite (BS)-PCR revealed 5mC within an exonic region of a housekeeping protein-coding gene (Bg14-3-3), supporting previous in silico predictions and whole genome BS-Seq analysis of this species' genome. Finally, we provide preliminary evidence for parasite-mediated host epigenetic reprogramming in the schistosome/snail system, as demonstrated by the increase in Bgdnmt1 and Bgmbd2/3 transcript abundance following Bge (B. glabrata embryonic cell line) exposure to parasite larval transformation products (LTP). CONCLUSIONS/SIGNIFICANCE The presence of a functional DNA methylation machinery in B. glabrata as well as the modulation of these gene products in response to schistosome products, suggests a vital role for DNA methylation during snail development/oviposition and parasite interactions. Further deciphering the role of this epigenetic process during Biomphalaria/Schistosoma co-evolutionary biology may reveal key factors associated with disease transmission and, moreover, enable the discovery of novel lifecycle intervention strategies.
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Affiliation(s)
- Kathrin K. Geyer
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Umar H. Niazi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David Duval
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Céline Cosseau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Chad Tomlinson
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Iain W. Chalmers
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Martin T. Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David J. Cutress
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Utibe Bickham-Wright
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Sabrina E. Munshi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Christoph Grunau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Timothy P. Yoshino
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
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18
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Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification. Biomolecules 2017; 7:biom7010014. [PMID: 28208632 PMCID: PMC5372726 DOI: 10.3390/biom7010014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/02/2017] [Accepted: 02/02/2017] [Indexed: 12/22/2022] Open
Abstract
Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S. pombe. Queuine, the respective base, is a hypermodified guanine analog that is synthesized from guanosine-5’-triphosphate (GTP) by bacteria. Interestingly, most eukaryotes have queuosine in their tRNA. However, they cannot synthesize it themselves, but rather salvage it from food or from gut microbes. The queuine obtained from these sources comes from the breakdown of tRNAs, where the queuine ultimately was synthesized by bacteria. Queuine thus has been termed a micronutrient. This review summarizes the current knowledge of Dnmt2 methylation and queuosine modification with respect to translation as well as the organismal consequences of the absence of these modifications. Models for the functional cooperation between these modifications and its wider implications are discussed.
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19
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Agrahari M, Gaurav AK, Bhattacharya A, Bhattacharya S. Cytosine DNA methylation at promoter of non LTR retrotransposon and heat shock protein gene (HSP70) of Entamoeba histolytica and lack of correlation with transcription status. Mol Biochem Parasitol 2017; 212:21-27. [PMID: 28082182 DOI: 10.1016/j.molbiopara.2017.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/26/2016] [Accepted: 01/05/2017] [Indexed: 02/08/2023]
Abstract
Non LTR retrotransposons (EhLINEs and EhSINEs) occupy 11% of the Entamoeba histolytica genome. Since promoter DNA methylation at cytosines has been correlated with transcriptional silencing of transposable elements in model organisms we checked whether this was the case in EhLINE1. We located promoter activity in a 841bp fragment at 5'-end of this element by luciferase reporter assay. From RNAseq and RT-PCR analyses we selected a transcriptionally active and silent copy to study cytosine DNA methylation of the promoter region by bisulfite sequencing. None of the cytosines were methylated in either copy. Further, we looked at methylation status of a few selected cytosines in all 5'-intact EhLINE1 copies by single nucleotide incorporation opposite cytosine in bisulfite-treated DNA, where dGTP would be incorporated if the cytosine was methylated. Again we did not find evidence of cytosine methylation, indicating that expression status of this element was not correlated with promoter DNA methylation. To test for any role of cytosine methylation in transcriptional regulation of the E. histolytica Hsp70 gene in which the promoter is fully methylated under normal growth conditions, we checked methylation status and found that the promoter remained fully methylated during heat-shock as well, although transcription was greatly enhanced by heat-shock, showing that cytosine methylation is not a repressive mark for EhHsp70. Our data present direct evidence that promoter methylation, a common mode of transposon silencing, is unlikely to be involved in transcriptional regulation of EhLINE1, and reinforce the conclusion that promoter DNA methylation may not be a major contributor to transcriptional regulation in E. histolytica.
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Affiliation(s)
- Mridula Agrahari
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Amit Kumar Gaurav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
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Jeltsch A, Ehrenhofer-Murray A, Jurkowski TP, Lyko F, Reuter G, Ankri S, Nellen W, Schaefer M, Helm M. Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation. RNA Biol 2016; 14:1108-1123. [PMID: 27232191 PMCID: PMC5699548 DOI: 10.1080/15476286.2016.1191737] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A group of homologous nucleic acid modification enzymes called Dnmt2, Trdmt1, Pmt1, DnmA, and Ehmet in different model organisms catalyze the transfer of a methyl group from the cofactor S-adenosyl-methionine (SAM) to the carbon-5 of cytosine residues. Originally considered as DNA MTases, these enzymes were shown to be tRNA methyltransferases about a decade ago. Between the presumed involvement in DNA modification-related epigenetics, and the recent foray into the RNA modification field, significant progress has characterized Dnmt2-related research. Here, we review this progress in its diverse facets including molecular evolution, structural biology, biochemistry, chemical biology, cell biology and epigenetics.
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Affiliation(s)
- Albert Jeltsch
- a Institute of Biochemistry , Stuttgart University , Stuttgart , Germany
| | | | - Tomasz P Jurkowski
- a Institute of Biochemistry , Stuttgart University , Stuttgart , Germany
| | - Frank Lyko
- c Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center , Heidelberg , Germany
| | - Gunter Reuter
- d Institute of Biology, Developmental Genetics, Martin Luther University Halle , Halle , Germany
| | - Serge Ankri
- e Department of Molecular Microbiology , The Bruce Rappaport Faculty of Medicine , Technion , Haifa , Israel
| | - Wolfgang Nellen
- f Abteilung für Genetik, Universität Kassel , Kassel , Germany
| | - Matthias Schaefer
- g Medical University of Vienna, Center for Anatomy & Cell Biology , Vienna , Austria
| | - Mark Helm
- h Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Mainz , Germany
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21
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Ashapkin VV, Kutueva LI, Vanyushin BF. Dnmt2 is the most evolutionary conserved and enigmatic cytosine DNA methyltransferase in eukaryotes. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416030029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Bollmann SR, Fang Y, Press CM, Tyler BM, Grünwald NJ. Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora. FRONTIERS IN PLANT SCIENCE 2016; 7:284. [PMID: 27014308 PMCID: PMC4791657 DOI: 10.3389/fpls.2016.00284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/22/2016] [Indexed: 05/10/2023]
Abstract
Gene regulation by small RNA pathways is ubiquitous among eukaryotes, but little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora, a genus of filamentous oomycetes, contains many devastating plant pathogens, causing multibillion-dollar damage to crops, ornamental plants, and natural environments. The genomes of several oomycetes including Phytophthora species such as the soybean pathogen P. sojae, have been sequenced, allowing evolutionary analysis of small RNA-processing enzymes. This study examined the evolutionary origins of the oomycete small RNA-related genes Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) through broad phylogenetic analyses of the key domains. Two Dicer gene homologs, DCL1 and DCL2, and one RDR homolog were cloned and analyzed from P. sojae. Gene expression analysis revealed only minor changes in transcript levels among different life stages. Oomycete DCL1 homologs clustered with animal and plant Dicer homologs in evolutionary trees, whereas oomycete DCL2 homologs clustered basally to the tree along with Drosha homologs. Phylogenetic analysis of the RDR homologs confirmed a previous study that suggested the last common eukaryote ancestor possessed three RDR homologs, which were selectively retained or lost in later lineages. Our analysis clarifies the position of some Unikont and Chromalveolate RDR lineages within the tree, including oomycete homologs. Finally, we analyzed alterations in the domain structure of oomycete Dicer and RDR homologs, specifically focusing on the proposed domain transfer of the DEAD-box helicase domain from Dicer to RDR. Implications of the oomycete domain structure are discussed, and possible roles of the two oomycete Dicer homologs are proposed.
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Affiliation(s)
- Stephanie R. Bollmann
- Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA
| | - Yufeng Fang
- Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia TechBlacksburg, VA, USA
| | - Caroline M. Press
- Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA
| | - Brett M. Tyler
- Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA
| | - Niklaus J. Grünwald
- Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA
- Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA
- *Correspondence: Niklaus J. Grünwald
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Schmith A, Spaller T, Gaube F, Fransson Å, Boesler B, Ojha S, Nellen W, Hammann C, Söderbom F, Winckler T. A host factor supports retrotransposition of the TRE5-A population in Dictyostelium cells by suppressing an Argonaute protein. Mob DNA 2015; 6:14. [PMID: 26339297 PMCID: PMC4559204 DOI: 10.1186/s13100-015-0045-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/26/2015] [Indexed: 11/30/2022] Open
Abstract
Background In the compact and haploid genome of Dictyostelium discoideum control of transposon activity is of particular importance to maintain viability. The non-long terminal repeat retrotransposon TRE5-A amplifies continuously in D. discoideum cells even though it produces considerable amounts of minus-strand (antisense) RNA in the presence of an active RNA interference machinery. Removal of the host-encoded C-module-binding factor (CbfA) from D. discoideum cells resulted in a more than 90 % reduction of both plus- and minus-strand RNA of TRE5-A and a strong decrease of the retrotransposition activity of the cellular TRE5-A population. Transcriptome analysis revealed an approximately 230-fold overexpression of the gene coding for the Argonaute-like protein AgnC in a CbfA-depleted mutant. Results The D. discoideum genome contains orthologs of RNA-dependent RNA polymerases, Dicer-like proteins, and Argonaute proteins that are supposed to represent RNA interference pathways. We analyzed available mutants in these genes for altered expression of TRE5-A. We found that the retrotransposon was overexpressed in mutants lacking the Argonaute proteins AgnC and AgnE. Because the agnC gene is barely expressed in wild-type cells, probably due to repression by CbfA, we employed a new method of promoter-swapping to overexpress agnC in a CbfA-independent manner. In these strains we established an in vivo retrotransposition assay that determines the retrotransposition frequency of the cellular TRE5-A population. We observed that both the TRE5-A steady-state RNA level and retrotransposition rate dropped to less than 10 % of wild-type in the agnC overexpressor strains. Conclusions The data suggest that TRE5-A amplification is controlled by a distinct pathway of the Dictyostelium RNA interference machinery that does not require RNA-dependent RNA polymerases but involves AgnC. This control is at least partially overcome by the activity of CbfA, a factor derived from the retrotransposon’s host. This unusual regulation of mobile element activity most likely had a profound effect on genome evolution in D. discoideum. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0045-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anika Schmith
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
| | - Thomas Spaller
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
| | - Friedemann Gaube
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
| | - Åsa Fransson
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Uppsala, Sweden ; Present address: Aprea AB, Karolinska Institutet Science Park, Nobels väg 3, 17175 Solna, Sweden
| | - Benjamin Boesler
- Institute of Biology - Genetics, University of Kassel, Kassel, Germany
| | - Sandeep Ojha
- Ribogenetics@Biochemistry Lab, Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Jacobs University Bremen, Bremen, Germany
| | - Wolfgang Nellen
- Institute of Biology - Genetics, University of Kassel, Kassel, Germany ; Present address: Department of Biology, Brawijaya University, Jl. Veteran, Malang, East Java Indonesia
| | - Christian Hammann
- Ribogenetics@Biochemistry Lab, Department of Life Sciences and Chemistry, Molecular Life Sciences Research Center, Jacobs University Bremen, Bremen, Germany
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Thomas Winckler
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Jena, Semmelweisstrasse 10, 07743 Jena, Germany
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Haag S, Warda AS, Kretschmer J, Günnigmann MA, Höbartner C, Bohnsack MT. NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs. RNA (NEW YORK, N.Y.) 2015; 21:1532-43. [PMID: 26160102 PMCID: PMC4536315 DOI: 10.1261/rna.051524.115] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 06/01/2015] [Indexed: 05/04/2023]
Abstract
Many cellular RNAs require modification of specific residues for their biogenesis, structure, and function. 5-methylcytosine (m(5)C) is a common chemical modification in DNA and RNA but in contrast to the DNA modifying enzymes, only little is known about the methyltransferases that establish m(5)C modifications in RNA. The putative RNA methyltransferase NSUN6 belongs to the family of Nol1/Nop2/SUN domain (NSUN) proteins, but so far its cellular function has remained unknown. To reveal the target spectrum of human NSUN6, we applied UV crosslinking and analysis of cDNA (CRAC) as well as chemical crosslinking with 5-azacytidine. We found that human NSUN6 is associated with tRNAs and acts as a tRNA methyltransferase. Furthermore, we uncovered tRNA(Cys) and tRNA(Thr) as RNA substrates of NSUN6 and identified the cytosine C72 at the 3' end of the tRNA acceptor stem as the target nucleoside. Interestingly, target recognition in vitro depends on the presence of the 3'-CCA tail. Together with the finding that NSUN6 localizes to the cytoplasm and largely colocalizes with marker proteins for the Golgi apparatus and pericentriolar matrix, our data suggest that NSUN6 modifies tRNAs in a late step in their biogenesis.
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Affiliation(s)
- Sara Haag
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Ahmed S Warda
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Jens Kretschmer
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Manuel A Günnigmann
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
| | - Markus T Bohnsack
- Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany Göttingen Centre for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany
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25
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Meyer RC, Hönig G, Brandt R, Arana-Ceballos F, Neitsch C, Reuter G, Altmann T, Kuhlmann M. Overexpression of Arabidopsis thaliana ERI, the homolog of C. elegans Enhancer of RNAinterference, leads to enhanced growth. FRONTIERS IN PLANT SCIENCE 2015; 6:531. [PMID: 26257748 PMCID: PMC4510415 DOI: 10.3389/fpls.2015.00531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 06/29/2015] [Indexed: 05/27/2023]
Abstract
Organisms adopt a wide range of strategies to adapt to change. Gene silencing describes the ability of organisms to modulate the expression of susceptible genes at certain times at the transcriptional or the translational level. In all known eukaryotic organisms 21-nt long short interfering RNAs (siRNAs) are the effector molecules of post-transcriptional gene silencing (PTGS), while 24-nt long siRNAs are involved in PTGS in plants. Mutant studies in Caenorhabditis elegans lead to the identification of the enzyme ERI (Enhancer of RNAinterference) with enhanced PTGS. Although the genes involved in growth vigor and growth rate are still unknown, it becomes clearer that the population of small RNAs plays a role in the very early phase of plant development. To pinpoint the link between growth and siRNAs, the expression of Arabidopsis uni-gene Enhancer of RNAi (ERI) homolog from C. elegans was modulated. Increased degradation of small RNAs was achieved by ectopic AtERI overexpression in planta. Based on global small RNA analysis, AtERI overexpression affects mainly the population of 21 mers, excluding miRNAs. To identify target genes, AtERI gain-of-function mutants were analyzed, and differentially abundant small RNAs were identified. Plants with an elevated level of AtERI were bigger in all three light intensities analyzed, indicating an inhibitory function of particular small RNAs in plant growth, with differences in relative growth rates depending on developmental stage and light intensity. Understanding the role of these siRNAs could open new avenues for enhancing plant growth.
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Affiliation(s)
- Rhonda C. Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Stadt Seeland, Germany
| | - Gunnar Hönig
- Department of Developmental Genetics, Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ronny Brandt
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Stadt Seeland, Germany
| | - Fernando Arana-Ceballos
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Stadt Seeland, Germany
| | - Cathleen Neitsch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Stadt Seeland, Germany
| | - Gunter Reuter
- Department of Developmental Genetics, Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Stadt Seeland, Germany
| | - Markus Kuhlmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Stadt Seeland, Germany
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Boesler B, Meier D, Förstner KU, Friedrich M, Hammann C, Sharma CM, Nellen W. Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1. J Biol Chem 2014; 289:35124-38. [PMID: 25352599 DOI: 10.1074/jbc.m114.612663] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The retrotransposon DIRS-1 is the most abundant retroelement in Dictyostelium discoideum and constitutes the pericentromeric heterochromatin of the six chromosomes in D. discoideum. The vast majority of cellular siRNAs is derived from DIRS-1, suggesting that the element is controlled by RNAi-related mechanisms. We investigated the role of two of the five Argonaute proteins of D. discoideum, AgnA and AgnB, in DIRS-1 silencing. Deletion of agnA resulted in the accumulation of DIRS-1 transcripts, the expression of DIRS-1-encoded proteins, and the loss of most DIRS-1-derived secondary siRNAs. Simultaneously, extrachromosomal single-stranded DIRS-1 DNA accumulated in the cytoplasm of agnA- strains. These DNA molecules appear to be products of reverse transcription and thus could represent intermediate structures before transposition. We further show that transitivity of endogenous siRNAs is impaired in agnA- strains. The deletion of agnB alone had no strong effect on DIRS-1 transposon regulation. However, in agnA-/agnB- double mutant strains strongly reduced accumulation of extrachromosomal DNA compared with the single agnA- strains was observed.
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Affiliation(s)
- Benjamin Boesler
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Doreen Meier
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Konrad U Förstner
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany, and
| | - Michael Friedrich
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Laboratory, School of Engineering and Science, Molecular Life Sciences Research Center, Jacobs University, Campus Ring 1, DE-28759 Bremen, Germany
| | - Cynthia M Sharma
- Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany, and
| | - Wolfgang Nellen
- From the Department of Genetics, FB10, Kassel University, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany,
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27
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Entamoeba histolytica adaptation to glucose starvation: a matter of life and death. Curr Opin Microbiol 2014; 20:139-45. [DOI: 10.1016/j.mib.2014.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 06/11/2014] [Accepted: 06/13/2014] [Indexed: 12/25/2022]
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Wiegand S, Meier D, Seehafer C, Malicki M, Hofmann P, Schmith A, Winckler T, Földesi B, Boesler B, Nellen W, Reimegård J, Käller M, Hällman J, Emanuelsson O, Avesson L, Söderbom F, Hammann C. The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals. Nucleic Acids Res 2013; 42:3330-45. [PMID: 24369430 PMCID: PMC3950715 DOI: 10.1093/nar/gkt1337] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Dictyostelium intermediate repeat sequence 1 (DIRS-1) is the founding member of a poorly characterized class of retrotransposable elements that contain inverse long terminal repeats and tyrosine recombinase instead of DDE-type integrase enzymes. In Dictyostelium discoideum, DIRS-1 forms clusters that adopt the function of centromeres, rendering tight retrotransposition control critical to maintaining chromosome integrity. We report that in deletion strains of the RNA-dependent RNA polymerase RrpC, full-length and shorter DIRS-1 messenger RNAs are strongly enriched. Shorter versions of a hitherto unknown long non-coding RNA in DIRS-1 antisense orientation are also enriched in rrpC– strains. Concurrent with the accumulation of long transcripts, the vast majority of small (21 mer) DIRS-1 RNAs vanish in rrpC– strains. RNASeq reveals an asymmetric distribution of the DIRS-1 small RNAs, both along DIRS-1 and with respect to sense and antisense orientation. We show that RrpC is required for post-transcriptional DIRS-1 silencing and also for spreading of RNA silencing signals. Finally, DIRS-1 mis-regulation in the absence of RrpC leads to retrotransposon mobilization. In summary, our data reveal RrpC as a key player in the silencing of centromeric retrotransposon DIRS-1. RrpC acts at the post-transcriptional level and is involved in spreading of RNA silencing signals, both in the 5′ and 3′ directions.
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Affiliation(s)
- Stephan Wiegand
- Ribogenetics@Biochemistry Lab, School of Engineering and Science, Molecular Life Sciences Research Center, Jacobs University Bremen, Campus Ring 1, DE-28759 Bremen, Germany, Abteilung Genetik, Universität Kassel, Heinrich-Plett-Strasse 40, DE-34132 Kassel, Germany, Friedrich-Schiller-Universität Jena, Institut für Pharmazie, Lehrstuhl für Pharmazeutische Biologie, Semmelweisstraße 10, DE-07743 Jena, Germany, Division of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, SE-171 65 Solna, Sweden, Garvan Institute of Medical Research, 384 Victoria St Darlinghurst, NSW 2010, Australia, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, PO Box 596, S-75124 Uppsala, Sweden and Science for Life Laboratory, SE-75124 Uppsala, Sweden
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Durdevic Z, Schaefer M. Dnmt2 methyltransferases and immunity: An ancient overlooked connection between nucleotide modification and host defense? Bioessays 2013; 35:1044-9. [DOI: 10.1002/bies.201300088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Zeljko Durdevic
- Division of Epigenetics; DKFZ-ZMBH Alliance, German Cancer Research Center; Heidelberg Germany
| | - Matthias Schaefer
- Division of Epigenetics; DKFZ-ZMBH Alliance, German Cancer Research Center; Heidelberg Germany
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30
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Müller S, Windhof IM, Maximov V, Jurkowski T, Jeltsch A, Förstner KU, Sharma CM, Gräf R, Nellen W. Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homologue (DnmA). Nucleic Acids Res 2013; 41:8615-27. [PMID: 23877245 PMCID: PMC3794594 DOI: 10.1093/nar/gkt634] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Although the DNA methyltransferase 2 family is highly conserved during evolution and recent reports suggested a dual specificity with stronger activity on transfer RNA (tRNA) than DNA substrates, the biological function is still obscure. We show that the Dictyostelium discoideum Dnmt2-homologue DnmA is an active tRNA methyltransferase that modifies C38 in tRNAAsp(GUC)in vitro and in vivo. By an ultraviolet-crosslinking and immunoprecipitation approach, we identified further DnmA targets. This revealed specific tRNA fragments bound by the enzyme and identified tRNAGlu(CUC/UUC) and tRNAGly(GCC) as new but weaker substrates for both human Dnmt2 and DnmA in vitro but apparently not in vivo. Dnmt2 enzymes form transient covalent complexes with their substrates. The dynamics of complex formation and complex resolution reflect methylation efficiency in vitro. Quantitative PCR analyses revealed alterations in dnmA expression during development, cell cycle and in response to temperature stress. However, dnmA expression only partially correlated with tRNA methylation in vivo. Strikingly, dnmA expression in the laboratory strain AX2 was significantly lower than in the NC4 parent strain. As expression levels and binding of DnmA to a target in vivo are apparently not necessarily accompanied by methylation, we propose an additional biological function of DnmA apart from methylation.
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Affiliation(s)
- Sara Müller
- Department of Genetics, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany, Institute of Biochemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany, Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Str. 2/Bau D15, 97080 Würzburg and Universität Potsdam, Institut für Biochemie und Biologie, Abt. Zellbiologie, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam - Golm
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31
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Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes. BMC Genomics 2013; 14:462. [PMID: 23837670 PMCID: PMC3710501 DOI: 10.1186/1471-2164-14-462] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 07/03/2013] [Indexed: 12/22/2022] Open
Abstract
Background The phylum Platyhelminthes (flatworms) contains an important group of bilaterian organisms responsible for many debilitating and chronic infectious diseases of human and animal populations inhabiting the planet today. In addition to their biomedical and veterinary relevance, some platyhelminths are also frequently used models for understanding tissue regeneration and stem cell biology. Therefore, the molecular (genetic and epigenetic) characteristics that underlie trophic specialism, pathogenicity or developmental maturation are likely to be pivotal in our continued studies of this important metazoan group. Indeed, in contrast to earlier studies that failed to detect evidence of cytosine or adenine methylation in parasitic flatworm taxa, our laboratory has recently defined a critical role for cytosine methylation in Schistosoma mansoni oviposition, egg maturation and ovarian development. Thus, in order to identify whether this epigenetic modification features in other platyhelminth species or is a novelty of S. mansoni, we conducted a study simultaneously surveying for DNA methylation machinery components and DNA methylation marks throughout the phylum using both parasitic and non-parasitic representatives. Results Firstly, using both S. mansoni DNA methyltransferase 2 (SmDNMT2) and methyl-CpG binding domain protein (SmMBD) as query sequences, we illustrate that essential DNA methylation machinery components are well conserved throughout the phylum. Secondly, using both molecular (methylation specific amplification polymorphism, MSAP) and immunological (enzyme-linked immunoabsorbent assay, ELISA) methodologies, we demonstrate that representative species (Echinococcus multilocularis, Protopolystoma xenopodis, Schistosoma haematobium, Schistosoma japonicum, Fasciola hepatica and Polycelis nigra) within all four platyhelminth classes (Cestoda, Monogenea, Trematoda and ‘Turbellaria’) contain methylated cytosines within their genome compartments. Conclusions Collectively, these findings provide the first direct evidence for a functionally conserved and enzymatically active DNA methylation system throughout the Platyhelminthes. Defining how this epigenetic feature shapes phenotypic diversity and development within the phylum represents an exciting new area of metazoan biology.
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Wiegand S, Hammann C. The 5' spreading of small RNAs in Dictyostelium discoideum depends on the RNA-dependent RNA polymerase RrpC and on the dicer-related nuclease DrnB. PLoS One 2013; 8:e64804. [PMID: 23724097 PMCID: PMC3661229 DOI: 10.1371/journal.pone.0064804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/16/2013] [Indexed: 11/19/2022] Open
Abstract
RNA interference (RNAi) is a gene-regulatory mechanism in eukarya that is based on the presence of double stranded RNA and that can act on both, the transcription or post-transcriptional level. In many species, RNA-dependent RNA polymerases (RdRPs) are required for RNAi. To study the function of the three RdRPs in the amoeba Dictyostelium discoideum, we have deleted the encoding genes rrpA, rrpB and rrpC in all possible combinations. In these strains, expression of either antisense or hairpin RNA constructs against the transgene lacZ resulted in a 50% reduced β-Galactosidase activity. Northern blots surprisingly revealed unchanged lacZ mRNA levels, indicative of post-transcriptional regulation. Only in rrpC knock out strains, low levels of β-gal small interfering RNAs (siRNAs) could be detected in antisense RNA expressing strains. In contrast to this, and at considerably higher levels, all hairpin RNA expressing strains featured β-gal siRNAs. Spreading of the silencing signal to mRNA sequences 5′ of the original hairpin trigger was observed in all strains, except when the rrpC gene or that of the dicer-related nuclease DrnB was deleted. Thus, our data indicate that transitivity of an RNA silencing signal exists in D. discoideum and that it requires the two enzymes RrpC and DrnB.
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Affiliation(s)
- Stephan Wiegand
- Ribogenetics@Biochemistry Lab, School of Engineering and Science, MOLIFE Research Center, Jacobs University Bremen, Bremen, Germany
| | - Christian Hammann
- Ribogenetics@Biochemistry Lab, School of Engineering and Science, MOLIFE Research Center, Jacobs University Bremen, Bremen, Germany
- * E-mail:
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Sibbritt T, Patel HR, Preiss T. Mapping and significance of the mRNA methylome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:397-422. [PMID: 23681756 DOI: 10.1002/wrna.1166] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 12/25/2022]
Abstract
Internal methylation of eukaryotic mRNAs in the form of N6-methyladenosine (m(6)A) and 5-methylcytidine (m(5)C) has long been known to exist, but progress in understanding its role was hampered by difficulties in identifying individual sites. This was recently overcome by high-throughput sequencing-based methods that mapped thousands of sites for both modifications throughout mammalian transcriptomes, with most sites found in mRNAs. The topology of m(6)A in mouse and human revealed both conserved and variable sites as well as plasticity in response to extracellular cues. Within mRNAs, m(5)C and m(6)A sites were relatively depleted in coding sequences and enriched in untranslated regions, suggesting functional interactions with post-transcriptional gene control. Finer distribution analyses and preexisting literature point toward roles in the regulation of mRNA splicing, translation, or decay, through an interplay with RNA-binding proteins and microRNAs. The methyltransferase (MTase) METTL3 'writes' m(6)A marks on mRNA, whereas the demethylase FTO can 'erase' them. The RNA:m(5)C MTases NSUN2 and TRDMT1 have roles in tRNA methylation but they also act on mRNA. Proper functioning of these enzymes is important in development and there are clear links to human disease. For instance, a common variant of FTO is a risk allele for obesity carried by 1 billion people worldwide and mutations cause a lethal syndrome with growth retardation and brain deficits. NSUN2 is linked to cancer and stem cell biology and mutations cause intellectual disability. In this review, we summarize the advances, open questions, and intriguing possibilities in this emerging field that might be called RNA modomics or epitranscriptomics.
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Affiliation(s)
- Tennille Sibbritt
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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Becker M, Müller S, Nellen W, Jurkowski TP, Jeltsch A, Ehrenhofer-Murray AE. Pmt1, a Dnmt2 homolog in Schizosaccharomyces pombe, mediates tRNA methylation in response to nutrient signaling. Nucleic Acids Res 2012; 40:11648-58. [PMID: 23074192 PMCID: PMC3526270 DOI: 10.1093/nar/gks956] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe carries a cytosine 5-methyltransferase homolog of the Dnmt2 family (termed pombe methyltransferase 1, Pmt1), but contains no detectable DNA methylation. Here, we found that Pmt1, like other Dnmt2 homologs, has in vitro methylation activity on cytosine 38 of tRNAAsp and, to a lesser extent, of tRNAGlu, despite the fact that it contains a non-consensus residue in catalytic motif IV as compared with its homologs. In vivo tRNA methylation also required Pmt1. Unexpectedly, however, its in vivo activity showed a strong dependence on the nutritional status of the cell because Pmt1-dependent tRNA methylation was induced in cells grown in the presence of peptone or with glutamate as a nitrogen source. Furthermore, this induction required the serine/threonine kinase Sck2, but not the kinases Sck1, Pka1 or Tor1 and was independent of glucose signaling. Taken together, this work reveals a novel connection between nutrient signaling and tRNA methylation that thus may link tRNA methylation to processes downstream of nutrient signaling like ribosome biogenesis and translation initiation.
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Affiliation(s)
- Maria Becker
- Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, 45117 Essen, Germany
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Avesson L, Reimegård J, Wagner EGH, Söderbom F. MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs. RNA (NEW YORK, N.Y.) 2012; 18:1771-1782. [PMID: 22875808 PMCID: PMC3446702 DOI: 10.1261/rna.033175.112] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/11/2012] [Indexed: 06/01/2023]
Abstract
The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs.
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Affiliation(s)
- Lotta Avesson
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, S-75124 Uppsala, Sweden
| | - Johan Reimegård
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, S-75124 Uppsala, Sweden
| | - E. Gerhart H. Wagner
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, S-75124 Uppsala, Sweden
- Science for Life Laboratory, SE-75124 Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, S-75124 Uppsala, Sweden
- Science for Life Laboratory, SE-75124 Uppsala, Sweden
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36
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Schulz EC, Roth HM, Ankri S, Ficner R. Structure analysis of Entamoeba histolytica DNMT2 (EhMeth). PLoS One 2012; 7:e38728. [PMID: 22737219 PMCID: PMC3380923 DOI: 10.1371/journal.pone.0038728] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/14/2012] [Indexed: 11/25/2022] Open
Abstract
In eukaryotes, DNA methylation is an important epigenetic modification that is generally involved in gene regulation. Methyltransferases (MTases) of the DNMT2 family have been shown to have a dual substrate specificity acting on DNA as well as on three specific tRNAs (tRNAAsp, tRNAVal, tRNAGly). Entamoeba histolytica is a major human pathogen, and expresses a single DNA MTase (EhMeth) that belongs to the DNMT2 family and shows high homology to the human enzyme as well as to the bacterial DNA MTase M.HhaI. The molecular basis for the recognition of the substrate tRNAs and discrimination of non-cognate tRNAs is unknown. Here we present the crystal structure of the cytosine-5-methyltransferase EhMeth at a resolution of 2.15 Å, in complex with its reaction product S-adenosyl-L-homocysteine, revealing all parts of a DNMT2 MTase, including the active site loop. Mobility shift assays show that in vitro the full length tRNA is required for stable complex formation with EhMeth.
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Affiliation(s)
- Eike C. Schulz
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Heide M. Roth
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Serge Ankri
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
- * E-mail:
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37
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Jurkowski TP, Shanmugam R, Helm M, Jeltsch A. Mapping the tRNA Binding Site on the Surface of Human DNMT2 Methyltransferase. Biochemistry 2012; 51:4438-44. [DOI: 10.1021/bi3002659] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Tomasz P. Jurkowski
- Biochemistry Laboratory, School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany, and Institute of Biochemistry,
Faculty of Chemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Raghuvaran Shanmugam
- Biochemistry Laboratory, School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany, and Institute of Biochemistry,
Faculty of Chemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, Staudinger
Weg 5, 55128 Mainz, Germany
| | - Albert Jeltsch
- Biochemistry Laboratory, School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany, and Institute of Biochemistry,
Faculty of Chemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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38
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Hsu DW, Chubb JR, Muramoto T, Pears CJ, Mahadevan LC. Dynamic acetylation of lysine-4-trimethylated histone H3 and H3 variant biology in a simple multicellular eukaryote. Nucleic Acids Res 2012; 40:7247-56. [PMID: 22600736 PMCID: PMC3424546 DOI: 10.1093/nar/gks367] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Dynamic acetylation of all lysine-4-trimethylated histone H3 is a complex phenomenon involved in Immediate-early gene induction in metazoan eukaryotes. Higher eukaryotes express repeated copies of three closely related H3 variants, inaccessible to genetic analysis. We demonstrate conservation of these phenomena in Dictyostelium which has three single-copy H3 variant genes. Although dynamic acetylation is targeted to two H3 variants which are K4-trimethylated, K9-acetylation is preferentially targeted to one. In cells lacking Set1 methyltransferase and any detectable K4-trimethylation, dynamic acetylation is lost demonstrating a direct link between the two. Gene replacement to express mutated H3 variants reveals a novel interaction between K4-trimethylation on different variants. Cells expressing only one variant show defects in growth, and in induction of a UV-inducible gene, demonstrating the functional importance of variant expression. These studies confirm that dynamic acetylation targeted to H3K4me3 arose early in evolution and reveal a very high level of specificity of histone variant utilization in a simple multicellular eukaryote.
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Affiliation(s)
- Duen-Wei Hsu
- Nuclear Signalling Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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39
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Squires JE, Preiss T. Function and detection of 5-methylcytosine in eukaryotic RNA. Epigenomics 2012; 2:709-15. [PMID: 22122054 DOI: 10.2217/epi.10.47] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Modified nucleosides play an important role in RNA function and have been identified in multiple RNA types, including tRNAs, rRNAs, mRNAs and small regulatory RNAs. Among these, 5-methylcytosine (m(5)C) has been detected in rRNAs and tRNAs, and early reports suggested its presence in mRNAs. Known and well studied as an epigenetic mark in DNA, the prevalence and function of m(5)C in RNA is either incompletely explored (i.e., in tRNA and rRNA) or virtually unknown (i.e., in mRNA and other noncoding RNA). Two eukaryotic methyltransferases have been demonstrated to place m(5)C in RNA; however, their substrate specificity and cellular functions are not completely understood. With the recent development of m(5)C detection in RNA by bisulfite sequencing, comprehensive analyses to determine its occurrence and biological roles are now feasible. In this article we review the occurrence, function and biochemical detection of m(5)C in eukaryotic RNA, and provide perspectives on the biological roles of this modification in the transcriptome.
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Affiliation(s)
- Jeffrey E Squires
- Victor Chang Cardiac Research Institute, Molecular Genetics Division, Darlinghurst, NSW 2010, Australia
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40
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Jurkowski TP, Jeltsch A. On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2. PLoS One 2011; 6:e28104. [PMID: 22140515 PMCID: PMC3227630 DOI: 10.1371/journal.pone.0028104] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 11/01/2011] [Indexed: 12/19/2022] Open
Abstract
The Dnmt2 enzymes show strong amino acid sequence similarity with eukaryotic and prokaryotic DNA-(cytosine C5)-methyltransferases. Yet, Dnmt2 enzymes from several species were shown to methylate tRNA-Asp and had been proposed that eukaryotic DNA methyltransferases evolved from a Dnmt2-like tRNA methyltransferase ancestor [Goll et al., 2006, Science, 311, 395-8]. It was the aim of this study to investigate if this hypothesis could be supported by evidence from sequence alignments. We present phylogenetic analyses based on sequence alignments of the methyltransferase catalytic domains of more than 2300 eukaryotic and prokaryotic DNA-(cytosine C5)-methyltransferases and analyzed the distribution of DNA methyltransferases in eukaryotic species. The Dnmt2 homologues were reliably identified by an additional conserved CFT motif next to motif IX. All DNA methyltransferases and Dnmt2 enzymes were clearly separated from other RNA-(cytosine-C5)-methyltransferases. Our sequence alignments and phylogenetic analyses indicate that the last universal eukaryotic ancestor contained at least one member of the Dnmt1, Dnmt2 and Dnmt3 families of enzymes and additional RNA methyltransferases. The similarity of Dnmt2 enzymes with DNA methyltransferases and absence of similarity with RNA methyltransferases combined with their strong RNA methylation activity suggest that the ancestor of Dnmt2 was a DNA methyltransferase and an early Dnmt2 enzyme changed its substrate preference to tRNA. There is no phylogenetic evidence that Dnmt2 was the precursor of eukaryotic Dnmts. Most likely, the eukaryotic Dnmt1 and Dnmt3 families of DNA methyltransferases had an independent origin in the prokaryotic DNA methyltransferase sequence space.
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Affiliation(s)
- Tomasz P. Jurkowski
- School of Engineering and Science, Jacobs University Bremen, Campus Ring Bremen, Germany
| | - Albert Jeltsch
- School of Engineering and Science, Jacobs University Bremen, Campus Ring Bremen, Germany
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41
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Stevense M, Chubb JR, Muramoto T. Nuclear organization and transcriptional dynamics in Dictyostelium. Dev Growth Differ 2011; 53:576-86. [PMID: 21585360 DOI: 10.1111/j.1440-169x.2011.01271.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Dictyostelium model has a set of features uniquely well-suited to developing our understanding of transcriptional control. The complete Dictyostelium discoideum genome sequence has revealed that many of the molecular components regulating transcription in larger eukaryotes are conserved in Dictyostelium, from transcription factors and chromatin components to the enzymes and signals that regulate them. In addition, the system permits visualization of single gene firing events in living cells, which provides a more detailed view of transcription and its relationships to cell and developmental processes. This review will bring together the available knowledge of the structure and dynamics of the Dictyostelium nucleus and discuss recent transcription imaging studies and their implications for stability and accuracy of cell decisions.
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Affiliation(s)
- Michelle Stevense
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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42
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Goll MG, Halpern ME. DNA methylation in zebrafish. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:193-218. [PMID: 21507352 DOI: 10.1016/b978-0-12-387685-0.00005-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA methylation is crucial for normal development and cellular differentiation in many large-genome eukaryotes. The small tropical freshwater fish Danio rerio (zebrafish) has recently emerged as a powerful system for the study of DNA methylation, especially in the context of development. This review summarizes our current knowledge of DNA methylation in zebrafish and provides evidence for the general conservation of this system with mammals. In addition, emerging strategies are highlighted that use the fish model to address some of the key unanswered questions in DNA methylation research.
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Affiliation(s)
- Mary G Goll
- Developmental Biology Program, Sloan-Kettering Institute, New York, USA
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43
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Cytosine methylation regulates oviposition in the pathogenic blood fluke Schistosoma mansoni. Nat Commun 2011; 2:424. [PMID: 21829186 PMCID: PMC3265374 DOI: 10.1038/ncomms1433] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Accepted: 07/13/2011] [Indexed: 12/31/2022] Open
Abstract
Similar to other metazoan pathogens, Schistosoma mansoni undergoes transcriptional and developmental regulation during its complex lifecycle and host interactions. DNA methylation as a mechanism to control these processes has, to date, been discounted in this parasite. Here we show the first evidence for cytosine methylation in the S. mansoni genome. Transcriptional coregulation of novel DNA methyltransferase (SmDnmt2) and methyl-CpG-binding domain proteins mirrors the detection of cytosine methylation abundance and implicates the presence of a functional DNA methylation machinery. Genome losses in cytosine methylation upon SmDnmt2 silencing and the identification of a hypermethylated, repetitive intron within a predicted forkhead gene confirm this assertion. Importantly, disruption of egg production and egg maturation by 5-azacytidine establishes an essential role for 5-methylcytosine in this parasite. These findings provide the first functional confirmation for this epigenetic modification in any worm species and link the cytosine methylation machinery to platyhelminth oviposition processes. The chronic disease schistosomiasis is caused by the blood fluke Schistosoma mansoni. By studying DNA modifications throughout the lifecycle of the pathogen, the authors identify DNA methylation as a factor in egg development and suggest that the epigenetic machinery responsible may be a therapeutic target.
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44
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Tovy A, Ankri S. Epigenetics in the unicellular parasite Entamoeba histolytica. Future Microbiol 2011; 5:1875-84. [PMID: 21198420 DOI: 10.2217/fmb.10.140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amoebiasis is a serious infectious disease that is caused by the unicellular parasite, Entamoeba histolytica. This parasite is mainly found in developing countries, and are named owing to its ability to destroy tissues. The molecular mechanisms that regulate the virulence of this parasite are not well understood. In recent years, an increasing interest in the epigenetic regulation of the parasite's virulence has emerged. In this article, an overview of our current knowledge about the role of DNA methylation, histone modifications and RNA-associated silencing in the biology of E. histolytica is provided. The relevance of some features of the parasite's unique epigenetic machinery to the development of new antiamoebic therapeutic molecules is discussed.
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Affiliation(s)
- Ayala Tovy
- Department of Microbiology, Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology & the Rappaport Institute, Haifa, Israel
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45
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Boesler C, Kruse J, Söderbom F, Hammann C. Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum. J Biol Chem 2011; 286:17693-703. [PMID: 21454536 DOI: 10.1074/jbc.m110.208306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The amoeba Dictyostelium discoideum is a well established model organism for studying numerous aspects of cellular and developmental functions. Its ribosomal RNA (rRNA) is encoded in an extrachromosomal palindrome that exists in ∼100 copies in the cell. In this study, we have set out to investigate the sequence of the expressed rRNA. For this, we have ligated the rRNA ends and performed RT-PCR on these circular RNAs. Sequencing revealed that the mature 26 S, 17 S, 5.8 S, and 5 S rRNAs have sizes of 3741, 1871, 162, and 112 nucleotides, respectively. Unlike the published data, all mature rRNAs of the same type uniformly display the same start and end nucleotides in the analyzed AX2 strain. We show the existence of a short lived primary transcript covering the rRNA transcription unit of 17 S, 5.8 S, and 26 S rRNA. Northern blots and RT-PCR reveal that from this primary transcript two precursor molecules of the 17 S and two precursors of the 26 S rRNA are generated. We have also determined the sequences of these precursor molecules, and based on these data, we propose a model for the maturation of the rRNAs in Dictyostelium discoideum that we compare with the processing of the rRNA transcription unit of Saccharomyces cerevisiae.
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Affiliation(s)
- Carsten Boesler
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, 64287 Darmstadt, Germany
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46
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Wiegand S, Kruse J, Gronemann S, Hammann C. Efficient generation of gene knockout plasmids for Dictyostelium discoideum using one-step cloning. Genomics 2011; 97:321-5. [PMID: 21316445 DOI: 10.1016/j.ygeno.2011.02.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/03/2011] [Indexed: 11/18/2022]
Abstract
The amoeba Dictyostelium discoideum is a well-established model organism for studying numerous aspects of cellular and developmental functions. Its rather small (~34Mb) chromosomal genome and the high efficiency of gene disruption by homologous recombination have enabled researchers to dissect various specific gene functions. We describe here the use of one-step cloning for the fast and efficient generation of deletion vectors that are produced in a one-step reaction by inserting two PCR products into an organism-specific, generic acceptor system. This worked efficiently for all 16 tested constructs directed against genes in the amoeba Dictyostelium discoideum. Saving cost and time, the used protocol represents a significant advancement in the generation of such plasmids compared to the conventionally applied restriction enzyme/ligation approach. Using appropriate selection markers, similar systems could also be useful in other organisms, where genes can be knocked out by homologous recombination.
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Affiliation(s)
- Stephan Wiegand
- Department for Microbiology and Genetics, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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47
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Krauss V, Reuter G. DNA methylation in Drosophila--a critical evaluation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:177-91. [PMID: 21507351 DOI: 10.1016/b978-0-12-387685-0.00003-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Drosophila belongs to the so-called "Dnmt2 only" organisms, and does not contain any of the canonical DNA methyltransferases (Dnmt1 and Dnmt3). Furthermore, no functional homologs of known 5-methylcytosine reader proteins are found. Nevertheless, there is strong evidence for DNA methylation in this organism. It has been suggested that DNA methylation in Drosophila is simply a byproduct of Dnmt2, which is a DNA methyltransferase (Dnmt) according to structure and type of catalysis but functions in vivo as a tRNA methyltransferase. However, concerning the very specific timing of cytosine methylation in Drosophila, their suggested functions in control of retrotransposon silencing and genome stability, and the obvious DNA methylation activity of Dnmt2 enzymes in the protozoans Dictyostelium discoideum and Entamoeba histolytica, we tend to disagree with this notation. Dnmt2 probably serves, and not only in Drosophila, as a methyltransferase of both specific DNA and tRNA targets.
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Affiliation(s)
- Veiko Krauss
- Developmental Genetics, Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg, Halle/S, Germany
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48
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Natural history of eukaryotic DNA methylation systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:25-104. [PMID: 21507349 DOI: 10.1016/b978-0-12-387685-0.00002-0] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methylation of cytosines and adenines in DNA is a widespread epigenetic mark in both prokaryotes and eukaryotes. In eukaryotes, it has a profound influence on chromatin structure and dynamics. Recent advances in genomics and biochemistry have considerably elucidated the functions and provenance of these DNA modifications. DNA methylases appear to have emerged first in bacterial restriction-modification (R-M) systems from ancient RNA-modifying enzymes, in transitions that involved acquisition of novel catalytic residues and DNA-recognition features. DNA adenine methylases appear to have been acquired by ciliates, heterolobosean amoeboflagellates, and certain chlorophyte algae. Six distinct clades of cytosine methylases, including the DNMT1, DNMT2, and DNMT3 clades, were acquired by eukaryotes through independent lateral transfer of their precursors from bacteria or bacteriophages. In addition to these, multiple adenine and cytosine methylases were acquired by several families of eukaryotic transposons. In eukaryotes, the DNA-methylase module was often combined with distinct modified and unmodified peptide recognition domains and other modules mediating specialized interactions, for example, the RFD module of DNMT1 which contains a permuted Sm domain linked to a helix-turn-helix domain. In eukaryotes, the evolution of DNA methylases appears to have proceeded in parallel to the elaboration of histone-modifying enzymes and the RNAi system, with functions related to counter-viral and counter-transposon defense, and regulation of DNA repair and differential gene expression being their primary ancestral functions. Diverse DNA demethylation systems that utilize base-excision repair via DNA glycosylases and cytosine deaminases appear to have emerged in multiple eukaryotic lineages. Comparative genomics suggests that the link between cytosine methylation and DNA glycosylases probably emerged first in a novel R-M system in bacteria. Recent studies suggest that the 5mC is not a terminal DNA modification, with enzymes of the Tet/JBP family of 2-oxoglutarate- and iron-dependent dioxygenases further hydroxylating it to form 5-hydroxymethylcytosine (5hmC). These enzymes emerged first in bacteriophages and appear to have been transferred to eukaryotes on one or more occasions. Eukaryotes appear to have recruited three major types of DNA-binding domains (SRA/SAD, TAM/MBD, and CXXC) in discriminating DNA with methylated or unmethylated cytosines. Analysis of the domain architectures of these domains and the DNA methylases suggests that early in eukaryotic evolution they developed a close functional link with SET-domain methylases and Jumonji-related demethylases that operate on peptides in chromatin proteins. In several eukaryotes, other functional connections were elaborated in the form of various combinations between domains related to DNA methylation and those involved in ATP-dependent chromatin remodeling and RNAi. In certain eukaryotes, such as mammals and angiosperms, novel dependencies on the DNA methylation system emerged, which resulted in it affecting unexpected aspects of the biology of these organisms such as parent-offspring interactions. In genomic terms, this was reflected in the emergence of new proteins related to methylation, such as Stella. The well-developed methylation systems of certain heteroloboseans, stramenopiles, chlorophytes, and haptophyte indicate that these might be new model systems to explore the relevance of DNA modifications in eukaryotes.
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Lack of evidence for DNA methylation of Invader4 retroelements in Drosophila and implications for Dnmt2-mediated epigenetic regulation. Nat Genet 2010; 42:920-1; author reply 921. [PMID: 20980983 DOI: 10.1038/ng1110-920] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Tovy A, Hofmann B, Helm M, Ankri S. In vitro tRNA methylation assay with the Entamoeba histolytica DNA and tRNA methyltransferase Dnmt2 (Ehmeth) enzyme. J Vis Exp 2010:2390. [PMID: 21048666 DOI: 10.3791/2390] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Protozoan parasites are among the most devastating infectious agents of humans responsible for a variety of diseases including amebiasis, which is one of the three most common causes of death from parasitic disease. The agent of amebiasis is the amoeba parasite Entamoeba histolytica that exists under two stages: the infective cyst found in food or water and the invasive trophozoite living in the intestine. The clinical manifestations of amebiasis range from being asymptomatic to colitis, dysentery or liver abscesses. E. histolytica is one of the rare unicellular parasite with 5-methylcytosine (5mC) in its genome. It contains a single DNA methyltransferase, Ehmeth, that belongs to the Dnmt2 family. A role for Dnmt2 in the control of repetitive elements has been established in E. histolytica, Dictyostelium discoideum and Drosophila. Our recent work has shown that Ehmeth methylates tRNA(Asp), and this finding indicates that this enzyme has a dual DNA/tRNA(Asp) methyltransferase activity. This observation is in agreement with the dual activity that has been reported for D. discoideum and D. melanogaster. The functional significance of the DNA/tRNA specificity of Dnmt2 enzymes is still unknown. To address this question, a method to determine the tRNA methyltransferase activity of Dnmt2 proteins was established. In this video, we describe a straightforward approach to prepare an adequate tRNA substrate for Dnmt2 and a method to measure its tRNA methyltransferase activity.
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Affiliation(s)
- Ayala Tovy
- Faculty of Medicine, Rappaport Institute, Technion - Israel Institute of Technology
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