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Yen YH, Zheng DY, Yang SY, Gwo JC, Fugmann SD. The cytokine genes of Oncorhynchus masou formosanus include a defective interleukin-4/13A gene. Dev Comp Immunol 2024; 155:105156. [PMID: 38423493 DOI: 10.1016/j.dci.2024.105156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Oncorhynchus masou formosanus (Formosa landlocked salmon) is a critically endangered salmonid fish endemic to Taiwan. To begin to understand how its drastic change in lifestyle from anadromous to exclusively river-dwelling is reflected in its immune genes, we characterized the genes encoding six cytokines (IL-2A, IL-2B, IL-4/13A, IL-4/13B1, IL-4/13B2, and IL-17A/F2a) important for T cell responses as no genomic data is available for this fish. Interestingly, all genes appeared homozygous indicative of a genetic bottleneck. The IL2 and IL17A/F2a genes and their products are highly similar to their characterized homologs in Oncorhynchus mykiss (rainbow trout) and other salmonid fish. Two notable differences were observed in IL4/13 family important for type 2 immune responses. First, O. m. formosanus carries not only one but two genes encoding IL-4/13B1 proteins and expansions of these genes are present in other salmonid fish. Second, the OmfoIL4/13A gene carries a 228 bp deletion that results in a premature stop codon and hence a non-functional IL-4/13A cytokine. This suggests a reduced ability for T cell responses against parasitic infections in this species.
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Affiliation(s)
- Ying-Hsuan Yen
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - De Yu Zheng
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Shu Yuan Yang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Jin-Chywan Gwo
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Sebastian D Fugmann
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Department of Nephrology, Chang Gung Memorial Hospital, Linkou, Taiwan; Center of Molecular and Clinical Immunology, Chang Gung University, Taiwan.
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2
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Hsueh SW, Jian YH, Fugmann SD, Yang SY. Polystyrene-colonizing bacteria are enriched for long-chain alkane degradation pathways. PLoS One 2023; 18:e0292137. [PMID: 37788234 PMCID: PMC10547174 DOI: 10.1371/journal.pone.0292137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/13/2023] [Indexed: 10/05/2023] Open
Abstract
One of the most promising strategies for the management of plastic waste is microbial biodegradation, but efficient degraders for many types of plastics are still lacking, including those for polystyrene (PS). Genomics has emerged as a powerful tool for mining environmental microbes that may have the ability to degrade different types of plastics. In this study, we use 16S rRNA sequencing to analyze the microbiomes for multiple PS samples collected from sites with different vegetation in Taiwan to reveal potential common properties between species that exhibit growth advantages on PS surfaces. Phylum enrichment analysis identified Cyanobacteria and Deinococcus-Thermus as being the most over-represented groups on PS, and both phyla include species known to reside in extreme environments and could encode unique enzymes that grant them properties suitable for colonization on PS surfaces. Investigation of functional enrichment using reference genomes of PS-enriched species highlighted carbon metabolic pathways, especially those related to hydrocarbon degradation. This is corroborated by the finding that genes encoding long-chain alkane hydroxylases such as AlmA are more prevalent in the genomes of PS-associated bacteria. Our analyses illustrate how plastic in the environment support the colonization by different microbes compared to surrounding soil. In addition, our results point to the possibility that alkane hydroxylases could confer growth advantages of microbes on PS.
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Affiliation(s)
- Shu Wei Hsueh
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - You-Hua Jian
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Sebastian D. Fugmann
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Nephrology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Shu Yuan Yang
- Department and Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
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3
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Chou ST, Lin TM, Yang HY, Fugmann SD. Functional characterization of the MyD88 homologs in Strongylocentrotus purpuratus. Dev Comp Immunol 2023; 139:104580. [PMID: 36306972 DOI: 10.1016/j.dci.2022.104580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Toll-like receptor signaling is an evolutionarily conserved pathway to induce the expression of immune mediators in response to encounters with pathogens. MyD88 is a central adapter connecting the intracellular domain of the receptors to downstream kinases. Here, we conducted a comprehensive assessment of the MyD88 family in an echinoderm, Strongylocentrotus purpuratus. Of five SpMyD88s only two closely related proteins, SpMyD88A and SpMyD88B, are functional in mammalian cell lines as their overexpression facilitates the activation of the downstream transcription factor NF-κB. This requires the presence of the endogenous mammalian MyD88s, and domain swapping indicated that the death domains of S. purpuratus MyD88 are unable to efficiently connect to the respective domains of the vertebrate IRAK kinases. This suggests that the interaction surfaces between the signaling mediators in this conserved signaling pathway are not as conserved as previously thought but were likely shaped and evolved by pathogenic selection over evolutionary timescales.
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Affiliation(s)
- Shu-Ting Chou
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Tse-Mao Lin
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Huang-Yu Yang
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Department of Nephrology, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Sebastian D Fugmann
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan; Center of Molecular and Clinical Immunology, Chang Gung University, Taiwan; Department of Nephrology, Chang Gung Memorial Hospital, Linkou, Taiwan.
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4
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Liu MC, Fugmann SD. Measuring Mutator Enzyme Activity Using an E. coli-Based Colony Formation Assay. Methods Mol Biol 2022; 2421:103-114. [PMID: 34870814 DOI: 10.1007/978-1-0716-1944-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mutator enzymes alter the nucleotide sequences of DNA or RNA molecules; immune systems utilize them to destroy the integrity of pathogen genomes and to optimize immune mediators of the host. Their dysregulation has been linked to tumorigenesis in various tissues. Defining and comparing the activities of such mutator enzymes requires a robust versatile assay that is independent of their biological context as in vivo mutation rates are typically low. Here we provide detailed protocols for two widely used E. coli-based approaches that detect the activities of ectopically expressed cytidine deaminases on two distinct reporter genes: an extrachromosomal kanamycin-resistance gene or an endogenous chromosomal substrate, the rpoB gene-encoding RNA polymerase. The generation of mutations is in both cases measured in a colony formation assay. With appropriate modifications, these assays can be extended to study other mutator enzymes.
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Affiliation(s)
- Mei-Chen Liu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sebastian D Fugmann
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
- Center for Molecular and Clinical Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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5
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Li YR, Lai HW, Huang HH, Chen HC, Fugmann SD, Yang SY. Trajectory mapping of the early Drosophila germline reveals controls of zygotic activation and sex differentiation. Genome Res 2021; 31:1011-1023. [PMID: 33858841 PMCID: PMC8168578 DOI: 10.1101/gr.271148.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/07/2021] [Indexed: 01/29/2023]
Abstract
Germ cells in Drosophila melanogaster are specified maternally shortly after fertilization and are transcriptionally quiescent until their zygotic genome is activated to sustain further development. To understand the molecular basis of this process, we analyzed the progressing transcriptomes of early male and female germ cells at the single-cell level between germline specification and coalescence with somatic gonadal cells. Our data comprehensively cover zygotic activation in the germline genome, and analyses on genes that exhibit germline-restricted expression reveal that polymerase pausing and differential RNA stability are important mechanisms that establish gene expression differences between the germline and soma. In addition, we observe an immediate bifurcation between the male and female germ cells as zygotic transcription begins. The main difference between the two sexes is an elevation in X Chromosome expression in females relative to males, signifying incomplete dosage compensation, with a few select genes exhibiting even higher expression increases. These indicate that the male program is the default mode in the germline that is driven to female development with a second X Chromosome.
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Affiliation(s)
- Yi-Ru Li
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan
| | - Hsiao Wen Lai
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan
| | - Hsiao Han Huang
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan
| | - Hsing-Chun Chen
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan
| | - Sebastian D Fugmann
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan.,Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan.,Department of Nephrology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan 333 Taiwan
| | - Shu Yuan Yang
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan.,Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan.,Department of Gynecology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan 333 Taiwan
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6
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Fugmann SD, Cheng JF, Huang HH. Transcriptome analysis of distinct coelomocyte populations in Strongylocentrotus purpuratus. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.73.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Coelomocytes are important cellular mediators of immunity in echinoderms. In the purple sea urchin (Strongylocentrotus purpuratus) these cells can readily be divided into phagocytes, vibratile cells, red spherule cells, and colorless spherule cells based on their morphology. While some information has been reported about genes that are expressed in specific types of coelomocytes, a comprehensive analysis of the gene expression pattern in each cell type was not available. Using a density gradient coelomocytes from individual adult urchins were separated into three populations (phagocytes, a mixture of vibratile and colorless spherule cells, and red spherule cells), RNA was isolated, and next generation sequencing was employed to determine the transcriptome of each cell population. All three cell populations showed clear differences in their gene expression patterns, and the differences in transcript levels for selected genes that were found to be uniquely expressed in one cell type were confirmed by qRT-PCR using cDNA obtained from additional sea urchins. This bulk population data was then complemented by single-cell RNAseq to obtain information about suitable population and sub-population markers for subsequent studies of coelomocyte biology.
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7
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Liu MC, Liao WY, Buckley KM, Yang SY, Rast JP, Fugmann SD. AID/APOBEC-like cytidine deaminases are ancient innate immune mediators in invertebrates. Nat Commun 2018; 9:1948. [PMID: 29769532 PMCID: PMC5956068 DOI: 10.1038/s41467-018-04273-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/17/2018] [Indexed: 12/26/2022] Open
Abstract
In the course of both innate and adaptive immunity, cytidine deaminases within the activation induced cytidine deaminase (AID)/apolipoprotein B editing complex (APOBEC) family modulate immune responses by mutating specific nucleic acid sequences of hosts and pathogens. The evolutionary emergence of these mediators, however, seems to coincide precisely with the emergence of adaptive immunity in vertebrates. Here, we show a family of genes in species within two divergent invertebrate phyla-the echinoderm Strongylocentrotus purpuratus and the brachiopod Lingula anatina-that encode proteins with similarities in amino acid sequence and enzymatic activities to the vertebrate AID/APOBECs. The expression of these invertebrate factors is enriched in tissues undergoing constant, direct interactions with microbes and can be induced upon pathogen challenge. Our findings suggest that AID/APOBEC proteins, and their function in immunity, emerged far earlier than previously thought. Thus, cytidine deamination is probably an ancient innate immune mechanism that predates the protostome/deuterostome divergence.
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Affiliation(s)
- Mei-Chen Liu
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan District, Tao-Yuan, 333, Taiwan
| | - Wen-Yun Liao
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan District, Tao-Yuan, 333, Taiwan
| | - Katherine M Buckley
- Biological Sciences, Sunnybrook Research Institute, 2075 Bayview Ave., Toronto, ON, M4N 3M5, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, MG5 1LC, ON, Canada
- Department of Immunology, University of Toronto, Toronto, M5S 1A8, ON, Canada
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Shu Yuan Yang
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan District, Tao-Yuan, 333, Taiwan
- Division of Biochemistry, Molecular and Cellular Biology, Graduate Institute of Biomedical Sciences, Chang Gung University, Kwei-Shan District, Tao-Yuan, 333, Taiwan
- Department of Pathology, Chang Gung Memorial Hospital, Tao-Yuan, 333, Taiwan
| | - Jonathan P Rast
- Biological Sciences, Sunnybrook Research Institute, 2075 Bayview Ave., Toronto, ON, M4N 3M5, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, MG5 1LC, ON, Canada
- Department of Immunology, University of Toronto, Toronto, M5S 1A8, ON, Canada
- Pathology & Laboratory Medicine, Emory University School of Medicine, 1462 Clifton Road, Atlanta, GA, 30322, USA
| | - Sebastian D Fugmann
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan District, Tao-Yuan, 333, Taiwan.
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Kwei-Shan District, Tao-Yuan, 333, Taiwan.
- Chang Gung Immunology Consortium, Chang Gung Memorial Hospital and Chang Gung University, Kwei-Shan District, Tao-Yuan, 333, Taiwan.
- Department of General Surgery, Chang Gung Memorial Hospital, Tao-Yuan, 333, Taiwan.
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8
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Wang XR, Ling LB, Huang HH, Lin JJ, Fugmann SD, Yang SY. Evidence for parallel evolution of a gene involved in the regulation of spermatogenesis. Proc Biol Sci 2017; 284:rspb.2017.0324. [PMID: 28539513 DOI: 10.1098/rspb.2017.0324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/13/2017] [Indexed: 01/01/2023] Open
Abstract
PHD finger protein 7 (Phf7) is a male germline specific gene in Drosophila melanogaster that can trigger the male germline sexual fate and regulate spermatogenesis, and its human homologue can rescue fecundity defects in male flies lacking this gene. These findings prompted us to investigate conservation of reproductive strategies through studying the evolutionary origin of this gene. We find that Phf7 is present only in select species including mammals and some insects, whereas the closely related G2/M-phase specific E3 ubiquitin protein ligase (G2e3) is in the genome of most metazoans. Interestingly, phylogenetic analyses showed that vertebrate and insect Phf7 genes did not evolve from a common Phf7 ancestor but rather through independent duplication events from an ancestral G2e3 This is an example of parallel evolution in which a male germline factor evolved at least twice from a pre-existing template to develop new regulatory mechanisms of spermatogenesis.
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Affiliation(s)
- Xin Rui Wang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - Li Bin Ling
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - Hsiao Han Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - Jau Jyun Lin
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - Sebastian D Fugmann
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan.,Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, 333, Taiwan.,Department of General Surgery, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Shu Yuan Yang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan .,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan.,Department of Pathology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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9
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Carmona LM, Fugmann SD, Schatz DG. Collaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination. Genes Dev 2016; 30:909-17. [PMID: 27056670 PMCID: PMC4840297 DOI: 10.1101/gad.278432.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/09/2016] [Indexed: 12/03/2022]
Abstract
Here, Carmona et al. show that two ancestral RAG1 proteins, Transib transposase and purple sea urchin RAG1-like, have a latent ability to initiate V(D)J recombination when coexpressed with RAG2 and that in vitro transposition by Transib transposase is stimulated by RAG2. They propose that evolution of RAG1/RAG2 began with a Transib transposon whose intrinsic recombination activity was enhanced by capture of an ancestral RAG2, allowing for the development of adaptive immunity. The recombination-activating gene 1 (RAG1) and RAG2 proteins initiate V(D)J recombination, the process that assembles the B- and T-lymphocyte antigen receptor genes of jawed vertebrates. RAG1 and RAG2 are thought to have arisen from a transposable element, but the origins of this element are not understood. We show that two ancestral RAG1 proteins, Transib transposase and purple sea urchin RAG1-like, have a latent ability to initiate V(D)J recombination when coexpressed with RAG2 and that in vitro transposition by Transib transposase is stimulated by RAG2. Conversely, we report low levels of V(D)J recombination by RAG1 in the absence of RAG2. Recombination by RAG1 alone differs from canonical V(D)J recombination in having lost the requirement for asymmetric DNA substrates, implicating RAG2 in the origins of the “12/23 rule,” a fundamental regulatory feature of the reaction. We propose that evolution of RAG1/RAG2 began with a Transib transposon whose intrinsic recombination activity was enhanced by capture of an ancestral RAG2, allowing for the development of adaptive immunity.
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Affiliation(s)
- Lina Marcela Carmona
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
| | - Sebastian D Fugmann
- Department of Biomedical Sciences, Chang Gung University, Tao-Yuan City 33302, Taiwan; Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Chang Gung University, Tao-Yuan City 33302, Taiwan
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, 06520, USA; Howard Hughes Medical Institute, New Haven, Connecticut 06511, USA
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10
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Singh N, Ravichandran S, Spelman K, Fugmann SD, Moaddel R. The identification of a novel SIRT6 modulator from Trigonella foenum-graecum using ligand fishing with protein coated magnetic beads. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 968:105-11. [PMID: 24704183 DOI: 10.1016/j.jchromb.2014.03.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 03/06/2014] [Accepted: 03/09/2014] [Indexed: 10/25/2022]
Abstract
SIRT6 is a histone deacetylase that has been proposed as a potential therapeutic target for metabolic disorders and the prevention of age-associated diseases. Thus the identification of compounds that modulate SIRT6 activity could be of great therapeutic importance. We have previously developed an H3K9 deacetylation guided assay with SIRT6 coated magnetic beads (SIRT6-MB). With the developed assay, we identified quercetin, naringenin and vitexin as SIRT6 inhibitors from T. foenum-graecum seed extract using a candidate approach. Currently, the predominant method for the identification of active compounds from a plant extract is carried out through a dereplication process. A novel targeted approach for the direct identification of active compounds from a complex matrix could save time and resources. Herein, we report the application of the SIRT6-MB for 'fishing' experiments utilizing T. foenum-graecum seed extract. In which orientin, and seventeen other compounds were identified as SIRT6 binders. This is the first use of this method for 'fishing' out active ligands from a botanical matrix, and sets the basis for the identification of active compounds from a complex matrix.
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Affiliation(s)
- N Singh
- Biomedical Research Center, National institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA
| | - S Ravichandran
- Advanced Biomedical Computing Center, Information Systems Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - K Spelman
- Health, Education & Research in Botanical Medicine, 2209 Dollarhide Way, Ashland, OR 97520, USA
| | - S D Fugmann
- Department of Biomedical Sciences, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Taiwan
| | - R Moaddel
- Biomedical Research Center, National institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA.
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11
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Fugmann SD. Form follows function - the three-dimensional structure of antigen receptor gene loci. Curr Opin Immunol 2014; 27:33-7. [PMID: 24549092 DOI: 10.1016/j.coi.2014.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 01/22/2014] [Indexed: 01/17/2023]
Abstract
Antigen receptor genes are assembled during lymphocyte development from individual gene segments by a somatic gene rearrangement process named V(D)J recombination. This process is tightly regulated to ensure the generation of an unbiased broad primary repertoire of immunoglobulins and T cell receptors, and to prevent aberrant recombination products that could initiate lymphomagenesis. One important mode of regulation that has recently been discovered for the immunoglobulin heavy chain (IGH) gene locus is the adoption of distinct three-dimensional structures of the locus. Changes in the spatial conformation are thought to ensure the appropriate access of the V(D)J recombinase machinery at each developmental stage, and the formation of extensive chromosome loops has been implicated in allowing equal access to widely dispersed gene elements.
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Affiliation(s)
- Sebastian D Fugmann
- Department of Biomedical Sciences, Chang Gung University, 259 Wenhua 1st Rd, Kwei-Shan, Tao-Yuan 333, Taiwan.
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12
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Ravichandran S, Singh N, Donnelly D, Migliore M, Johnson P, Fishwick C, Luke BT, Martin B, Maudsley S, Fugmann SD, Moaddel R. Pharmacophore model of the quercetin binding site of the SIRT6 protein. J Mol Graph Model 2014; 49:38-46. [PMID: 24491483 DOI: 10.1016/j.jmgm.2014.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 01/03/2014] [Accepted: 01/08/2014] [Indexed: 11/25/2022]
Abstract
SIRT6 is a histone deacetylase that has been proposed as a potential therapeutic target for metabolic disorders and the prevention of age-associated diseases. We have previously reported on the identification of quercetin and vitexin as SIRT6 inhibitors, and studied structurally related flavonoids including luteolin, kaempferol, apigenin and naringenin. It was determined that the SIRT6 protein remained active after immobilization and that a single frontal displacement could correctly predict the functional activity of the immobilized enzyme. The previous study generated a preliminary pharmacophore for the quercetin binding site on SIRT6, containing 3 hydrogen bond donors and one hydrogen bond acceptor. In this study, we have generated a refined pharmacophore with an additional twelve quercetin analogs. The resulting model had a positive linear behavior between the experimental elution time verses the fit values obtained from the model with a correlation coefficient of 0.8456.
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Affiliation(s)
- S Ravichandran
- Advanced Biomedical Computing Center, SAIC-Frederick, Inc., Information Systems Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - N Singh
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, NIH, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - D Donnelly
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - M Migliore
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - P Johnson
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - C Fishwick
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - B T Luke
- Advanced Biomedical Computing Center, SAIC-Frederick, Inc., Information Systems Program, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - B Martin
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, NIH, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - S Maudsley
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, NIH, 251 Bayview Boulevard, Baltimore, MD 21224, USA
| | - S D Fugmann
- Department of Biomedical Sciences, Chang Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Taiwan
| | - R Moaddel
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, NIH, 251 Bayview Boulevard, Baltimore, MD 21224, USA.
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13
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Singh N, Ravichandran S, Norton DD, Fugmann SD, Moaddel R. Synthesis and characterization of a SIRT6 open tubular column: predicting deacetylation activity using frontal chromatography. Anal Biochem 2013; 436:78-83. [PMID: 23376017 DOI: 10.1016/j.ab.2013.01.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/14/2013] [Accepted: 01/18/2013] [Indexed: 02/02/2023]
Abstract
SIRT6 is a histone deacetylase that has been proposed as a potential therapeutic target for metabolic disorders and the prevention of age-associated diseases. Thus the identification of compounds that modulate SIRT6 activity could be of great therapeutic importance. We have previously reported on the identification of quercetin and vitexin as SIRT6 inhibitors, using SIRT6-coated magnetic beads. In this study, we have immobilized SIRT6 onto the surface of an open tubular capillary and characterized the quercetin binding site using frontal displacement chromatography. Structurally related flavonoids were tested for their activity on SIRT6, including apigenin, naringenin, luteolin, and kaempferol. In addition to obtaining their binding activity using frontal affinity chromatographic techniques, we also ranked the compounds based on their ability to displace quercetin. The data suggest that a single displacement curve is representative of the enzymatic activity of the tested ligand. In addition, using the inhibition data obtained in this study, we developed a preliminary pharmacophore model that confirmed the experimental data.
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Affiliation(s)
- Nagendra Singh
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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14
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Abstract
A systematic analysis of LPS-induced gene expression in macrophages by Bhatt et al. demonstrates that inflammatory responses are governed primarily at the level of transcription initiation. Unexpectedly, full-length nascent RNAs that contain introns appear to accumulate on chromatin, presumably to complete processing, prior to release of functional mRNA for export to the cytoplasm.
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Affiliation(s)
- Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, 251 Bayview Boulevard, Baltimore, MD 21224, USA.
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15
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Yasuda M, Wilson DR, Fugmann SD, Moaddel R. Synthesis and characterization of SIRT6 protein coated magnetic beads: identification of a novel inhibitor of SIRT6 deacetylase from medicinal plant extracts. Anal Chem 2011; 83:7400-7. [PMID: 21854049 DOI: 10.1021/ac201403y] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
SIRT6 is a histone deacetylase that has been proposed as a potential therapeutic target for metabolic disorders and the prevention of age-associated diseases. Thus, the identification of compounds that modulate SIRT6 activity could be of great therapeutic importance. The aim of this study was to develop a screening method for the identification of novel modulators of SIRT6 from a natural plant extract. We immobilized SIRT6 onto the surface of magnetic beads, and assessed SIRT6 enzymatic activity on synthetic acetylated histone tails (H3K9Ac) by measuring products of the deacetylation process. The SIRT6 coated magnetic beads were then suspended in fenugreek seed extract (Trigonella foenum-graecum) as a bait to identify active ligands that suppress SIRT6 activity. While the entire extract also inhibited SIRT6 activity in a cell-based assay, the inhibitory effect of two flavonoids from this extract, quercetin and vitexin, was only detected in vitro. This is the first report on the use of protein-coated magnetic beads for the identification of an active ligand from a botanical matrix, and it sets the basis for the de novo identification of SIRT6 modulators from complex biological mixtures.
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Affiliation(s)
- M Yasuda
- Biomedical Research Center, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, Maryland 21224-6825, USA
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16
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Abstract
Secondary Ig gene diversification relies on activation-induced cytidine deaminase (AID) to create U:G mismatches that are subsequently fixed by mutagenic repair pathways. AID activity is focused to Ig loci by cis-regulatory DNA sequences named targeting elements. In this study, we show that in contrast to prevailing thought in the field, the targeting elements in the chicken IGL locus are distinct from classical transcriptional enhancers. These mutational enhancer elements (MEEs) are required over and above transcription to recruit AID-mediated mutagenesis to Ig loci. We identified a small 222-bp fragment in the chicken IGL locus that enhances mutagenesis without boosting transcription, and this sequence represents a key component of an MEE. Lastly, MEEs are evolutionarily conserved among birds, both in sequence and function, and contain several highly conserved sequence modules that are likely involved in recruiting trans-acting targeting factors. We propose that MEEs represent a novel class of cis-regulatory elements for which the function is to control genomic integrity.
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Affiliation(s)
- Naga Rama Kothapalli
- Molecular Immunology Unit, Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Biomedical Research Center, Baltimore, MD 21224, USA
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17
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Abstract
The programmed degradation of the RAG-2 enzyme upon entry to S phase restricts V(D)J recombination to the G0-G1 phase of the cell cycle. In this issue of Immunity, Zhang et al. (2011) show that this is critical to prevent lymphoma formation.
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Affiliation(s)
- Sebastian D Fugmann
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Biomedical Research Center, 251 Bayview Blvd., Baltimore, MD 21224, USA.
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18
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Kothapalli NR, Norton DD, Fugmann SD. Classical Mus musculus Igκ enhancers support transcription but not high level somatic hypermutation from a V-lambda promoter in chicken DT40 cells. PLoS One 2011; 6:e18955. [PMID: 21533098 PMCID: PMC3080390 DOI: 10.1371/journal.pone.0018955] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 03/21/2011] [Indexed: 01/28/2023] Open
Abstract
Somatic hypermutation (SHM) of immunoglobulin genes is initiated by activation-induced cytidine deaminase (AID) in activated B cells. This process is strictly dependent on transcription. Hence, cis-acting transcriptional control elements have been proposed to target SHM to immunoglobulin loci. The Mus musculus Igκ locus is regulated by the intronic enhancer (iE/MAR) and the 3′ enhancer (3′E), and multiple studies using transgenic and knock-out approaches in mice and cell lines have reported somewhat contradictory results about the function of these enhancers in AID-mediated sequence diversification. Here we show that the M. musculus iE/MAR and 3′E elements are active solely as transcriptional enhancer when placed in the context of the IGL locus in Gallus gallus DT40 cells, but they are very inefficient in targeting AID-mediated mutation events to this locus. This suggests that either key components of the cis-regulatory targeting elements reside outside the murine Igκ transcriptional enhancer sequences, or that the targeting of AID activity to Ig loci occurs by largely species-specific mechanisms.
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Affiliation(s)
- Naga Rama Kothapalli
- Laboratory of Molecular Biology and Immunology, Molecular Immunology Unit, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
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19
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Kothapalli NR, Fugmann SD. Targeting of AID-mediated sequence diversification to immunoglobulin genes. Curr Opin Immunol 2011; 23:184-9. [PMID: 21295456 DOI: 10.1016/j.coi.2010.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 12/07/2010] [Accepted: 12/13/2010] [Indexed: 11/17/2022]
Abstract
Activation-induced cytidine deaminase (AID) is a key enzyme for antibody-mediated immune responses. Antibodies are encoded by the immunoglobulin genes and AID acts as a transcription-dependent DNA mutator on these genes to improve antibody affinity and effector functions. An emerging theme in field is that many transcribed genes are potential targets of AID, presenting an obvious danger to genomic integrity. Thus there are mechanisms in place to ensure that mutagenic outcomes of AID activity are specifically restricted to the immunoglobulin loci. Cis-regulatory targeting elements mediate this effect and their mode of action is probably a combination of immunoglobulin gene specific activation of AID and a perversion of faithful DNA repair towards error-prone outcomes.
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Affiliation(s)
- Naga Rama Kothapalli
- Molecular Immunology Unit, Laboratory of Molecular Biology and Immunology, National Institute on Aging/National Institutes of Health, Biomedical Research Center, 251 Bayview Blvd., Baltimore, MD 21224, USA
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20
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Abstract
The secondary immunoglobulin gene diversification processes, somatic hypermutation (SHM), immunoglobulin gene conversion (GCV), and class switch recombination, are important for efficient humoral immune responses. They require the action of activation-induced cytidine deaminase, an enzyme that deaminates cytosine in the context of single-stranded DNA. The chicken DT40 B-cell line is an important model system for exploring the mechanisms of SHM and GCV, as both processes occur constitutively without the need for stimulation. In addition, standard gene targeting strategies can be used for defined manipulations of the DT40 genome. Thus, these cells represent an excellent model of choice for genetic studies of SHM and GCV. Problems arising from defects in early B-cell development that are of concern when using genetically engineered mice are avoided in this system. Here, we describe how to perform gene targeting in DT40 cells and how to determine the effects of such modifications on SHM and GCV.
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Affiliation(s)
- Nagarama Kothapalli
- Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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21
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Abstract
Adaptive immunity is mediated through numerous genetic and cellular processes that generate favourable somatic variants of antigen-binding receptors under evolutionary selection pressure by pathogens and other factors. Advances in our understanding of immunity in mammals and other model organisms are revealing the underlying basis and complexity of this remarkable system. Although the evolution of adaptive immunity has been thought to occur by the acquisition of novel molecular capabilities, an increasing amount of information from new model systems suggest that co-option and redirection of pre-existing systems are the main source of innovation. We combine evidence from a wide range of organisms to obtain an integrated view of the origins and patterns of divergence in adaptive immunity.
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Affiliation(s)
- Gary W Litman
- Department of Molecular Genetics, All Children's Hospital, St. Petersburg, Florida 33701, USA.
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22
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Abstract
The recombination activating genes 1 and 2 (Rag1 and Rag2) encode the key enzyme that is required for the generation of the highly diversified antigen receptor repertoire central to adaptive immunity. The longstanding model proposed that this gene pair was acquired by horizontal gene transfer to explain its abrupt appearance in the vertebrate lineage. The analyses of the enormous amount of sequence data created by many genome sequencing projects now provide the basis for a more refined model as to how this unique gene pair evolved from a selfish DNA transposon into a sophisticated DNA recombinase essential for immunity.
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Affiliation(s)
- Sebastian D Fugmann
- Laboratory of Cellular and Molecular Biology, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd., Suite 100, Baltimore, MD 21224, USA.
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23
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Wilson DR, Norton DD, Fugmann SD. The PHD domain of the sea urchin RAG2 homolog, SpRAG2L, recognizes dimethylated lysine 4 in histone H3 tails. Dev Comp Immunol 2008; 32:1221-1230. [PMID: 18499250 PMCID: PMC2518978 DOI: 10.1016/j.dci.2008.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Revised: 03/26/2008] [Accepted: 03/27/2008] [Indexed: 05/26/2023]
Abstract
V(D)J recombination is a somatic gene rearrangement process that assembles antigen receptor genes from individual segments during lymphocyte development. The access of the RAG1/RAG2 recombinase to these gene segments is regulated at the level of chromatin modifications, in particular histone tail modifications. Trimethylation of lysine 4 in histone H3 (H3K4me3) correlates with actively recombining gene elements, and this mark is recognized and interpreted by the plant homeodomain (PHD) of RAG2. Here we report that the PHD domain of the only known invertebrate homolog of RAG2, the SpRAG2L protein of the purple sea urchin (Strongylocentrotus purpuratus) also binds to methylated histones, but with a unique preference for H3K4me2. While the cognate substrate for the sea urchin RAG1L/RAG2L complex remains elusive, the affinity for histone tails and the nuclear localization of ectopically expressed SpRAG2L strongly support the model that this enzyme complex exerts its activity on DNA in the context of chromatin.
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Affiliation(s)
- David R. Wilson
- Molecular Immunology Unit, Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
| | - Darrell D. Norton
- Molecular Immunology Unit, Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
| | - Sebastian D. Fugmann
- Molecular Immunology Unit, Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
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24
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Kothapalli N, Norton DD, Fugmann SD. Cutting Edge: A cis-Acting DNA Element Targets AID-Mediated Sequence Diversification to the Chicken Ig Light Chain Gene Locus. J Immunol 2008; 180:2019-23. [DOI: 10.4049/jimmunol.180.4.2019] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Gopal AR, Fugmann SD. AID-mediated diversification within the IgL locus of chicken DT40 cells is restricted to the transcribed IgL gene. Mol Immunol 2007; 45:2062-8. [PMID: 18023479 DOI: 10.1016/j.molimm.2007.10.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Accepted: 10/11/2007] [Indexed: 12/19/2022]
Abstract
Somatic hypermutation (SHM) and gene conversion (GCV) are closely related processes that increase the diversity the primary immunoglobulin repertoire. In both processes the activation-induced cytidine deaminase (AID) converts cytosine residues to uracils within the DNA of the immunoglobulin (Ig) genes in a transcription-dependent manner, and subsequent error-prone repair processes lead to changes in the antigen recognition site of the encoded receptors. This activity is specifically recruited to the Ig loci by unknown mechanisms. Our analyses of the chicken B-cell line DT40, and derivatives thereof, now revealed that even the closest neighbors of the Ig light chain (IgL) gene are protected from AID activity, albeit being transcribed and thus acting as potential targets of AID. Our findings are in support of a model in which cis-acting DNA boundary elements restrict AID activity to the IgL locus and guard the genome in the vicinity of the IgL gene from deleterious mutations.
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Affiliation(s)
- Anjali R Gopal
- Molecular Immunology Unit, Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
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26
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Drejer-Teel AH, Fugmann SD, Schatz DG. The beyond 12/23 restriction is imposed at the nicking and pairing steps of DNA cleavage during V(D)J recombination. Mol Cell Biol 2007; 27:6288-99. [PMID: 17636023 PMCID: PMC2099602 DOI: 10.1128/mcb.00835-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The beyond 12/23 (B12/23) rule ensures inclusion of a Dbeta gene segment in the assembled T-cell receptor (TCR) beta variable region exon and is manifest by a failure of direct Vbeta-to-Jbeta gene segment joining. The restriction is enforced during the DNA cleavage step of V(D)J recombination by the recombination-activating gene 1 and 2 (RAG1/2) proteins and the recombination signal sequences (RSSs) flanking the TCRbeta gene segments. Nothing is known about the step(s) at which DNA cleavage is defective or how TCRbeta locus sequences contribute to these defects. To address this, we examined the steps of DNA cleavage by the RAG proteins using TCRbeta locus V, D, and J RSS oligonucleotide substrates. The results demonstrate that the B12/23 rule is enforced through slow nicking of Jbeta substrates and to some extent through poor synapsis of Vbeta and Jbeta substrates. Nicking is controlled largely by the coding flank and, unexpectedly, the RSS spacer, while synapsis is controlled primarily by the RSS nonamer. The results demonstrate that different Jbeta substrates are crippled at different steps of cleavage by distinct combinations of defects in the various DNA elements and strongly suggest that the DNA nicking step of V(D)J recombination can be rate limiting in vivo.
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Affiliation(s)
- Anna H Drejer-Teel
- Department of Genetics, Yale University School of Medicine, 330 Cedar St., New Haven, Connecticut 06510, USA
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27
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Yang SY, Fugmann SD, Gramlich HS, Schatz DG. Activation-induced cytidine deaminase-mediated sequence diversification is transiently targeted to newly integrated DNA substrates. J Biol Chem 2007; 282:25308-13. [PMID: 17613522 DOI: 10.1074/jbc.m704231200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The molecular features that allow activation-induced cytidine deaminase (AID) to target Ig and certain non-Ig genes are not understood, although transcription has been implicated as one important parameter. We explored this issue by testing the mutability of a non-Ig transcription cassette in Ig and non-Ig loci of the chicken B cell line DT40. The cassette did not act as a stable long term mutation target but was able to be mutated in an AID-dependent manner for a limited time post-integration. This indicates that newly integrated DNA has molecular characteristics that render it susceptible to modification by AID, with implications for how targeting and mis-targeting of AID occurs.
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Affiliation(s)
- Shu Yuan Yang
- Department of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06520-8011, USA
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28
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Abstract
It is thought that gene conversion (GCV) and somatic hypermutation (SHM) of immunoglobulin (Ig) genes occur in two steps: the generation of uracils in DNA by activation-induced cytidine deaminase, followed by their subsequent repair by various DNA repair pathways to generate sequence-diversified products. It is not known how either of the two steps is targeted specifically to Ig loci. Because of the tight link between transcription and SHM, we have investigated the role of endogenous Ig light chain (IgL) transcriptional control elements in GCV/SHM in the chicken B cell line DT40. Promoter substitution experiments led to identification of a strong RNA polymerase II promoter incapable of supporting efficient GCV/SHM. This surprising finding indicates that high levels of transcription are not sufficient for robust GCV/SHM in Ig loci. Deletion of the IgL enhancer in a context in which high-level transcription was not compromised showed that the enhancer is not necessary for GCV/SHM. Our results indicate that cis-acting elements are important for Ig gene diversification, and we propose that targeting specificity is achieved through the combined action of several Ig locus elements that include the promoter.
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Affiliation(s)
- Shu Yuan Yang
- Section of Immunobiology and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA
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29
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Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science 2006; 314:941-52. [PMID: 17095691 PMCID: PMC3159423 DOI: 10.1126/science.1133609] [Citation(s) in RCA: 795] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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30
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Hibino T, Loza-Coll M, Messier C, Majeske AJ, Cohen AH, Terwilliger DP, Buckley KM, Brockton V, Nair SV, Berney K, Fugmann SD, Anderson MK, Pancer Z, Cameron RA, Smith LC, Rast JP. The immune gene repertoire encoded in the purple sea urchin genome. Dev Biol 2006; 300:349-65. [PMID: 17027739 DOI: 10.1016/j.ydbio.2006.08.065] [Citation(s) in RCA: 414] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 08/21/2006] [Accepted: 08/28/2006] [Indexed: 01/01/2023]
Abstract
Echinoderms occupy a critical and largely unexplored phylogenetic vantage point from which to infer both the early evolution of bilaterian immunity and the underpinnings of the vertebrate adaptive immune system. Here we present an initial survey of the purple sea urchin genome for genes associated with immunity. An elaborate repertoire of potential immune receptors, regulators and effectors is present, including unprecedented expansions of innate pathogen recognition genes. These include a diverse array of 222 Toll-like receptor (TLR) genes and a coordinate expansion of directly associated signaling adaptors. Notably, a subset of sea urchin TLR genes encodes receptors with structural characteristics previously identified only in protostomes. A similarly expanded set of 203 NOD/NALP-like cytoplasmic recognition proteins is present. These genes have previously been identified only in vertebrates where they are represented in much lower numbers. Genes that mediate the alternative and lectin complement pathways are described, while gene homologues of the terminal pathway are not present. We have also identified several homologues of genes that function in jawed vertebrate adaptive immunity. The most striking of these is a gene cluster with similarity to the jawed vertebrate Recombination Activating Genes 1 and 2 (RAG1/2). Sea urchins are long-lived, complex organisms and these findings reveal an innate immune system of unprecedented complexity. Whether the presumably intense selective processes that molded these gene families also gave rise to novel immune mechanisms akin to adaptive systems remains to be seen. The genome sequence provides immediate opportunities to apply the advantages of the sea urchin model toward problems in developmental and evolutionary immunobiology.
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Affiliation(s)
- Taku Hibino
- Sunnybrook Research Institute and Department of Medical Biophysics, University of Toronto, 2075 Bayview Ave., Room S-126b, Toronto, Ontario, Canada M4N 3M5
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31
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Abstract
The diversity of antigen receptors in the adaptive immune system of jawed vertebrates is generated by a unique process of somatic gene rearrangement known as V(D)J recombination. The Rag1 and Rag2 proteins are the key mediators of this process. They are encoded by a compact gene cluster that has exclusively been identified in animal species displaying V(D)J-mediated immunity, and no homologous gene pair has been identified in other organisms. This distinctly restricted phylogenetic distribution has led to the hypothesis that one or both of the Rag genes were coopted after horizontal gene transfer and assembled into a Rag1/2 gene cluster in a common jawed vertebrate ancestor. Here, we identify and characterize a closely linked pair of genes, SpRag1L and SpRag2L, from an invertebrate, the purple sea urchin (Strongylocentrotus purpuratus) with similarity in both sequence and genomic organization to the vertebrate Rag1 and Rag2 genes. They are coexpressed during development and in adult tissues, and recombinant versions of the proteins form a stable complex with each other as well as with Rag1 and Rag2 proteins from several vertebrate species. We thus conclude that SpRag1L and SpRag2L represent homologs of vertebrate Rag1 and Rag2. In combination with the apparent absence of V(D)J recombination in echinoderms, this finding strongly suggests that linked Rag1- and Rag2-like genes were already present and functioning in a different capacity in the common ancestor of living deuterostomes, and that their specific role in the adaptive immune system was acquired much later in an early jawed vertebrate.
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Affiliation(s)
- Sebastian D. Fugmann
- *Laboratory of Cellular and Molecular Biology, National Institute on Aging, Baltimore, MD 21224
| | - Cynthia Messier
- Sunnybrook and Women’s Research Institute and Department of Medical Biophysics, University of Toronto, 2075 Bayview Avenue, Room S-126B, Toronto, ON, Canada M4N 3M5; and
| | - Laura A. Novack
- *Laboratory of Cellular and Molecular Biology, National Institute on Aging, Baltimore, MD 21224
| | - R. Andrew Cameron
- Division of Biology, 156-29 California Institute of Technology, Pasadena, CA 91125
| | - Jonathan P. Rast
- Sunnybrook and Women’s Research Institute and Department of Medical Biophysics, University of Toronto, 2075 Bayview Avenue, Room S-126B, Toronto, ON, Canada M4N 3M5; and
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Rush JS, Fugmann SD, Schatz DG. Staggered AID-dependent DNA double strand breaks are the predominant DNA lesions targeted to S mu in Ig class switch recombination. Int Immunol 2005; 16:549-57. [PMID: 15039385 DOI: 10.1093/intimm/dxh057] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Class switch recombination (CSR) is the process whereby B cells alter the effector properties of their Ig molecules. Whilst much is known about the cellular regulation of this process, many of the molecular details remain elusive. Recent evidence suggests that CSR involves blunt DNA double strand breaks (dsbs), and that formation of these dsbs requires the function of the activation-induced cytidine deaminase (AID). We sought to characterize the structural properties and kinetics of induction of the DNA lesions associated with CSR. Using ligation-mediated PCR, we found that AID-dependent DNA dsbs were specifically induced in the S mu region of murine B cells stimulated to undergo CSR. While blunt dsbs were detected, they were only a minor species, with staggered breaks being more than an order of magnitude more abundant. In addition, these breaks could be detected at equal frequency at upstream and downstream portions of S mu, and were induced prior to expression of newly switched isotypes. Collectively, these results provide direct evidence that staggered, S mu-targeted AID-dependent dsbs are the predominant DNA lesion associated with CSR, with important implications for the mechanisms by which CSR DNA lesions are made and processed.
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Affiliation(s)
- James S Rush
- Section of Immunobiology, Howard Hughes Medical Institute and Yale School of Medicine, New Haven, CT, USA
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Affiliation(s)
- Shyam Unniraman
- Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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Abstract
Class switch recombination (CSR), somatic hypermutation, and gene conversion are immunoglobulin diversification mechanisms that are strictly dependent on the activity of the activation-induced cytidine deaminase (AID). The precise role and substrate(s) of AID in these processes remain to be well defined. The closest homologue of AID is APOBEC-1, a bona fide mRNA-editing enzyme, which shares with AID the ability to deaminate cytidines within single-stranded DNA in vitro and in prokaryotic cells. To determine whether APOBEC-1 can therefore substitute for AID in activated B cells, we expressed human AID, a catalytic mutant thereof, and rat APOBEC-1 in AID-deficient murine B cells. Whereas AID rescued CSR, neither the inactive mutant nor APOBEC-1 could complement AID deficiency. This indicates that cytidine deaminase activity is necessary but not sufficient to initiate CSR, and suggests that AID is specifically targeted to its cognate substrate, the immunoglobulin genes or a distinct mRNA, by an as-yet-unknown mechanism.
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Affiliation(s)
- Sebastian D Fugmann
- Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of Medicine, New Haven, USA
| | - James S Rush
- Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of Medicine, New Haven, USA
| | - David G Schatz
- Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of Medicine, New Haven, USA
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Lee AI, Fugmann SD, Cowell LG, Ptaszek LM, Kelsoe G, Schatz DG. A functional analysis of the spacer of V(D)J recombination signal sequences. PLoS Biol 2003; 1:E1. [PMID: 14551903 PMCID: PMC212687 DOI: 10.1371/journal.pbio.0000001] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2003] [Accepted: 07/10/2003] [Indexed: 11/18/2022] Open
Abstract
During lymphocyte development, V(D)J recombination assembles antigen receptor genes from component V, D, and J gene segments. These gene segments are flanked by a recombination signal sequence (RSS), which serves as the binding site for the recombination machinery. The murine Jbeta2.6 gene segment is a recombinationally inactive pseudogene, but examination of its RSS reveals no obvious reason for its failure to recombine. Mutagenesis of the Jbeta2.6 RSS demonstrates that the sequences of the heptamer, nonamer, and spacer are all important. Strikingly, changes solely in the spacer sequence can result in dramatic differences in the level of recombination. The subsequent analysis of a library of more than 4,000 spacer variants revealed that spacer residues of particular functional importance are correlated with their degree of conservation. Biochemical assays indicate distinct cooperation between the spacer and heptamer/nonamer along each step of the reaction pathway. The results suggest that the spacer serves not only to ensure the appropriate distance between the heptamer and nonamer but also regulates RSS activity by providing additional RAG:RSS interaction surfaces. We conclude that while RSSs are defined by a "digital" requirement for absolutely conserved nucleotides, the quality of RSS function is determined in an "analog" manner by numerous complex interactions between the RAG proteins and the less-well conserved nucleotides in the heptamer, the nonamer, and, importantly, the spacer. Those modulatory effects are accurately predicted by a new computational algorithm for "RSS information content." The interplay between such binary and multiplicative modes of interactions provides a general model for analyzing protein-DNA interactions in various biological systems.
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Affiliation(s)
- Alfred Ian Lee
- 1Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of MedicineNew Haven, ConnecticutUnited States of America
| | - Sebastian D Fugmann
- 1Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of MedicineNew Haven, ConnecticutUnited States of America
| | - Lindsay G Cowell
- 2Department of Immunology, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Leon M Ptaszek
- 3Ruttenberg Cancer Center, Mount Sinai School of Medicine of New York UniversityNew York, New YorkUnited States of America
| | - Garnett Kelsoe
- 2Department of Immunology, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - David G Schatz
- 1Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of MedicineNew Haven, ConnecticutUnited States of America
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Jung D, Bassing CH, Fugmann SD, Cheng HL, Schatz DG, Alt FW. Extrachromosomal recombination substrates recapitulate beyond 12/23 restricted VDJ recombination in nonlymphoid cells. Immunity 2003; 18:65-74. [PMID: 12530976 DOI: 10.1016/s1074-7613(02)00507-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
V(D)J recombination occurs efficiently only between gene segments flanked by recombination signals (RSs) containing 12 and 23 base pair spacers (the 12/23 rule). A further limitation "beyond the 12/23 rule" (B12/23) exists at the TCRbeta locus and ensures Dbeta usage. Herein, we show that extrachromosomal V(D)J recombination substrates recapitulate B12/23 restriction in nonlymphoid cells. We further demonstrate that the Vbeta coding flank, the 12-RS heptamer/nonamer, and the 23-RS spacer each can significantly influence B12/23 restriction. Finally, purified core RAG1 and RAG2 proteins (together with HMG2) also reproduce B12/23 restriction in a cell-free system. Our findings indicate that B12/23 restriction of V(D)J recombination is cemented at the level of interactions between the RAG proteins and TCRbeta RS sequences.
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Affiliation(s)
- David Jung
- Howard Hughes Medical Institute, The Children's Hospital, Harvard Medical School, Boston, MA, USA
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Affiliation(s)
- Sebastian D Fugmann
- Howard Hughes Medical Institute and Section of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
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Abstract
RAG1 and RAG2 are the key components of the V(D)J recombinase machinery that catalyses the somatic gene rearrangements of antigen receptor genes during lymphocyte development. In the first step of V(D)J recombination--DNA cleavage--the RAG proteins act together as an endonuclease to excise the DNA between two individual gene segments. They are also thought to be involved in the subsequent DNA joining step. In vitro, the RAG proteins catalyze the integration of the excised DNA element into target DNA completing a process similar to bacterial transposition. In vivo, this reaction is suppressed by an unknown mechanism. The individual roles of RAG1 and RAG2 in V(D)J recombination and transposition reactions are discussed based on mutation analyses and structure predictions.
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Affiliation(s)
- S D Fugmann
- Howard Hughes Medical Institute, New Haven, CT 06520-8011, USA.
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Abstract
In V(D)J recombination, the RAG1 and RAG2 proteins are the essential components of the complex that catalyzes DNA cleavage. RAG1 has been shown to play a central role in DNA binding and catalysis. In contrast, the molecular roles of RAG2 in V(D)J recombination are unknown. To address this, we individually mutated 36 evolutionarily conserved basic and hydroxy group containing residues within RAG2. Biochemical analysis of the recombinant RAG2 proteins led to the identification of a number of basic residue mutants defective in catalysis in vitro and V(D)J recombination in vivo. Five of these were deficient in binding of the RAG1-RAG2 complex to its cognate DNA target sequence while interacting normally with RAG1. Our findings provide support for the direct involvement of RAG2 in DNA binding during all steps of the cleavage reaction.
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Affiliation(s)
- S D Fugmann
- Section of Immunobiology, Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06520, USA
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Abstract
V(D)J recombination proceeds through a series of protein:DNA complexes mediated in part by the RAG1 and RAG2 proteins. These proteins are responsible for sequence-specific DNA recognition and DNA cleavage, and they appear to perform multiple postcleavage roles in the reaction as well. Here we review the interaction of the RAG proteins with DNA, the chemistry of the cleavage reaction, and the higher order complexes in which these events take place. We also discuss postcleavage functions of the RAG proteins, including recent evidence indicating that they initiate the process of coding end processing by nicking hairpin DNA termini. Finally, we discuss the evolutionary and functional implications of the finding that RAG1 and RAG2 constitute a transposase, and we consider RAG protein biochemistry in the context of several bacterial transposition systems. This suggests a model of the RAG protein active site in which two divalent metal ions serve alternating and opposite roles as activators of attacking hydroxyl groups and stabilizers of oxyanion leaving groups.
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Affiliation(s)
- S D Fugmann
- Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520-8011, USA
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Fugmann SD, Villey IJ, Ptaszek LM, Schatz DG. Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex. Mol Cell 2000; 5:97-107. [PMID: 10678172 DOI: 10.1016/s1097-2765(00)80406-2] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
During V(D)J recombination, the RAG1 and RAG2 proteins cooperate to catalyze a series of DNA bond breakage and strand transfer reactions. The structure, location, and number of active sites involved in RAG-mediated catalysis have as yet not been determined. Using protein secondary structure prediction algorithms, we have identified a region of RAG1 with possible structural similarities to the active site regions of transposases and retroviral integrases. Based on this information, we have identified two aspartic acid residues in RAG1 (D600 and D708) that function specifically in catalysis. The results support a model in which RAG1 contains a single, divalent metal ion binding active site structurally related to the active sites of transposases/integrases and responsible for all catalytic functions of the RAG protein complex.
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Affiliation(s)
- S D Fugmann
- Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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Fugmann SD, Müller S, Friedrich W, Bartram CR, Schwarz K. Mutations in the gene for the common gamma chain (gammac) in X-linked severe combined immunodeficiency. Hum Genet 1998; 103:730-1. [PMID: 9921912 DOI: 10.1007/pl00008710] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
X-linked severe combined immunodeficiency (XSCID) constitutes a disorder of the immune system caused by mutations in the gene encoding the common gamma chain (gammac), a subunit of the IL-2, IL-4, IL-7, IL-9 and IL-15 receptors, which are necessary for lymphocyte development and function. In this study the IL2RG gene of 31 patients with severe combined immunodeficiency (SCID) was examined by nonradioactive single-strand conformation polymorphism and sequence analysis. Among the 11 patients with XSCID, ten different mutations were identified in the IL2RG gene, including eight novel mutations. Ninety percent of the mothers of the XSCID patients are carriers of the mutated allele. One patient showed low numbers of B-cells, a striking deviation from the classical B-cell-positive and T-cell-negative phenotype.
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Affiliation(s)
- S D Fugmann
- Department of Transfusion Medicine, University of Ulm, Germany
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