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Massri M, Toonen EJ, Sarg B, Kremser L, Grasse M, Fleischer V, Torres-Quesada O, Hengst L, Skjoedt MO, Bayarri-Olmos R, Rosbjerg A, Garred P, Orth-Höller D, Prohászka Z, Würzner R. Complement C7 and clusterin form a complex in circulation. Front Immunol 2024; 15:1330095. [PMID: 38333209 PMCID: PMC10850381 DOI: 10.3389/fimmu.2024.1330095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024] Open
Abstract
Introduction The complement system is part of innate immunity and is comprised of an intricate network of proteins that are vital for host defense and host homeostasis. A distinct mechanism by which complement defends against invading pathogens is through the membrane attack complex (MAC), a lytic structure that forms on target surfaces. The MAC is made up of several complement components, and one indispensable component of the MAC is C7. The role of C7 in MAC assembly is well documented, however, inherent characteristics of C7 are yet to be investigated. Methods To shed light on the molecular characteristics of C7, we examined the properties of serum-purified C7 acquired using polyclonal and novel monoclonal antibodies. The properties of serum‑purified C7 were investigated through a series of proteolytic analyses, encompassing Western blot and mass spectrometry. The nature of C7 protein-protein interactions were further examined by a novel enzyme-linked immunosorbent assay (ELISA), as well as size‑exclusion chromatography. Results Protein analyses showcased an association between C7 and clusterin, an inhibitory complement regulator. The distinct association between C7 and clusterin was also demonstrated in serum-purified clusterin. Further assessment revealed that a complex between C7 and clusterin (C7-CLU) was detected. The C7-CLU complex was also identified in healthy serum and plasma donors, highlighting the presence of the complex in circulation. Discussion Clusterin is known to dissociate the MAC structure by binding to polymerized C9, nevertheless, here we show clusterin binding to the native form of a terminal complement protein in vivo. The presented data reveal that C7 exhibits characteristics beyond that of MAC assembly, instigating further investigation of the effector role that the C7-CLU complex plays in the complement cascade.
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Affiliation(s)
- Mariam Massri
- Institute of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Bettina Sarg
- Institute of Medical Biochemsitry, Protein Core Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Leopold Kremser
- Institute of Medical Biochemsitry, Protein Core Facility, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Marco Grasse
- Institute of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Verena Fleischer
- Institute of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Omar Torres-Quesada
- Institute of Medical Biochemistry, Medical University of Innsbruck, Biocenter, Innsbruck, Austria
- Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Ludger Hengst
- Institute of Medical Biochemistry, Medical University of Innsbruck, Biocenter, Innsbruck, Austria
| | - Mikkel-Ole Skjoedt
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Immunology & Microbiology , University of Copenhagen, Copenhagen, Denmark
| | - Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne Rosbjerg
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Dorothea Orth-Höller
- Institute of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
- MB-LAB Clinical Microbiology Laboratory, Innsbruck, Austria
| | - Zoltán Prohászka
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
- Research Group for Immunology and Hematology, Semmelweis University-Eötvös Loránd Research Network (Office for Supported Research Groups), Budapest, Hungary
| | - Reinhard Würzner
- Institute of Hygiene & Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. The diverse structural modes of tRNA binding and recognition. J Biol Chem 2023; 299:104966. [PMID: 37380076 PMCID: PMC10424219 DOI: 10.1016/j.jbc.2023.104966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
tRNAs are short noncoding RNAs responsible for decoding mRNA codon triplets, delivering correct amino acids to the ribosome, and mediating polypeptide chain formation. Due to their key roles during translation, tRNAs have a highly conserved shape and large sets of tRNAs are present in all living organisms. Regardless of sequence variability, all tRNAs fold into a relatively rigid three-dimensional L-shaped structure. The conserved tertiary organization of canonical tRNA arises through the formation of two orthogonal helices, consisting of the acceptor and anticodon domains. Both elements fold independently to stabilize the overall structure of tRNAs through intramolecular interactions between the D- and T-arm. During tRNA maturation, different modifying enzymes posttranscriptionally attach chemical groups to specific nucleotides, which not only affect translation elongation rates but also restrict local folding processes and confer local flexibility when required. The characteristic structural features of tRNAs are also employed by various maturation factors and modification enzymes to assure the selection, recognition, and positioning of specific sites within the substrate tRNAs. The cellular functional repertoire of tRNAs continues to extend well beyond their role in translation, partly, due to the expanding pool of tRNA-derived fragments. Here, we aim to summarize the most recent developments in the field to understand how three-dimensional structure affects the canonical and noncanonical functions of tRNA.
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Affiliation(s)
- Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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Bergeron D, Faucher-Giguère L, Emmerichs AK, Choquet K, Song KS, Deschamps-Francoeur G, Fafard-Couture É, Rivera A, Couture S, Churchman LS, Heyd F, Abou Elela S, Scott MS. Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences. Genome Biol 2023; 24:160. [PMID: 37415181 PMCID: PMC10324135 DOI: 10.1186/s13059-023-03002-y] [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: 10/25/2022] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Small nucleolar RNAs (snoRNAs) are abundant noncoding RNAs best known for their involvement in ribosomal RNA maturation. In mammals, most expressed snoRNAs are embedded in introns of longer genes and produced through transcription and splicing of their host. Intronic snoRNAs were long viewed as inert passengers with little effect on host expression. However, a recent study reported a snoRNA influencing the splicing and ultimate output of its host gene. Overall, the general contribution of intronic snoRNAs to host expression remains unclear. RESULTS Computational analysis of large-scale human RNA-RNA interaction datasets indicates that 30% of detected snoRNAs interact with their host transcripts. Many snoRNA-host duplexes are located near alternatively spliced exons and display high sequence conservation suggesting a possible role in splicing regulation. The study of the model SNORD2-EIF4A2 duplex indicates that the snoRNA interaction with the host intronic sequence conceals the branch point leading to decreased inclusion of the adjacent alternative exon. Extended SNORD2 sequence containing the interacting intronic region accumulates in sequencing datasets in a cell-type-specific manner. Antisense oligonucleotides and mutations that disrupt the formation of the snoRNA-intron structure promote the splicing of the alternative exon, shifting the EIF4A2 transcript ratio away from nonsense-mediated decay. CONCLUSIONS Many snoRNAs form RNA duplexes near alternative exons of their host transcripts, placing them in optimal positions to control host output as shown for the SNORD2-EIF4A2 model system. Overall, our study supports a more widespread role for intronic snoRNAs in the regulation of their host transcript maturation.
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Affiliation(s)
- Danny Bergeron
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Laurence Faucher-Giguère
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Ann-Kathrin Emmerichs
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Laboratory of RNA Biochemistry, Takustrasse 6, 14195, Berlin, Germany
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Kristina Sungeun Song
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Étienne Fafard-Couture
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Andrea Rivera
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Sonia Couture
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Florian Heyd
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Laboratory of RNA Biochemistry, Takustrasse 6, 14195, Berlin, Germany
| | - Sherif Abou Elela
- Département de Microbiologie Et d'infectiologie, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Département de Biochimie Et Génomique Fonctionnelle, Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
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Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants. Genes (Basel) 2021; 12:genes12060822. [PMID: 34071968 PMCID: PMC8228828 DOI: 10.3390/genes12060822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as "bridges" in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.
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Liehr T. Repetitive Elements in Humans. Int J Mol Sci 2021; 22:ijms22042072. [PMID: 33669810 PMCID: PMC7922087 DOI: 10.3390/ijms22042072] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called 'genetic background', being able to at least potentially influence disease susceptibilities. Here, the known 'bad boys' among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany
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