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Davidge B, McDermott SM, Carnes J, Lewis I, Tracy M, Stuart KD. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes in Trypanosoma brucei. RNA 2023; 29:1591-1609. [PMID: 37474258 PMCID: PMC10578492 DOI: 10.1261/rna.079691.123] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life-cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multiprotein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing, and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations, most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the zinc fingers (ZFs), an intrinsically disordered region (IDR), and several within or near the carboxy-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing, whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.
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Affiliation(s)
- Brittney Davidge
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Isaac Lewis
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Maxwell Tracy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Kenneth D Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
- Department of Global Health, University of Washington, Seattle, Washington 98195, USA
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2
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Davidge B, McDermott SM, Carnes J, Lewis I, Tracy M, Stuart KD. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA Editing Catalytic Complexes in Trypanosoma brucei. bioRxiv 2023:2023.04.19.537538. [PMID: 37131796 PMCID: PMC10153193 DOI: 10.1101/2023.04.19.537538] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multi-protein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the ZFs, an intrinsically disordered region (IDR) and several within or near the C-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.
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Affiliation(s)
- Brittney Davidge
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Isaac Lewis
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Maxwell Tracy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Kenneth D Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
- Department of Pediatrics, University of Washington, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
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3
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Espinel-Mesa DX, González Rugeles CI, Mantilla Hernández JC, Stashenko EE, Villegas-Lanau CA, Quimbaya Ramírez JJ, García Sánchez LT. Immunomodulation and Antioxidant Activities as Possible Trypanocidal and Cardioprotective Mechanisms of Major Terpenes from Lippia alba Essential Oils in an Experimental Model of Chronic Chagas Disease. Antioxidants (Basel) 2021; 10:antiox10111851. [PMID: 34829722 PMCID: PMC8614928 DOI: 10.3390/antiox10111851] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022] Open
Abstract
In the late phase of Trypanosoma cruzi infection, parasite persistence and an exaggerated immune response accompanied by oxidative stress play a crucial role in the genesis of Chronic Chagasic Cardiomyopathy (CCC). Current treatments (Benznidazole (BNZ) and Nifurtimox) can effect only the elimination of the parasite, but are ineffective for late stage treatment and for preventing heart damage and disease progression. In vivo trypanocidal and cardioprotective activity has been reported for Lippia alba essential oils (EOs), ascribed to their two major terpenes, limonene and caryophyllene oxide. To investigate the role of antioxidant and immunomodulatory mechanisms behind these properties, chronic-T. cruzi-infected rats were treated with oral synergistic mixtures of the aforementioned EOs. For this purpose, the EOs were optimized through limonene-enrichment fractioning and by the addition of exogenous caryophyllene oxide (LIMOX) and used alone or in combined therapy with subtherapeutic doses of BNZ (LIMOXBNZ). Clinical, toxicity, inflammatory, oxidative, and parasitological (qPCR) parameters were assessed in cardiac tissue. These therapies demonstrated meaningful antioxidant and immunomodulatory activity on markers involved in CCC pathogenesis (IFN-γ, TNF-α, IL-4, IL-10, and iNOS), which could explain their significant trypanocidal properties and their noteworthy role in preventing, and even reversing, the progression of cardiac damage in chronic Chagas disease.
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Affiliation(s)
- Denerieth Ximena Espinel-Mesa
- Infectious Diseases Postgraduate Program, Instituto de Investigación Masira, Universidad de Santander, Bucaramanga 680006, Santander, Colombia; (D.X.E.-M.); (J.J.Q.R.)
| | - Clara Isabel González Rugeles
- Immunology and Molecular Epidemiology Group, School of Microbiology, Universidad Industrial de Santander, Bucaramanga 680002, Santander, Colombia;
| | | | - Elena E. Stashenko
- National Research Center for the Agroindustrialization of Tropical Aromatic and Medicinal Plant Species—CENIVAM, Universidad Industrial de Santander, Bucaramanga 680002, Santander, Colombia;
| | | | - John Jaime Quimbaya Ramírez
- Infectious Diseases Postgraduate Program, Instituto de Investigación Masira, Universidad de Santander, Bucaramanga 680006, Santander, Colombia; (D.X.E.-M.); (J.J.Q.R.)
| | - Liliana Torcoroma García Sánchez
- Infectious Diseases Postgraduate Program, Instituto de Investigación Masira, Universidad de Santander, Bucaramanga 680006, Santander, Colombia; (D.X.E.-M.); (J.J.Q.R.)
- Correspondence:
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Yerabham ASK, Müller-Schiffmann A, Ziehm T, Stadler A, Köber S, Indurkhya X, Marreiros R, Trossbach SV, Bradshaw NJ, Prikulis I, Willbold D, Weiergräber OH, Korth C. Biophysical insights from a single chain camelid antibody directed against the Disrupted-in-Schizophrenia 1 protein. PLoS One 2018; 13:e0191162. [PMID: 29324815 DOI: 10.1371/journal.pone.0191162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 12/31/2017] [Indexed: 01/17/2023] Open
Abstract
Accumulating evidence suggests an important role for the Disrupted-in-Schizophrenia 1 (DISC1) protein in neurodevelopment and chronic mental illness. In particular, the C-terminal 300 amino acids of DISC1 have been found to mediate important protein-protein interactions and to harbor functionally important phosphorylation sites and disease-associated polymorphisms. However, long disordered regions and oligomer-forming subdomains have so far impeded structural analysis. VHH domains derived from camelid heavy chain only antibodies are minimal antigen binding modules with appreciable solubility and stability, which makes them well suited for the stabilizing proteins prior to structural investigation. Here, we report on the generation of a VHH domain derived from an immunized Lama glama, displaying high affinity for the human DISC1 C region (aa 691-836), and its characterization by surface plasmon resonance, size exclusion chromatography and immunological techniques. The VHH-DISC1 (C region) complex was also used for structural investigation by small angle X-ray scattering analysis. In combination with molecular modeling, these data support predictions regarding the three-dimensional fold of this DISC1 segment as well as its steric arrangement in complex with our VHH antibody.
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Garza JA, Taylor AB, Sherwood LJ, Hart PJ, Hayhurst A. Unveiling a Drift Resistant Cryptotope within Marburgvirus Nucleoprotein Recognized by Llama Single-Domain Antibodies. Front Immunol 2017; 8:1234. [PMID: 29038656 PMCID: PMC5630700 DOI: 10.3389/fimmu.2017.01234] [Citation(s) in RCA: 13] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022] Open
Abstract
Marburg virus (MARV) is a highly lethal hemorrhagic fever virus that is increasingly re-emerging in Africa, has been imported to both Europe and the US, and is also a Tier 1 bioterror threat. As a negative sense RNA virus, MARV has error prone replication which can yield progeny capable of evading countermeasures. To evaluate this vulnerability, we sought to determine the epitopes of 4 llama single-domain antibodies (sdAbs or VHH) specific for nucleoprotein (NP), each capable of forming MARV monoclonal affinity reagent sandwich assays. Here, we show that all sdAb bound the C-terminal region of NP, which was produced recombinantly to derive X-ray crystal structures of the three best performing antibody-antigen complexes. The common epitope is a trio of alpha helices that form a novel asymmetric basin-like depression that accommodates each sdAb paratope via substantial complementarity-determining region (CDR) restructuring. Shared core contacts were complemented by unique accessory contacts on the sides and overlooks of the basin yielding very different approach routes for each sdAb to bind the antigen. The C-terminal region of MARV NP was unable to be crystallized alone and required engagement with sdAb to form crystals suggesting the antibodies acted as crystallization chaperones. While gross structural homology is apparent between the two most conserved helices of MARV and Ebolavirus, the positions and morphologies of the resulting basins were markedly different. Naturally occurring amino acid variations occurring in bat and human Marburgvirus strains all mapped to surfaces distant from the predicted sdAb contacts suggesting a vital role for the NP interface in virus replication. As an essential internal structural component potentially interfacing with a partner protein it is likely the C-terminal epitope remains hidden or “cryptic” until virion disruption occurs. Conservation of this epitope over 50 years of Marburgvirus evolution should make these sdAb useful foundations for diagnostics and therapeutics resistant to drift.
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Affiliation(s)
- John Anthony Garza
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Alexander Bryan Taylor
- X-Ray Crystallography Core Laboratory, Department of Biochemistry and Structural Biology, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Laura Jo Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Peter John Hart
- X-Ray Crystallography Core Laboratory, Department of Biochemistry and Structural Biology, Institutional Research Cores, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX, United States
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, United States
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Abstract
To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins.
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Affiliation(s)
- Joshua Holcomb
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nicholas Spellmon
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yingxue Zhang
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Maysaa Doughan
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chunying Li
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA, USA
| | - Zhe Yang
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
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Fernandes CFC, Pereira SDS, Luiz MB, Zuliani JP, Furtado GP, Stabeli RG. Camelid Single-Domain Antibodies As an Alternative to Overcome Challenges Related to the Prevention, Detection, and Control of Neglected Tropical Diseases. Front Immunol 2017. [PMID: 28649245 PMCID: PMC5465246 DOI: 10.3389/fimmu.2017.00653] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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] [Indexed: 12/31/2022] Open
Abstract
Due mainly to properties such as high affinity and antigen specificity, antibodies have become important tools for biomedical research, diagnosis, and treatment of several human diseases. When the objective is to administer them for therapy, strategies are used to reduce the heterologous protein immunogenicity and to improve pharmacokinetic and pharmacodynamic characteristics. Size minimization contributes to ameliorate these characteristics, while preserving the antigen-antibody interaction site. Since the discovery that camelids produce functional antibodies devoid of light chains, studies have proposed the use of single domains for biosensors, monitoring and treatment of tumors, therapies for inflammatory and neurodegenerative diseases, drug delivery, or passive immunotherapy. Despite an expected increase in antibody and related products in the pharmaceutical market over the next years, few research initiatives are related to the development of alternatives for helping to manage neglected tropical diseases (NTDs). In this review, we summarize developments of camelid single-domain antibodies (VHH) in the field of NTDs. Particular attention is given to VHH-derived products, i.e., VHHs fused to nanoparticles, constructed for the development of rapid diagnostic kits; fused to oligomeric matrix proteins for viral neutralization; and conjugated with proteins for the treatment of human parasites. Moreover, paratransgenesis technology using VHHs is an interesting approach to control parasite development in vectors. With enormous biotechnological versatility, facility and low cost for heterologous production, and greater ability to recognize different epitopes, VHHs have appeared as an opportunity to overcome challenges related to the prevention, detection, and control of human diseases, especially NTDs.
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Affiliation(s)
| | | | - Marcos B Luiz
- Fundação Oswaldo Cruz, Fiocruz Rondônia, Porto Velho, Rondônia, Brazil
| | - Juliana P Zuliani
- Fundação Oswaldo Cruz, Fiocruz Rondônia, Porto Velho, Rondônia, Brazil.,Departamento de Medicina da Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil
| | | | - Rodrigo G Stabeli
- Departamento de Medicina da Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil.,Plataforma Bi-Institucional de Medicina Translacional (Fiocruz-USP), Ribeirão Preto, São Paulo, Brazil
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8
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Abstract
Uridine insertion and deletion RNA editing generates functional mitochondrial mRNAs in Trypanosoma brucei Editing is catalyzed by three distinct ∼20S editosomes that have a common set of 12 proteins, but are typified by mutually exclusive RNase III endonucleases with distinct cleavage specificities and unique partner proteins. Previous studies identified a network of protein-protein interactions among a subset of common editosome proteins, but interactions among the endonucleases and their partner proteins, and their interactions with common subunits were not identified. Here, chemical cross-linking and mass spectrometry, comparative structural modeling, and genetic and biochemical analyses were used to define the molecular architecture and subunit organization of purified editosomes. We identified intra- and interprotein cross-links for all editosome subunits that are fully consistent with editosome protein structures and previously identified interactions, which we validated by genetic and biochemical studies. The results were used to create a highly detailed map of editosome protein domain proximities, leading to identification of molecular interactions between subunits, insights into the functions of noncatalytic editosome proteins, and a global understanding of editosome architecture.
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9
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Aphasizheva I, Aphasizhev R. U-Insertion/Deletion mRNA-Editing Holoenzyme: Definition in Sight. Trends Parasitol 2015; 32:144-156. [PMID: 26572691 DOI: 10.1016/j.pt.2015.10.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [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: 09/03/2015] [Revised: 10/06/2015] [Accepted: 10/12/2015] [Indexed: 11/16/2022]
Abstract
RNA editing is a process that alters DNA-encoded sequences and is distinct from splicing, 5' capping, and 3' additions. In 30 years since editing was discovered in mitochondria of trypanosomes, several functionally and evolutionarily unrelated mechanisms have been described in eukaryotes, archaea, and viruses. Editing events are predominantly post-transcriptional and include nucleoside insertions and deletions, and base substitutions and modifications. Here, we review the mechanism of uridine insertion/deletion mRNA editing in kinetoplastid protists typified by Trypanosoma brucei. This type of editing corrects frameshifts, introduces translation punctuation signals, and often adds hundreds of uridines to create protein-coding sequences. We focus on protein complexes responsible for editing reactions and their interactions with other elements of the mitochondrial gene expression pathway.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA.
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
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Czerwoniec A, Kasprzak JM, Bytner P, Dobrychłop M, Bujnicki JM. Structure and intrinsic disorder of the proteins of the Trypanosoma brucei editosome. FEBS Lett 2015; 589:2603-10. [PMID: 26226426 DOI: 10.1016/j.febslet.2015.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 06/01/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 01/02/2023]
Abstract
Mitochondrial pre-mRNAs in trypanosomatids undergo RNA editing to be converted into translatable mRNAs. The reaction is characterized by the insertion and deletion of uridine residues and is catalyzed by a macromolecular protein complex called the editosome. Despite intensive research, structural information for the majority of editosome proteins is still missing and no high resolution structure for the editosome exists. Here we present a comprehensive structural bioinformatics analysis of all proteins of the Trypanosoma brucei editosome. We specifically focus on the interplay between intrinsic order and disorder. According to computational predictions, editosome proteins involved in the basal reaction steps of the processing cycle are mostly ordered. By contrast, thirty percent of the amino acid content of the editosome is intrinsically disordered, which includes most prominently proteins with OB-fold domains. Based on the data we suggest a functional model, in which the structurally disordered domains of the complex are correlated with the RNA binding and RNA unfolding activity of the T. brucei editosome.
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Affiliation(s)
- Anna Czerwoniec
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland.
| | - Joanna M Kasprzak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Patrycja Bytner
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Mateusz Dobrychłop
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland.
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11
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Simpson L, Douglass SM, Lake JA, Pellegrini M, Li F. Comparison of the Mitochondrial Genomes and Steady State Transcriptomes of Two Strains of the Trypanosomatid Parasite, Leishmania tarentolae. PLoS Negl Trop Dis 2015. [PMID: 26204118 PMCID: PMC4512693 DOI: 10.1371/journal.pntd.0003841] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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] [Indexed: 12/20/2022] Open
Abstract
U-insertion/deletion RNA editing is a post-transcriptional mitochondrial RNA modification phenomenon required for viability of trypanosomatid parasites. Small guide RNAs encoded mainly by the thousands of catenated minicircles contain the information for this editing. We analyzed by NGS technology the mitochondrial genomes and transcriptomes of two strains, the old lab UC strain and the recently isolated LEM125 strain. PacBio sequencing provided complete minicircle sequences which avoided the assembly problem of short reads caused by the conserved regions. Minicircles were identified by a characteristic size, the presence of three short conserved sequences, a region of inherently bent DNA and the presence of single gRNA genes at a fairly defined location. The LEM125 strain contained over 114 minicircles encoding different gRNAs and the UC strain only ~24 minicircles. Some LEM125 minicircles contained no identifiable gRNAs. Approximate copy numbers of the different minicircle classes in the network were determined by the number of PacBio CCS reads that assembled to each class. Mitochondrial RNA libraries from both strains were mapped against the minicircle and maxicircle sequences. Small RNA reads mapped to the putative gRNA genes but also to multiple regions outside the genes on both strands and large RNA reads mapped in many cases over almost the entire minicircle on both strands. These data suggest that minicircle transcription is complete and bidirectional, with 3’ processing yielding the mature gRNAs. Steady state RNAs in varying abundances are derived from all maxicircle genes, including portions of the repetitive divergent region. The relative extents of editing in both strains correlated with the presence of a cascade of cognate gRNAs. These data should provide the foundation for a deeper understanding of this dynamic genetic system as well as the evolutionary variation of editing in different strains. U-insertion/deletion RNA editing is a unique post-transcriptional mRNA modification process that occurs in trypanosomatid parasites and is required for viability. The participation of guide RNAs which are transcribed from the thousands of catenated minicircles in determining the precise sites and number of U’s inserted and deleted to create translatable mRNAs is novel and significant in terms of the recently realized importance of small RNAs in biology. This study contributes the necessary bioinformatics foundation for a deeper understanding of this important genetic system in molecular detail using a model trypanosomatid, Leishmania tarentolae. We used Next Generation Sequencing methods to determine the complete maxicircle and minicircle genomes and to map maxicircle pre-edited and edited transcripts and minicircle transcripts. The transcription of minicircle-encoded guide RNAs was confirmed and novel information about minicircle gene expression was obtained. The biological context involved a comparison of two strains of the parasites, one recently isolated and having an intact mitochondrial genetic system and the other an old lab strain that has developed a partially defective mitochondrial genome. The data are important for an understanding of the mitochondrial genomic complexity and expression of this dynamic genetic system.
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Affiliation(s)
- Larry Simpson
- Department of Microbiology, Immunology and Molecular Genetics, Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| | - Stephen M. Douglass
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - James A. Lake
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Matteo Pellegrini
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Feng Li
- Dental Research Institute, School of Dentistry, University of California, Los Angeles, Los Angeles, California, United States of America
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12
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Marsden CJ, Eckersley S, Hebditch M, Kvist AJ, Milner R, Mitchell D, Warwicker J, Marley AE. The Use of Antibodies in Small-Molecule Drug Discovery. ACTA ACUST UNITED AC 2014; 19:829-38. [PMID: 24695620 DOI: 10.1177/1087057114527770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 07/08/2013] [Accepted: 12/08/2013] [Indexed: 12/17/2022]
Abstract
Antibodies are powerful research tools that can be used in many areas of biology to probe, measure, and perturb various biological structures. Successful drug discovery is dependent on the correct identification of a target implicated in disease, coupled with the successful selection, optimization, and development of a candidate drug. Because of their specific binding characteristics, with regard to specificity, affinity, and avidity, coupled with their amenability to protein engineering, antibodies have become a key tool in drug discovery, enabling the quantification, localization, and modulation of proteins of interest. This review summarizes the application of antibodies and other protein affinity reagents as specific research tools within the drug discovery process.
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13
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Pardon E, Laeremans T, Triest S, Rasmussen SGF, Wohlkönig A, Ruf A, Muyldermans S, Hol WGJ, Kobilka BK, Steyaert J. A general protocol for the generation of Nanobodies for structural biology. Nat Protoc 2014; 9:674-93. [PMID: 24577359 DOI: 10.1038/nprot.2014.039] [Citation(s) in RCA: 460] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is growing interest in using antibodies as auxiliary tools to crystallize proteins. Here we describe a general protocol for the generation of Nanobodies to be used as crystallization chaperones for the structural investigation of diverse conformational states of flexible (membrane) proteins and complexes thereof. Our technology has a competitive advantage over other recombinant crystallization chaperones in that we fully exploit the natural humoral response against native antigens. Accordingly, we provide detailed protocols for the immunization with native proteins and for the selection by phage display of in vivo-matured Nanobodies that bind conformational epitopes of functional proteins. Three representative examples illustrate that the outlined procedures are robust, making it possible to solve by Nanobody-assisted X-ray crystallography in a time span of 6-12 months.
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Affiliation(s)
- Els Pardon
- 1] Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium. [2] Structural Biology Research Center, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
| | - Toon Laeremans
- 1] Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium. [2] Structural Biology Research Center, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
| | - Sarah Triest
- 1] Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium. [2] Structural Biology Research Center, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
| | - Søren G F Rasmussen
- Department of Neuroscience and Pharmacology, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alexandre Wohlkönig
- 1] Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium. [2] Structural Biology Research Center, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
| | - Armin Ruf
- Pharma Research and Early Development (pRED), Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche, Basel, Switzerland
| | - Serge Muyldermans
- 1] Structural Biology Research Center, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium. [2] Cellular and Molecular Immunology, VUB, Brussels, Belgium
| | - Wim G J Hol
- Department of Biochemistry, Biomolecular Structure Center, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, California, USA
| | - Jan Steyaert
- 1] Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium. [2] Structural Biology Research Center, Vlaams Instituut voor Biotechnologie (VIB), Brussels, Belgium
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Khamrui S, Turley S, Pardon E, Steyaert J, Fan E, Verlinde CLMJ, Bergman LW, Hol WGJ. The structure of the D3 domain of Plasmodium falciparum myosin tail interacting protein MTIP in complex with a nanobody. Mol Biochem Parasitol 2013; 190:87-91. [PMID: 23831371 DOI: 10.1016/j.molbiopara.2013.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 02/11/2013] [Revised: 06/18/2013] [Accepted: 06/24/2013] [Indexed: 02/03/2023]
Abstract
Apicomplexan parasites enter host cells by many sophisticated steps including use of an ATP-powered invasion machinery. The machinery consists of multiple proteins, including a special myosin (MyoA) which moves along an actin fiber and which is connected to the myosin tail interaction protein (MTIP). Here we report a crystal structure of the major MyoA-binding domain (D3) of Plasmodium falciparum MTIP in complex with an anti-MTIP nanobody. In this complex, the MyoA-binding groove in MTIP-D3 is considerably less accessible than when occupied by the MyoA helix, due to a shift of two helices. The nanobody binds to an area slightly overlapping with the MyoA binding groove, covering a hydrophobic region next to the groove entrance. This provides a new avenue for arriving at compounds interfering with the invasion machinery since small molecules binding simultaneously to the nanobody binding site and the adjacent MyoA binding groove would prevent MyoA binding by MTIP.
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Affiliation(s)
- Susmita Khamrui
- Department of Biochemistry, Biomolecular Structure Center, School of Medicine, University of Washington, Seattle, WA 98195, United States
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15
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Bukowska MA, Grütter MG. New concepts and aids to facilitate crystallization. Curr Opin Struct Biol 2013; 23:409-16. [PMID: 23578532 DOI: 10.1016/j.sbi.2013.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 03/08/2013] [Accepted: 03/13/2013] [Indexed: 12/20/2022]
Abstract
Novel tools and technologies are required to obtain structural information of difficult to crystallize complex biological systems such as membrane proteins, multiprotein assemblies, transient conformational states and intrinsically disordered proteins. One promising approach is to select a high affinity and specificity-binding partner (crystallization chaperone), form a complex with the protein of interest and crystallize the complex. Often the chaperone reduces the conformational freedom of the target protein and additionally facilitates the formation of well-ordered crystals. This review provides an update on the recent successes in chaperone-assisted crystallography. We also stress the importance of synergistic approaches involving protein engineering, crystallization chaperones and crystallization additives. Recent examples demonstrate that investment in such approaches can be key to success.
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Sherwood LJ, Hayhurst A. Ebolavirus nucleoprotein C-termini potently attract single domain antibodies enabling monoclonal affinity reagent sandwich assay (MARSA) formulation. PLoS One 2013; 8:e61232. [PMID: 23577211 PMCID: PMC3618483 DOI: 10.1371/journal.pone.0061232] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [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: 12/31/2012] [Accepted: 03/06/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Antigen detection assays can play an important part in environmental surveillance and diagnostics for emerging threats. We are interested in accelerating assay formulation; targeting the agents themselves to bypass requirements for a priori genome information or surrogates. Previously, using in vitro affinity reagent selection on Marburg virus we rapidly established monoclonal affinity reagent sandwich assay (MARSA) where one recombinant antibody clone was both captor and tracer for polyvalent nucleoprotein (NP). Hypothesizing that the closely related Ebolavirus genus may share the same Achilles' heel, we redirected the scheme to see whether similar assays could be delivered and began to explore their mechanism. METHODS AND FINDINGS In parallel we selected panels of llama single domain antibodies (sdAb) from a semi-synthetic library against Zaire, Sudan, Ivory Coast, and Reston Ebola viruses. Each could perform as both captor and tracer in the same antigen sandwich capture assay thereby forming MARSAs. All sdAb were specific for NP and those tested required the C-terminal domain for recognition. Several clones were cross-reactive, indicating epitope conservation across the Ebolavirus genus. Analysis of two immune shark sdAb revealed they also targeted the C-terminal domain, and could be similarly employed, yet were less sensitive than a comparable llama sdAb despite stemming from immune selections. CONCLUSIONS The C-terminal domain of Ebolavirus NP is a strong attractant for antibodies and enables sensitive sandwich immunoassays to be rapidly generated using a single antibody clone. The polyvalent nature of nucleocapsid borne NP and display of the C-terminal region likely serves as a bountiful affinity sink during selections, and a highly avid target for subsequent immunoassay capture. Combined with the high degree of amino acid conservation through 37 years and across wide geographies, this domain makes an ideal handle for monoclonal affinity reagent driven antigen sandwich assays for the Ebolavirus genus.
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Affiliation(s)
- Laura J. Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
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Park YJ, Hol WGJ. Explorations of linked editosome domains leading to the discovery of motifs defining conserved pockets in editosome OB-folds. J Struct Biol 2012; 180:362-73. [PMID: 22902563 PMCID: PMC3483419 DOI: 10.1016/j.jsb.2012.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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: 05/21/2012] [Revised: 07/26/2012] [Accepted: 07/31/2012] [Indexed: 01/07/2023]
Abstract
Trypanosomatids form a group of protozoa which contain parasites of human, animals and plants. Several of these species cause major human diseases, including Trypanosoma brucei which is the causative agent of human African trypanosomiasis, also called sleeping sickness. These organisms have many highly unusual features including a unique U-insertion/deletion RNA editing process in the single mitochondrion. A key multi-protein complex, called the ∼20S editosome, or editosome, carries out a cascade of essential RNA-modifying reactions and contains a core of 12 different proteins of which six are the interaction proteins A1 to A6. Each of these interaction proteins comprises a C-terminal OB-fold and the smallest interaction protein A6 has been shown to interact with four other editosome OB-folds. Here we report the results of a "linked OB-fold" approach to obtain a view of how multiple OB-folds might interact in the core of the editosome. Constructs with variants of linked domains in 25 expression and co-expression experiments resulted in 13 soluble multi-OB-fold complexes. In several instances, these complexes were more homogeneous in size than those obtained from corresponding unlinked OB-folds. The crystal structure of A3(OB) linked to A6 could be elucidated and confirmed the tight interaction between these two OB domains as seen also in our recent complex of A3(OB) and A6 with nanobodies. In the current crystal structure of A3(OB) linked to A6, hydrophobic side chains reside in well-defined pockets of neighboring OB-fold domains. When analyzing the available crystal structures of editosome OB-folds, it appears that in five instances "Pocket 1" of A1(OB), A3(OB) and A6 is occupied by a hydrophobic side chain from a neighboring protein. In these three different OB-folds, Pocket 1 is formed by two conserved sequence motifs and an invariant arginine. These pockets might play a key role in the assembly or mechanism of the editosome by interacting with hydrophobic side chains from other proteins.
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Affiliation(s)
- Young-Jun Park
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Wim G. J. Hol
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA,To whom correspondence should be addressed. Telephone: +1 (206) 685 7044; Fax: +1 (206) 685 7002;
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18
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Kala S, Moshiri H, Mehta V, Yip CW, Salavati R. The oligonucleotide binding (OB)-fold domain of KREPA4 is essential for stable incorporation into editosomes. PLoS One 2012; 7:e46864. [PMID: 23056494 PMCID: PMC3464273 DOI: 10.1371/journal.pone.0046864] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 08/06/2012] [Accepted: 09/06/2012] [Indexed: 12/28/2022] Open
Abstract
Most mitochondrial mRNAs in trypanosomatid parasites require uridine insertion/deletion RNA editing, a process mediated by guide RNA (gRNA) and catalyzed by multi-protein complexes called editosomes. The six oligonucleotide/oligosaccharide binding (OB)-fold proteins (KREPA1-A6), are a part of the common core of editosomes. They form a network of interactions among themselves as well as with the insertion and deletion sub-complexes and are essential for the stability of the editosomes. KREPA4 and KREPA6 proteins bind gRNA in vitro and are known to interact directly in yeast two-hybrid analysis. In this study, using several approaches we show a minimal interaction surface of the KREPA4 protein that is required for this interaction. By screening a series of N- and C-terminally truncated KREPA4 fragments, we show that a predicted α-helix of KREPA4 OB-fold is required for its interaction with KREPA6. An antibody against the KREPA4 α-helix or mutations of this region can eliminate association with KREPA6; while a peptide fragment corresponding to the α-helix can independently interact with KREPA6, thereby supporting the identification of KREPA4-KREPA6 interface. We also show that the predicted OB-fold of KREPA4; independent of its interaction with gRNA, is responsible for the stable integration of KREPA4 in the editosomes, and editing complexes co-purified with the tagged OB-fold can catalyze RNA editing. Therefore, we conclude that while KREPA4 interacts with KREPA6 through the α-helix region of its OB-fold, the entire OB-fold is required for its integration in the functional editosome, through additional protein-protein interactions.
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Affiliation(s)
- Smriti Kala
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Houtan Moshiri
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Vaibhav Mehta
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Chun Wai Yip
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
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Park YJ, Budiarto T, Wu M, Pardon E, Steyaert J, Hol WGJ. The structure of the C-terminal domain of the largest editosome interaction protein and its role in promoting RNA binding by RNA-editing ligase L2. Nucleic Acids Res 2012; 40:6966-77. [PMID: 22561373 PMCID: PMC3413154 DOI: 10.1093/nar/gks369] [Citation(s) in RCA: 17] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 12/20/2022] Open
Abstract
Trypanosomatids, such as the sleeping sickness parasite Trypanosoma brucei, contain a ∼ 20S RNA-editing complex, also called the editosome, which is required for U-insertion/deletion editing of mitochondrial mRNAs. The editosome contains a core of 12 proteins including the large interaction protein A1, the small interaction protein A6, and the editing RNA ligase L2. Using biochemical and structural data, we identified distinct domains of T. brucei A1 which specifically recognize A6 and L2. We provide evidence that an N-terminal domain of A1 interacts with the C-terminal domain of L2. The C-terminal domain of A1 appears to be required for the interaction with A6 and also plays a key role in RNA binding by the RNA-editing ligase L2 in trans. Three crystal structures of the C-terminal domain of A1 have been elucidated, each in complex with a nanobody as a crystallization chaperone. These structures permitted the identification of putative dsRNA recognition sites. Mutational analysis of conserved residues of the C-terminal domain identified Arg703, Arg731 and Arg734 as key requirements for RNA binding. The data show that the editing RNA ligase activity is modulated by a novel mechanism, i.e. by the trans-acting RNA binding C-terminal domain of A1.
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Affiliation(s)
- Young-Jun Park
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA, Structural Biology Brussels, Vrije Universiteit Brussel and Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Tanya Budiarto
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA, Structural Biology Brussels, Vrije Universiteit Brussel and Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Meiting Wu
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA, Structural Biology Brussels, Vrije Universiteit Brussel and Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Els Pardon
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA, Structural Biology Brussels, Vrije Universiteit Brussel and Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Jan Steyaert
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA, Structural Biology Brussels, Vrije Universiteit Brussel and Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Wim G. J. Hol
- Biomolecular Structure Center, Department of Biochemistry, School of Medicine, University of Washington, Seattle, WA 98195, USA, Structural Biology Brussels, Vrije Universiteit Brussel and Department of Structural Biology, VIB, Pleinlaan 2, B-1050 Brussels, Belgium
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21
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Park YJ, Pardon E, Wu M, Steyaert J, Hol WGJ. Crystal structure of a heterodimer of editosome interaction proteins in complex with two copies of a cross-reacting nanobody. Nucleic Acids Res 2011; 40:1828-40. [PMID: 22039098 PMCID: PMC3287191 DOI: 10.1093/nar/gkr867] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [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] [Indexed: 12/27/2022] Open
Abstract
The parasite Trypanosoma brucei, the causative agent of sleeping sickness across sub-Saharan Africa, depends on a remarkable U-insertion/deletion RNA editing process in its mitochondrion. A approximately 20 S multi-protein complex, called the editosome, is an essential machinery for editing pre-mRNA molecules encoding the majority of mitochondrial proteins. Editosomes contain a common core of twelve proteins where six OB-fold interaction proteins, called A1-A6, play a crucial role. Here, we report the structure of two single-strand nucleic acid-binding OB-folds from interaction proteins A3 and A6 that surprisingly, form a heterodimer. Crystal growth required the assistance of an anti-A3 nanobody as a crystallization chaperone. Unexpectedly, this anti-A3 nanobody binds to both A3(OB) and A6, despite only ~40% amino acid sequence identity between the OB-folds of A3 and A6. The A3(OB)-A6 heterodimer buries 35% more surface area than the A6 homodimer. This is attributed mainly to the presence of a conserved Pro-rich loop in A3(OB). The implications of the A3(OB)-A6 heterodimer, and of a dimer of heterodimers observed in the crystals, for the architecture of the editosome are profound, resulting in a proposal of a 'five OB-fold center' in the core of the editosome.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry, Biomolecular Structure Center, School of Medicine, University of Washington, PO Box 357742, Seattle WA 98195, USA
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22
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Korotkov KV, Johnson TL, Jobling MG, Pruneda J, Pardon E, Héroux A, Turley S, Steyaert J, Holmes RK, Sandkvist M, Hol WGJ. Structural and functional studies on the interaction of GspC and GspD in the type II secretion system. PLoS Pathog 2011; 7:e1002228. [PMID: 21931548 PMCID: PMC3169554 DOI: 10.1371/journal.ppat.1002228] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [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: 05/19/2011] [Accepted: 07/21/2011] [Indexed: 12/02/2022] Open
Abstract
Type II secretion systems (T2SSs) are critical for secretion of many proteins from Gram-negative bacteria. In the T2SS, the outer membrane secretin GspD forms a multimeric pore for translocation of secreted proteins. GspD and the inner membrane protein GspC interact with each other via periplasmic domains. Three different crystal structures of the homology region domain of GspC (GspCHR) in complex with either two or three domains of the N-terminal region of GspD from enterotoxigenic Escherichia coli show that GspCHR adopts an all-β topology. N-terminal β-strands of GspC and the N0 domain of GspD are major components of the interface between these inner and outer membrane proteins from the T2SS. The biological relevance of the observed GspC–GspD interface is shown by analysis of variant proteins in two-hybrid studies and by the effect of mutations in homologous genes on extracellular secretion and subcellular distribution of GspC in Vibrio cholerae. Substitutions of interface residues of GspD have a dramatic effect on the focal distribution of GspC in V. cholerae. These studies indicate that the GspCHR–GspDN0 interactions observed in the crystal structure are essential for T2SS function. Possible implications of our structures for the stoichiometry of the T2SS and exoprotein secretion are discussed. Many bacterial pathogens affecting humans, animals and plants export diverse proteins across the cell membranes into the medium surrounding the bacteria. Some of these secreted proteins are involved in pathogenesis. One example is cholera toxin secreted by the bacterium Vibrio cholerae, a causative agent of cholera. The sophisticated type II secretion system is responsible for moving this toxin, and several other proteins, across the outer membrane. Here, we studied the interaction between the outer membrane pore of the type II secretion system, the secretin GspD, and the inner membrane protein GspC. We have solved three crystal structures of complexes between the interacting domains and identified critical contacts in the GspC–GspD interface. We also showed the importance of these contacts for assembly of the secretion system and for secretion of proteins by V. cholerae. Our studies provide a major piece in the puzzle of how the type II secretion system is assembled and how it functions. One day this knowledge might allow us to design compounds which interfere with this secretion process. Such compounds would be useful in the battle against bacteria affecting human health.
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Affiliation(s)
- Konstantin V. Korotkov
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, Washington, United States of America
| | - Tanya L. Johnson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Michael G. Jobling
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Jonathan Pruneda
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, Washington, United States of America
| | - Els Pardon
- Department of Molecular and Cellular Interactions, VIB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Annie Héroux
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Stewart Turley
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, Washington, United States of America
| | - Jan Steyaert
- Department of Molecular and Cellular Interactions, VIB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Randall K. Holmes
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Maria Sandkvist
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Wim G. J. Hol
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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23
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Aphasizhev R, Aphasizheva I. Uridine insertion/deletion editing in trypanosomes: a playground for RNA-guided information transfer. Wiley Interdiscip Rev RNA 2011; 2:669-85. [PMID: 21823228 PMCID: PMC3154072 DOI: 10.1002/wrna.82] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [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] [Indexed: 01/08/2023]
Abstract
RNA editing is a collective term referring to enzymatic processes that change RNA sequence apart from splicing, 5' capping or 3' extension. In this article, we focus on uridine insertion/deletion mRNA editing found exclusively in mitochondria of kinetoplastid protists. This type of editing corrects frameshifts, introduces start and stops codons, and often adds much of the coding sequence to create an open reading frame. The mitochondrial genome of trypanosomatids, the most extensively studied clade within the order Kinetoplastida, is composed of ∼50 maxicircles with limited coding capacity and thousands of minicircles. To produce functional mRNAs, a multitude of nuclear-encoded factors mediate interactions of maxicircle-encoded pre-mRNAs with a vast repertoire of minicircle-encoded guide RNAs. Editing reactions of mRNA cleavage, U-insertions or U-deletions, and ligation are catalyzed by the RNA editing core complex (RECC, the 20S editosome) while each step of this enzymatic cascade is directed by guide RNAs. These 50-60 nucleotide (nt) molecules are 3' uridylated by RET1 TUTase and stabilized via association with the gRNA binding complex (GRBC). Remarkably, the information transfer between maxicircle and minicircle transcriptomes does not rely on template-dependent polymerization of nucleic acids. Instead, intrinsic substrate specificities of key enzymes are largely responsible for the fidelity of editing. Conversely, the efficiency of editing is enhanced by assembling enzymes and RNA binding proteins into stable multiprotein complexes. WIREs RNA 2011 2 669-685 DOI: 10.1002/wrna.82 For further resources related to this article, please visit the WIREs website.
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MESH Headings
- Endonucleases/chemistry
- Endonucleases/genetics
- Endonucleases/metabolism
- Models, Biological
- Models, Molecular
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA Editing/genetics
- RNA Editing/physiology
- RNA Helicases/chemistry
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/chemistry
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Trypanosoma/genetics
- Trypanosoma/metabolism
- Uridine/chemistry
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, USA.
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24
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Steyaert J, Kobilka BK. Nanobody stabilization of G protein-coupled receptor conformational states. Curr Opin Struct Biol 2011; 21:567-72. [PMID: 21782416 DOI: 10.1016/j.sbi.2011.06.011] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 06/28/2011] [Accepted: 06/30/2011] [Indexed: 11/30/2022]
Abstract
Remarkable progress has been made in the field of G protein-coupled receptor (GPCR) structural biology during the past four years. Several obstacles to generating diffraction quality crystals of GPCRs have been overcome by combining innovative methods ranging from protein engineering to lipid-based screens and microdiffraction technology. The initial GPCR structures represent energetically stable inactive-state conformations. However, GPCRs signal through different G protein isoforms or G protein-independent effectors upon ligand binding suggesting the existence of multiple ligand-specific active states. These active-state conformations are unstable in the absence of specific cytosolic signaling partners representing new challenges for structural biology. Camelid single chain antibody fragments (nanobodies) show promise for stabilizing active GPCR conformations and as chaperones for crystallogenesis.
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Affiliation(s)
- Jan Steyaert
- Department of Molecular and Cellular Interactions, Vlaams Instituut voor Biotechnologie & Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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Abstract
BACKGROUND Single-domain antibody fragments possess structural features, such as a small dimension, an elevated stability, and the singularity of recognizing epitopes non-accessible for conventional antibodies that make them interesting for several research and biotechnological applications. RESULTS The discovery of the single-domain antibody's potentials has stimulated their use in an increasing variety of fields. The rapid accumulation of articles describing new applications and further developments of established approaches has made it, therefore, necessary to update the previous reviews with a new and more complete summary of the topic. CONCLUSIONS Beside the necessary task of updating, this work analyses in detail some applicative aspects of the single-domain antibodies that have been overseen in the past, such as their efficacy in affinity chromatography, as co-crystallization chaperones, protein aggregation controllers, enzyme activity tuners, and the specificities of the unconventional single-domain fragments.
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Affiliation(s)
- Ario de Marco
- University of Nova Gorica (UNG), Vipavska 13, PO Box 301-SI-5000, Rožna Dolina (Nova Gorica), Slovenia.
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26
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Abstract
Three distinct editosomes, typified by mutually exclusive KREN1, KREN2, or KREN3 endonucleases, are essential for mitochondrial RNA editing in Trypanosoma brucei. The three editosomes differ in substrate endoribonucleolytic cleavage specificity, which may reflect the vast number of editing sites that need insertion or deletion of uridine nucleotides (Us). Each editosome requires the single RNase III domain in each endonuclease for catalysis. Studies reported here show that the editing endonucleases do not form homodimeric domains, and may therefore function as intermolecular heterodimers, perhaps with KREPB4 and/or KREPB5. Editosomes isolated via TAP tag fused to KREPB6, KREPB7, or KREPB8 have a common set of 12 proteins. In addition, KREN3 is only found in KREPB6 editosomes, KREN2 is only found in KREPB7 editosomes, and KREN1 is only found in KREPB8 editosomes. These are the same associations previously found in editosomes isolated via the TAP-tagged endonucleases KREN1, KREN2, or KREN3. Furthermore, TAP-tagged KREPB6, KREPB7, and KREPB8 complexes isolated from cells in which expression of their respective endonuclease were knocked down were disrupted and lacked the heterotrimeric insertion subcomplex (KRET2, KREPA1, and KREL2). These results and published data suggest that KREPB6, KREPB7, and KREPB8 associate with the deletion subcomplex, whereas the KREN1, KREN2, and KREN3 endonucleases associate with the insertion subcomplex.
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Affiliation(s)
- Jason Carnes
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
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