1
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Adámik M, Soldánová Z, Drotárová M, Brečková K, Petr M, Helma R, Jenner LP, Vorlíčková M, Sýkorová E, Brázdová M. Human ARMC6 binds in vitro to both cancer genes and telomeric RNA, favoring G-quadruplex structure recognition. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195050. [PMID: 39029558 DOI: 10.1016/j.bbagrm.2024.195050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/25/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
Armadillo repeat-containing proteins (ARMCs) are a large family found throughout eukaryotes, which play prominent roles in cell adhesion, signaling and cytoskeletal regulation. The ARMC6 protein is highly conserved in primates, including humans, but to date does not have a clear function beyond initial hints of a link to cancer and telomerase activity. We report here in vitro experiments showing ARMC6 binding to DNA promoter sequences from several cancer-related genes (e.g., EGFR, VEGF and c-MYC), and also to the telomeric RNA repeat (TERRA). ARMC6 binding activity appears to recognize G-quadruplex motifs, which are being increasingly implicated as structure-based protein binding sites in chromosome maintenance and repair. In vivo investigation of ARMC6 function revealed that when this protein is overexpressed in human cell lines, there is different expression of genes connected with oncogenic pathways and those implicated in downstream non-canonical telomerase pathways (e.g., VEGF, hTERT, c-MYC, ESM1, MMP3). ARMC6 is already known to interact with human shelterin protein TRF2 and telomerase. The protein binds G-quadruplex structures and does so preferentially to RNA over DNA. As such, this protein may be an example of how a non-canonical nucleic acid structural motif allows mediation between gene regulation and telomeric chromatin rearrangement pathways.
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Affiliation(s)
- Matej Adámik
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Zuzana Soldánová
- Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého 1/3, 612 42 Brno, Czech Republic
| | - Magdaléna Drotárová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Katarína Brečková
- Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého 1/3, 612 42 Brno, Czech Republic
| | - Marek Petr
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Robert Helma
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Leon P Jenner
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic; Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého 1/3, 612 42 Brno, Czech Republic.
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2
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Carnes J, Gendrin C, McDermott SM, Stuart K. KRGG1 function in RNA editing in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2023; 29:228-240. [PMID: 36400448 PMCID: PMC9891254 DOI: 10.1261/rna.079418.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/11/2022] [Indexed: 05/20/2023]
Abstract
Mitochondrial gene expression in trypanosomes requires numerous multiprotein complexes that are unique to kinetoplastids. Among these, the most well characterized are RNA editing catalytic complexes (RECCs) that catalyze the guide RNA (gRNA)-specified insertion and deletion of uridines during mitochondrial mRNA maturation. This post-transcriptional resequencing of mitochondrial mRNAs can be extensive, involving dozens of different gRNAs and hundreds of editing sites with most of the mature mRNA sequences resulting from the editing process. Proper coordination of the editing with the cognate gRNAs is attributed to RNA editing substrate-binding complexes (RESCs), which are also required for RNA editing. Although the precise mechanism of RESC function is less well understood, their affinity for binding both editing substrates and products suggests that these complexes may provide a scaffold for RECC catalytic processing. KRGG1 has been shown to bind RNAs, and although affinity purification co-isolates RESC complexes, its role in RNA editing remains uncertain. We show here that KRGG1 is essential in BF parasites and required for normal editing. KRGG1 repression results in reduced amounts of edited A6 mRNA and increased amounts of edited ND8 mRNA. Sequence and structure analysis of KRGG1 identified a region of homology with RESC6, and both proteins have predicted tandem helical repeats that resemble ARM/HEAT motifs. The ARM/HEAT-like region is critical for function as exclusive expression of mutated KRGG1 results in growth inhibition and disruption of KRGG1 association with RESCs. These results indicate that KRGG1 is critical for RNA editing and its specific function is associated with RESC activity.
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Affiliation(s)
- Jason Carnes
- Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Claire Gendrin
- Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | | | - Kenneth Stuart
- Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics and Global Health, University of Washington, Seattle, Washington 98105, USA
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3
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Friedrich D, Marintchev A, Arthanari H. The metaphorical swiss army knife: The multitude and diverse roles of HEAT domains in eukaryotic translation initiation. Nucleic Acids Res 2022; 50:5424-5442. [PMID: 35552740 PMCID: PMC9177959 DOI: 10.1093/nar/gkac342] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
Biomolecular associations forged by specific interaction among structural scaffolds are fundamental to the control and regulation of cell processes. One such structural architecture, characterized by HEAT repeats, is involved in a multitude of cellular processes, including intracellular transport, signaling, and protein synthesis. Here, we review the multitude and versatility of HEAT domains in the regulation of mRNA translation initiation. Structural and cellular biology approaches, as well as several biophysical studies, have revealed that a number of HEAT domain-mediated interactions with a host of protein factors and RNAs coordinate translation initiation. We describe the basic structural architecture of HEAT domains and briefly introduce examples of the cellular processes they dictate, including nuclear transport by importin and RNA degradation. We then focus on proteins in the translation initiation system featuring HEAT domains, specifically the HEAT domains of eIF4G, DAP5, eIF5, and eIF2Bϵ. Comparative analysis of their remarkably versatile interactions, including protein-protein and protein-RNA recognition, reveal the functional importance of flexible regions within these HEAT domains. Here we outline how HEAT domains orchestrate fundamental aspects of translation initiation and highlight open mechanistic questions in the area.
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Affiliation(s)
- Daniel Friedrich
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Assen Marintchev
- Department of Physiology & Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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4
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Funk H, DiVita DJ, Sizemore HE, Wehrle K, Miller CLW, Fraley ME, Mullins AK, Guy AR, Phizicky EM, Guy MP. Identification of a Trm732 Motif Required for 2'- O-methylation of the tRNA Anticodon Loop by Trm7. ACS OMEGA 2022; 7:13667-13675. [PMID: 35559166 PMCID: PMC9088939 DOI: 10.1021/acsomega.1c07231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Posttranscriptional tRNA modifications are essential for proper gene expression, and defects in the enzymes that perform tRNA modifications are associated with numerous human disorders. Throughout eukaryotes, 2'-O-methylation of residues 32 and 34 of the anticodon loop of tRNA is important for proper translation, and in humans, a lack of these modifications results in non-syndromic X-linked intellectual disability. In yeast, the methyltransferase Trm7 forms a complex with Trm732 to 2'-O-methylate tRNA residue 32 and with Trm734 to 2'-O-methylate tRNA residue 34. Trm732 and Trm734 are required for the methylation activity of Trm7, but the role of these auxiliary proteins is not clear. Additionally, Trm732 and Trm734 homologs are implicated in biological processes not directly related to translation, suggesting that these proteins may have additional cellular functions. To identify critical amino acids in Trm732, we generated variants and tested their ability to function in yeast cells. We identified a conserved RRSAGLP motif in the conserved DUF2428 domain of Trm732 that is required for tRNA modification activity by both yeast Trm732 and its human homolog, THADA. The identification of Trm732 variants that lack tRNA modification activity will help to determine if other biological functions ascribed to Trm732 and THADA are directly due to tRNA modification or to secondary effects due to other functions of these proteins.
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Affiliation(s)
- Holly
M. Funk
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Daisy J. DiVita
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Hannah E. Sizemore
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Kendal Wehrle
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Catherine L. W. Miller
- Department
of Biochemistry and Biophysics, University
of Rochester School of Medicine, Rochester, New York 14642, United States
| | - Morgan E. Fraley
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Alex K. Mullins
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Adrian R. Guy
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Eric M. Phizicky
- Department
of Biochemistry and Biophysics, University
of Rochester School of Medicine, Rochester, New York 14642, United States
| | - Michael P. Guy
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
- Department
of Biochemistry and Biophysics, University
of Rochester School of Medicine, Rochester, New York 14642, United States
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5
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Scaltsoyiannes V, Corre N, Waltz F, Giegé P. Types and Functions of Mitoribosome-Specific Ribosomal Proteins across Eukaryotes. Int J Mol Sci 2022; 23:ijms23073474. [PMID: 35408834 PMCID: PMC8998825 DOI: 10.3390/ijms23073474] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are key organelles that combine features inherited from their bacterial endosymbiotic ancestor with traits that arose during eukaryote evolution. These energy producing organelles have retained a genome and fully functional gene expression machineries including specific ribosomes. Recent advances in cryo-electron microscopy have enabled the characterization of a fast-growing number of the low abundant membrane-bound mitochondrial ribosomes. Surprisingly, mitoribosomes were found to be extremely diverse both in terms of structure and composition. Still, all of them drastically increased their number of ribosomal proteins. Interestingly, among the more than 130 novel ribosomal proteins identified to date in mitochondria, most of them are composed of a-helices. Many of them belong to the nuclear encoded super family of helical repeat proteins. Here we review the diversity of functions and the mode of action held by the novel mitoribosome proteins and discuss why these proteins that share similar helical folds were independently recruited by mitoribosomes during evolution in independent eukaryote clades.
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Affiliation(s)
- Vassilis Scaltsoyiannes
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
| | - Nicolas Corre
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
| | - Florent Waltz
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Munich, Germany
- Correspondence: (F.W.); (P.G.); Tel.: +33-3-6715-5363 (P.G.); Fax: +33-3-8861-4442 (P.G.)
| | - Philippe Giegé
- CNRS, Institut de Biologie Moléculaire des Plantes, Université de Strasbourg, 67084 Strasbourg, France; (V.S.); (N.C.)
- Correspondence: (F.W.); (P.G.); Tel.: +33-3-6715-5363 (P.G.); Fax: +33-3-8861-4442 (P.G.)
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6
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Wobbe L. The Molecular Function of Plant mTERFs as Key Regulators of Organellar Gene Expression. PLANT & CELL PHYSIOLOGY 2021; 61:2004-2017. [PMID: 33067620 DOI: 10.1093/pcp/pcaa132] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/25/2020] [Indexed: 05/27/2023]
Abstract
The protein family of mTERFs (mitochondrial transcription termination factors) was initially studied in mammalian and insect mitochondria before the first Arabidopsis mTERF mutant was characterized. More than 10 years of research on the function of plant mTERFs in the flowering plants Arabidopsis thaliana, Zea mays and the green microalga Chlamydomonas reinhardtii has since highlighted that mTERFs are key regulators of organellar gene expression (OGE) in mitochondria and in chloroplasts. Additional functions to be fulfilled by plant mTERFs (e.g. splicing) and the fact that the expression of two organellar genomes had to be facilitated have led to a massive expansion of the plant mTERF portfolio compared to that found in mammals. Plant mTERFs are implicated in all steps of OGE ranging from the modulation of transcription to the maturation of tRNAs and hence translation. Furthermore, being regulators of OGE, mTERFs are required for a successful long-term acclimation to abiotic stress, retrograde signaling and interorganellar communication. Here, I review the recent progress in the elucidation of molecular mTERF functions.
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Affiliation(s)
- Lutz Wobbe
- Algae Biotechnology & Bioenergy Group, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universit�tsstrasse 27, Bielefeld 33615, Germany
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7
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Méteignier LV, Ghandour R, Zimmerman A, Kuhn L, Meurer J, Zoschke R, Hammani K. Arabidopsis mTERF9 protein promotes chloroplast ribosomal assembly and translation by establishing ribonucleoprotein interactions in vivo. Nucleic Acids Res 2021; 49:1114-1132. [PMID: 33398331 PMCID: PMC7826268 DOI: 10.1093/nar/gkaa1244] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/07/2020] [Accepted: 12/13/2020] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial transcription termination factor proteins are nuclear-encoded nucleic acid binders defined by degenerate tandem helical-repeats of ∼30 amino acids. They are found in metazoans and plants where they localize in organelles. In higher plants, the mTERF family comprises ∼30 members and several of these have been linked to plant development and response to abiotic stress. However, knowledge of the molecular basis underlying these physiological effects is scarce. We show that the Arabidopsis mTERF9 protein promotes the accumulation of the 16S and 23S rRNAs in chloroplasts, and interacts predominantly with the 16S rRNA in vivo and in vitro. Furthermore, mTERF9 is found in large complexes containing ribosomes and polysomes in chloroplasts. The comprehensive analysis of mTERF9 in vivo protein interactome identified many subunits of the 70S ribosome whose assembly is compromised in the null mterf9 mutant, putative ribosome biogenesis factors and CPN60 chaperonins. Protein interaction assays in yeast revealed that mTERF9 directly interact with these proteins. Our data demonstrate that mTERF9 integrates protein-protein and protein-RNA interactions to promote chloroplast ribosomal assembly and translation. Besides extending our knowledge of mTERF functional repertoire in plants, these findings provide an important insight into the chloroplast ribosome biogenesis.
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Affiliation(s)
- Louis-Valentin Méteignier
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Rabea Ghandour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Aude Zimmerman
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Jörg Meurer
- Plant Sciences, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Kamel Hammani
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
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8
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Li J, Ma X, Banerjee S, Baruah S, Schnicker NJ, Roh E, Ma W, Liu K, Bode AM, Dong Z. Structural basis for multifunctional roles of human Ints3 C-terminal domain. J Biol Chem 2021; 296:100112. [PMID: 33434574 PMCID: PMC7948952 DOI: 10.1074/jbc.ra120.016393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 11/06/2022] Open
Abstract
Proper repair of damaged DNA is critical for the maintenance of genome stability. A complex composed of Integrator subunit 3 (Ints3), single-stranded DNA-binding protein 1 (SSB1), and SSB-interacting protein 1 (SSBIP1) is required for efficient homologous recombination-dependent repair of double-strand breaks (DSBs) and ataxia-telangiectasia mutated (ATM)-dependent signaling pathways. It is known that in this complex the Ints3 N-terminal domain scaffolds SSB1 and SSBIP1. However, the molecular basis for the function of the Ints3 C-terminal domain remains unclear. Here, we present the crystal structure of the Ints3 C-terminal domain, uncovering a HEAT-repeat superhelical fold. Using structure and mutation analysis, we show that the C-terminal domain exists as a stable dimer. A basic groove and a cluster of conserved residues on two opposite sides of the dimer bind single-stranded RNA/DNA (ssRNA/ssDNA) and Integrator complex subunit 6 (Ints6), respectively. Dimerization is required for nucleic acid binding, but not for Ints6 binding. Additionally, in vitro experiments using HEK 293T cells demonstrate that Ints6 interaction is critical for maintaining SSB1 protein level. Taken together, our findings establish the structural basis of a multifunctional Ints3 C-terminal module, allowing us to propose a novel mode of nucleic acid recognition by helical repeat protein and paving the way for future mechanistic studies.
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Affiliation(s)
- Jian Li
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA; China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Xinli Ma
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA; China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Surajit Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, USA
| | - Sankar Baruah
- Protein and Crystallography Facility, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Nicholas J Schnicker
- Protein and Crystallography Facility, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Eunmiri Roh
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA; Department of Cosmetic Science, Kwangju Women's University, Gwangju, Republic of Korea
| | - Weiya Ma
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Kangdong Liu
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China; College of Medicine, Zhengzhou University, Zhengzhou, Henan, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Zigang Dong
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China; College of Medicine, Zhengzhou University, Zhengzhou, Henan, China.
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9
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Votaw KA, McCullagh M. Characterization of the Search Complex and Recognition Mechanism of the AlkD-DNA Glycosylase. J Phys Chem B 2018; 123:95-105. [PMID: 30525620 DOI: 10.1021/acs.jpcb.8b09555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA damage is a routine problem for cells, and pathways such as base excision repair have evolved to protect the genome by using DNA glycosylases to first recognize and excise lesions. The search mechanism of these enzymes is of particular interest due to the seemingly intractable problem of probing the billions of base pairs in the genome for potential damage. It has been hypothesized that glycosylases form multiple protein-DNA conformational states to efficiently search and recognize DNA lesions, ultimately only flipping out the damaged substrate into the active site. A unique DNA glycosylase, the Bacillus cereus AlkD enzyme, has been shown to excise damaged DNA without flipping the nucleobase into a protein binding pocket following lesion recognition. Here, we use microsecond-scale all-atom molecular dynamics simulations to characterize the AlkD recognition mechanism, putting it in perspective with other DNA glycosylases. We first identify and describe two distinct enzyme-DNA conformations of AlkD: the search complex (SC) and excision complex (EC). The SC is distinguished by the linearity of DNA, changes in four helical parameters in the vicinity of the lesion, and changes in distance between active site residues and the DNA. Free DNA simulations are used to demonstrate that the DNA structural deviations and increased active site interactions present in the EC are initiated by the recognition of a methylation-induced signal in the rises both 5' to the methylation and opposing this base. Our results support the hypothesis that subtle geometric distortions in DNA are recognized by AlkD and are consequently probed to initiate concerted protein and DNA conformational changes which prime excise without additional intermediate states. This mechanism is shown to be consistent among the three methylated DNA sequences that have been crystallized bound to AlkD.
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Affiliation(s)
- Kevin A Votaw
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523, United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523, United States
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10
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Shi R, Shen XX, Rokas A, Eichman BF. Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases. Bioessays 2018; 40:e1800133. [PMID: 30264543 DOI: 10.1002/bies.201800133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/27/2018] [Indexed: 11/08/2022]
Abstract
DNA glycosylases remove aberrant DNA nucleobases as the first enzymatic step of the base excision repair (BER) pathway. The alkyl-DNA glycosylases AlkC and AlkD adopt a unique structure based on α-helical HEAT repeats. Both enzymes identify and excise their substrates without a base-flipping mechanism used by other glycosylases and nucleic acid processing proteins to access nucleobases that are otherwise stacked inside the double-helix. Consequently, these glycosylases act on a variety of cationic nucleobase modifications, including bulky adducts, not previously associated with BER. The related non-enzymatic HEAT-like repeat (HLR) proteins, AlkD2, and AlkF, have unique nucleic acid binding properties that expand the functions of this relatively new protein superfamily beyond DNA repair. Here, we review the phylogeny, biochemistry, and structures of the HLR proteins, which have helped broaden our understanding of the mechanisms by which DNA glycosylases locate and excise chemically modified DNA nucleobases.
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Affiliation(s)
- Rongxin Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
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11
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Silvestrov P, Cisneros GA. Insights into conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations. Theor Chem Acc 2018; 137:78. [PMID: 30078993 PMCID: PMC6071674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Structural integrity of DNA molecules is necessary for their information storage function. Cells rely on a number of pathways to ensure that the damage to DNA induced by endogenous and exogenous reagents is repaired. AlkD, a base excision enzyme, removes a damaged nucleobase by cleaving a glycosidic bond. Unlike many other base excision enzymes, AlkD does not flip a damaged nucleobase into a designated reaction pocket, and as such can repair nucleobases with larger adducts, such as yatakemycin. In this study, the structure and dynamics of AlkD have been investigated by classical molecular dynamics simulations. Several systems including apo-AlkD, and AlkD in complex with DNA, both with and without the yatakemycin adduct have been simulated. Comparison of the results for the apo-AlkD with AlkD with substrate (damaged or undamaged) indicates a high degree of motion of helix αB in apo-AlkD, whereas this helix is observed to form various contacts when the substrate is bound. The calculated results are consistent with previous experimental studies that have suggested various residues involved in damage recognition, DNA binding, and base excision catalysis.
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Affiliation(s)
- Pavel Silvestrov
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
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12
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Silvestrov P, Cisneros GA. Insights into conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2255-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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13
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Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF. Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO J 2018; 37:63-74. [PMID: 29054852 PMCID: PMC5753038 DOI: 10.15252/embj.201797833] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/11/2017] [Accepted: 09/22/2017] [Indexed: 01/07/2023] Open
Abstract
DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications, and thus, the mechanisms by which glycosylases locate DNA damage are of particular interest. Bacterial AlkC and AlkD are specific for cationic alkylated nucleobases and have a distinctive HEAT-like repeat (HLR) fold. AlkD uses a unique non-base-flipping mechanism that enables excision of bulky lesions more commonly associated with nucleotide excision repair. In contrast, AlkC has a much narrower specificity for small lesions, principally N3-methyladenine (3mA). Here, we describe how AlkC selects for and excises 3mA using a non-base-flipping strategy distinct from that of AlkD. A crystal structure resembling a catalytic intermediate complex shows how AlkC uses unique HLR and immunoglobulin-like domains to induce a sharp kink in the DNA, exposing the damaged nucleobase to active site residues that project into the DNA This active site can accommodate and excise N3-methylcytosine (3mC) and N1-methyladenine (1mA), which are also repaired by AlkB-catalyzed oxidative demethylation, providing a potential alternative mechanism for repair of these lesions in bacteria.
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Affiliation(s)
- Rongxin Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Kori T Lay
- Department of Chemistry, University of California, Davis, CA, USA
| | - Philip K Yuen
- Department of Chemistry, University of California, Davis, CA, USA
| | - Sheila S David
- Department of Chemistry, University of California, Davis, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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14
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Li X, Liu S, Jiang J, Zhang L, Espinosa S, Hill RC, Hansen KC, Zhou ZH, Zhao R. CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing. Nat Commun 2017; 8:1035. [PMID: 29051543 PMCID: PMC5648754 DOI: 10.1038/s41467-017-01241-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/29/2017] [Indexed: 12/23/2022] Open
Abstract
U1 snRNP plays a critical role in 5'-splice site recognition and is a frequent target of alternative splicing factors. These factors transiently associate with human U1 snRNP and are not amenable for structural studies, while their Saccharomyces cerevisiae (yeast) homologs are stable components of U1 snRNP. Here, we report the cryoEM structure of yeast U1 snRNP at 3.6 Å resolution with atomic models for ten core proteins, nearly all essential domains of its RNA, and five stably associated auxiliary proteins. The foot-shaped yeast U1 snRNP contains a core in the "ball-and-toes" region architecturally similar to the human U1 snRNP. All auxiliary proteins are in the "arch-and-heel" region and connected to the core through the Prp42/Prp39 paralogs. Our demonstration that homodimeric human PrpF39 directly interacts with U1C-CTD, mirroring yeast Prp42/Prp39, supports yeast U1 snRNP as a model for understanding how transiently associated auxiliary proteins recruit human U1 snRNP in alternative splicing.
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Affiliation(s)
- Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Shiheng Liu
- Electron Imaging Center for Nanomachines University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA
| | - Jiansen Jiang
- Electron Imaging Center for Nanomachines University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Sara Espinosa
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Z Hong Zhou
- Electron Imaging Center for Nanomachines University of California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, 90095, USA.
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA.
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15
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Pugacheva V, Korotkov A, Korotkov E. Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming. Stat Appl Genet Mol Biol 2017; 15:381-400. [PMID: 27337743 DOI: 10.1515/sagmb-2015-0079] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of this study was to show that amino acid sequences have a latent periodicity with insertions and deletions of amino acids in unknown positions of the analyzed sequence. Genetic algorithm, dynamic programming and random weight matrices were used to develop a new mathematical algorithm for latent periodicity search. A multiple alignment of periods was calculated with help of the direct optimization of the position-weight matrix without using pairwise alignments. The developed algorithm was applied to analyze amino acid sequences of a small number of proteins. This study showed the presence of latent periodicity with insertions and deletions in the amino acid sequences of such proteins, for which the presence of latent periodicity was not previously known. The origin of latent periodicity with insertions and deletions is discussed.
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16
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Jenkins JL, Kielkopf CL. Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures. Trends Genet 2017; 33:336-348. [PMID: 28372848 PMCID: PMC5447463 DOI: 10.1016/j.tig.2017.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 01/08/2023]
Abstract
Somatic mutations of pre-mRNA splicing factors recur among patients with myelodysplastic syndrome (MDS) and related malignancies. Although these MDS-relevant mutations alter the splicing of a subset of transcripts, the mechanisms by which these single amino acid substitutions change gene expression remain controversial. New structures of spliceosome intermediates and associated protein complexes shed light on the molecular interactions mediated by 'hotspots' of the SF3B1 and U2AF1 pre-mRNA splicing factors. The frequently mutated SF3B1 residues contact the pre-mRNA splice site. Based on structural homology with other spliceosome subunits, and recent findings of altered RNA binding by mutant U2AF1 proteins, we suggest that affected U2AF1 residues also contact pre-mRNA. Altered pre-mRNA recognition emerges as a molecular theme among MDS-relevant mutations of pre-mRNA splicing factors.
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Affiliation(s)
- Jermaine L Jenkins
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Clara L Kielkopf
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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17
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Miranda RG, Rojas M, Montgomery MP, Gribbin KP, Barkan A. RNA-binding specificity landscape of the pentatricopeptide repeat protein PPR10. RNA (NEW YORK, N.Y.) 2017; 23:586-599. [PMID: 28108520 PMCID: PMC5340921 DOI: 10.1261/rna.059568.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/09/2017] [Indexed: 05/02/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins comprise a large family of helical repeat proteins that influence gene expression in mitochondria and chloroplasts. PPR tracts can bind RNA via a modular one repeat-one nucleotide mechanism in which the nucleotide is specified by the identities of several amino acids in each repeat. This mode of recognition, the so-called PPR code, offers opportunities for the prediction of native PPR binding sites and the design of proteins to bind specified RNAs. However, a deep understanding of the parameters that dictate the affinity and specificity of PPR-RNA interactions is necessary to realize these goals. We report a comprehensive analysis of the sequence specificity of PPR10, a protein that binds similar RNA sequences of ∼18 nucleotides (nt) near the chloroplast atpH and psaJ genes in maize. We assessed the contribution of each nucleotide in the atpH binding site to PPR10 affinity in vitro by analyzing the effects of single-nucleotide changes at each position. In a complementary approach, the RNAs bound by PPR10 from partially randomized RNA pools were analyzed by deep sequencing. The results revealed three patches in which nucleotide identity has a major impact on binding affinity. These include 5 nt for which protein contacts were not observed in a PPR10-RNA crystal structure and 4 nt that are not explained by current views of the PPR code. These findings highlight aspects of PPR-RNA interactions that pose challenges for binding site prediction and design.
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Affiliation(s)
- Rafael G Miranda
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Margarita Rojas
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | | | - Kyle P Gribbin
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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18
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Chen MZ, Mok SA, Ormsby AR, Muchowski PJ, Hatters DM. N-Terminal Fragments of Huntingtin Longer than Residue 170 form Visible Aggregates Independently to Polyglutamine Expansion. J Huntingtons Dis 2017; 6:79-91. [PMID: 28339398 DOI: 10.3233/jhd-160207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND A hallmark of Huntington's disease is the progressive aggregation of full length and N-terminal fragments of polyglutamine (polyQ)-expanded Huntingtin (Htt) into intracellular inclusions. The production of N-terminal fragments appears important for enabling pathology and aggregation; and hence the direct expression of a variety of N-terminal fragments are commonly used to model HD in animal and cellular models. OBJECTIVE It remains unclear how the length of the N-terminal fragments relates to polyQ - mediated aggregation. We investigated the fundamental intracellular aggregation process of eight different-length N-terminal fragments of Htt in both short (25Q) and long polyQ (97Q). METHODS N-terminal fragments were fused to fluorescent proteins and transiently expressed in mammalian cell culture models. These included the classic exon 1 fragment (90 amino acids) and longer forms of 105, 117, 171, 513, 536, 552, and 586 amino acids based on wild-type Htt (of 23Q) sequence length nomenclature. RESULTS N-terminal fragments of less than 171 amino acids only formed inclusions in polyQ-expanded form. By contrast the longer fragments formed inclusions irrespective of Q-length, with Q-length playing a negligible role in extent of aggregation. The inclusions could be classified into 3 distinct morphological categories. One type (Type A) was universally associated with polyQ expansions whereas the other two types (Types B and C) formed independently of polyQ length expansion. CONCLUSIONS PolyQ-expansion was only required for fragments of less than 171 amino acids to aggregate. Longer fragments aggregated predominately through a non-polyQ mechanism, involving at least one, and probably more distinct clustering mechanisms.
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Affiliation(s)
- Moore Z Chen
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC, Australia
| | - Sue-Ann Mok
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Angelique R Ormsby
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC, Australia
| | | | - Danny M Hatters
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC, Australia
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19
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Listeria monocytogenes DNA Glycosylase AdlP Affects Flagellar Motility, Biofilm Formation, Virulence, and Stress Responses. Appl Environ Microbiol 2016; 82:5144-52. [PMID: 27316964 PMCID: PMC4988193 DOI: 10.1128/aem.00719-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/09/2016] [Indexed: 12/16/2022] Open
Abstract
The temperature-dependent alteration of flagellar motility gene expression is critical for the foodborne pathogen Listeria monocytogenes to respond to a changing environment. In this study, a genetic determinant, L. monocytogenesf2365_0220 (lmof2365_0220), encoding a putative protein that is structurally similar to the Bacillus cereus alkyl base DNA glycosylase (AlkD), was identified. This determinant was involved in the transcriptional repression of flagellar motility genes and was named adlP (encoding an AlkD-like protein [AdlP]). Deletion of adlP activated the expression of flagellar motility genes at 37°C and disrupted the temperature-dependent inhibition of L. monocytogenes motility. The adlP null strains demonstrated decreased survival in murine macrophage-like RAW264.7 cells and less virulence in mice. Furthermore, the deletion of adlP significantly decreased biofilm formation and impaired the survival of bacteria under several stress conditions, including the presence of a DNA alkylation compound (methyl methanesulfonate), an oxidative agent (H2O2), and aminoglycoside antibiotics. Our findings strongly suggest that adlP may encode a bifunctional protein that transcriptionally represses the expression of flagellar motility genes and influences stress responses through its DNA glycosylase activity. IMPORTANCE We discovered a novel protein that we named AlkD-like protein (AdlP). This protein affected flagellar motility, biofilm formation, and virulence. Our data suggest that AdlP may be a bifunctional protein that represses flagellar motility genes and influences stress responses through its DNA glycosylase activity.
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20
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Byrnes J, Hauser K, Norona L, Mejia E, Simmerling C, Garcia-Diaz M. Base Flipping by MTERF1 Can Accommodate Multiple Conformations and Occurs in a Stepwise Fashion. J Mol Biol 2016; 428:2542-2556. [PMID: 26523681 PMCID: PMC4851923 DOI: 10.1016/j.jmb.2015.10.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/14/2015] [Accepted: 10/20/2015] [Indexed: 11/28/2022]
Abstract
Human mitochondrial transcription termination occurs within the leu-tRNA gene and is mediated by the DNA binding protein MTERF1. The crystal structure of MTERF1 bound to the canonical termination sequence reveals a rare base flipping event that involves the eversion of three nucleotides. These nucleotides are stabilized by stacking interactions with three MTERF1 residues, which are essential not only for base flipping but also for termination activity. To further understand the mechanism of base flipping, we examined each of the individual stacking interactions in structural, energetic and functional detail. Individual substitutions of Arg162, Tyr288 and Phe243 have revealed unequal contributions to overall termination activity. Furthermore, our work identifies an important role for Phe322 in the base flipping mechanism and we demonstrate how Phe322 and Phe243 are important for coupling base flipping between the heavy and light strand DNA chains. We propose a stepwise model for the base flipping process that recapitulates our observations. Finally, we show that MTERF1 has the ability to accommodate alternate active conformations. The adaptability of base flipping has implications for MTERF1 function and for the putative function of MTERF1 at alternative binding sites in human mitochondria.
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Affiliation(s)
- James Byrnes
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kevin Hauser
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Leah Norona
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Edison Mejia
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
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21
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Bohne AV, Schwenkert S, Grimm B, Nickelsen J. Roles of Tetratricopeptide Repeat Proteins in Biogenesis of the Photosynthetic Apparatus. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:187-227. [PMID: 27017009 DOI: 10.1016/bs.ircmb.2016.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Biosynthesis of the photosynthetic apparatus is a complex operation, which includes the concerted synthesis and assembly of lipids, pigments and metal cofactors, and dozens of proteins. Research conducted in recent years has shown that these processes, as well as the stabilization and repair of this molecular machinery, are facilitated by transiently acting regulatory proteins, many of which belong to the superfamily of helical repeat proteins. Here, we focus on one of its families in photoautotrophic model organisms, the tetratricopeptide repeat (TPR) proteins, which participate in almost all of these steps and are crucial for biogenesis of the thylakoid membrane.
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Affiliation(s)
- A-V Bohne
- Molecular Plant Sciences, Ludwig-Maximilians-University, Munich, Germany
| | - S Schwenkert
- Botany, Ludwig-Maximilians-University, Munich, Germany
| | - B Grimm
- Institute of Biology/Plant Physiology, Humboldt University, Berlin, Germany
| | - J Nickelsen
- Molecular Plant Sciences, Ludwig-Maximilians-University, Munich, Germany.
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22
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Hauser K, Essuman B, He Y, Coutsias E, Garcia-Diaz M, Simmerling C. A human transcription factor in search mode. Nucleic Acids Res 2015; 44:63-74. [PMID: 26673724 PMCID: PMC4705650 DOI: 10.1093/nar/gkv1091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022] Open
Abstract
Transcription factors (TF) can change shape to bind and recognize DNA, shifting the energy landscape from a weak binding, rapid search mode to a higher affinity recognition mode. However, the mechanism(s) driving this conformational change remains unresolved and in most cases high-resolution structures of the non-specific complexes are unavailable. Here, we investigate the conformational switch of the human mitochondrial transcription termination factor MTERF1, which has a modular, superhelical topology complementary to DNA. Our goal was to characterize the details of the non-specific search mode to complement the crystal structure of the specific binding complex, providing a basis for understanding the recognition mechanism. In the specific complex, MTERF1 binds a significantly distorted and unwound DNA structure, exhibiting a protein conformation incompatible with binding to B-form DNA. In contrast, our simulations of apo MTERF1 revealed significant flexibility, sampling structures with superhelical pitch and radius complementary to the major groove of B-DNA. Docking these structures to B-DNA followed by unrestrained MD simulations led to a stable complex in which MTERF1 was observed to undergo spontaneous diffusion on the DNA. Overall, the data support an MTERF1-DNA binding and recognition mechanism driven by intrinsic dynamics of the MTERF1 superhelical topology.
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Affiliation(s)
- Kevin Hauser
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Yiqing He
- Great Neck South High School, Great Neck, NY 11023, USA
| | - Evangelos Coutsias
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Carlos Simmerling
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
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23
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Pellegrini M. Tandem Repeats in Proteins: Prediction Algorithms and Biological Role. Front Bioeng Biotechnol 2015; 3:143. [PMID: 26442257 PMCID: PMC4585158 DOI: 10.3389/fbioe.2015.00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/07/2015] [Indexed: 12/30/2022] Open
Abstract
Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR.
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Affiliation(s)
- Marco Pellegrini
- Laboratory for Integrative Systems Medicine (LISM), Istituto di Informatica e Telematica, and Istituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche , Pisa , Italy
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24
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Payne KAP, Fisher K, Sjuts H, Dunstan MS, Bellina B, Johannissen L, Barran P, Hay S, Rigby SEJ, Leys D. Epoxyqueuosine Reductase Structure Suggests a Mechanism for Cobalamin-dependent tRNA Modification. J Biol Chem 2015; 290:27572-81. [PMID: 26378237 PMCID: PMC4646009 DOI: 10.1074/jbc.m115.685693] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Indexed: 01/11/2023] Open
Abstract
Queuosine (Q) is a hypermodified RNA base that replaces guanine in the wobble positions of 5′-GUN-3′ tRNA molecules. Q is exclusively made by bacteria, and the corresponding queuine base is a micronutrient salvaged by eukaryotic species. The final step in Q biosynthesis is the reduction of the epoxide precursor, epoxyqueuosine, to yield the Q cyclopentene ring. The epoxyqueuosine reductase responsible, QueG, shares distant homology with the cobalamin-dependent reductive dehalogenase (RdhA), however the role played by cobalamin in QueG catalysis has remained elusive. We report the solution and structural characterization of Streptococcus thermophilus QueG, revealing the enzyme harbors a redox chain consisting of two [4Fe-4S] clusters and a cob(II)alamin in the base-off form, similar to RdhAs. In contrast to the shared redox chain architecture, the QueG active site shares little homology with RdhA, with the notable exception of a conserved Tyr that is proposed to function as a proton donor during reductive dehalogenation. Docking of an epoxyqueuosine substrate suggests the QueG active site places the substrate cyclopentane moiety in close proximity of the cobalt. Both the Tyr and a conserved Asp are implicated as proton donors to the epoxide leaving group. This suggests that, in contrast to the unusual carbon-halogen bond chemistry catalyzed by RdhAs, QueG acts via Co-C bond formation. Our study establishes the common features of Class III cobalamin-dependent enzymes, and reveals an unexpected diversity in the reductive chemistry catalyzed by these enzymes.
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Affiliation(s)
- Karl A P Payne
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
| | - Karl Fisher
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
| | - Hanno Sjuts
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
| | - Mark S Dunstan
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
| | - Bruno Bellina
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
| | - Linus Johannissen
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
| | - Sam Hay
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
| | - Stephen E J Rigby
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
| | - David Leys
- From the Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester M1 7DN, United Kingdom
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25
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Mullins EA, Shi R, Kotsch LA, Eichman BF. A New Family of HEAT-Like Repeat Proteins Lacking a Critical Substrate Recognition Motif Present in Related DNA Glycosylases. PLoS One 2015; 10:e0127733. [PMID: 25978435 PMCID: PMC4433238 DOI: 10.1371/journal.pone.0127733] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 04/20/2015] [Indexed: 12/21/2022] Open
Abstract
DNA glycosylases are important repair enzymes that eliminate a diverse array of aberrant nucleobases from the genomes of all organisms. Individual bacterial species often contain multiple paralogs of a particular glycosylase, yet the molecular and functional distinctions between these paralogs are not well understood. The recently discovered HEAT-like repeat (HLR) DNA glycosylases are distributed across all domains of life and are distinct in their specificity for cationic alkylpurines and mechanism of damage recognition. Here, we describe a number of phylogenetically diverse bacterial species with two orthologs of the HLR DNA glycosylase AlkD. One ortholog, which we designate AlkD2, is substantially less conserved. The crystal structure of Streptococcus mutans AlkD2 is remarkably similar to AlkD but lacks the only helix present in AlkD that penetrates the DNA minor groove. We show that AlkD2 possesses only weak DNA binding affinity and lacks alkylpurine excision activity. Mutational analysis of residues along this DNA binding helix in AlkD substantially reduced binding affinity for damaged DNA, for the first time revealing the importance of this structural motif for damage recognition by HLR glycosylases.
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Affiliation(s)
- Elwood A. Mullins
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Rongxin Shi
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Lyle A. Kotsch
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brandt F. Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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Boulouis A, Drapier D, Razafimanantsoa H, Wostrikoff K, Tourasse NJ, Pascal K, Girard-Bascou J, Vallon O, Wollman FA, Choquet Y. Spontaneous dominant mutations in chlamydomonas highlight ongoing evolution by gene diversification. THE PLANT CELL 2015; 27:984-1001. [PMID: 25804537 PMCID: PMC4558696 DOI: 10.1105/tpc.15.00010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/10/2015] [Accepted: 03/05/2015] [Indexed: 05/04/2023]
Abstract
We characterized two spontaneous and dominant nuclear mutations in the unicellular alga Chlamydomonas reinhardtii, ncc1 and ncc2 (for nuclear control of chloroplast gene expression), which affect two octotricopeptide repeat (OPR) proteins encoded in a cluster of paralogous genes on chromosome 15. Both mutations cause a single amino acid substitution in one OPR repeat. As a result, the mutated NCC1 and NCC2 proteins now recognize new targets that we identified in the coding sequences of the chloroplast atpA and petA genes, respectively. Interaction of the mutated proteins with these targets leads to transcript degradation; however, in contrast to the ncc1 mutation, the ncc2 mutation requires on-going translation to promote the decay of the petA mRNA. Thus, these mutants reveal a mechanism by which nuclear factors act on chloroplast mRNAs in Chlamydomonas. They illustrate how diversifying selection can allow cells to adapt the nuclear control of organelle gene expression to environmental changes. We discuss these data in the wider context of the evolution of regulation by helical repeat proteins.
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Affiliation(s)
- Alix Boulouis
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Dominique Drapier
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Hélène Razafimanantsoa
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Katia Wostrikoff
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Nicolas J Tourasse
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Kevin Pascal
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Jacqueline Girard-Bascou
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Olivier Vallon
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Francis-André Wollman
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
| | - Yves Choquet
- Unité Mixte de Recherche 7141, CNRS/UPMC, Institut de Biologie Physico-Chimique, F-75005 Paris, France
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27
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A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization. Proc Natl Acad Sci U S A 2014; 111:18554-9. [PMID: 25512524 DOI: 10.1073/pnas.1407634112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding factor (PUF) proteins bind sequence specifically to mRNA targets using a single-stranded RNA-binding domain comprising eight Pumilio (PUM) repeats. PUM repeats have now been identified in proteins that function in pre-rRNA processing, including human Puf-A and yeast Puf6. This is a role not previously ascribed to PUF proteins. Here we present crystal structures of human Puf-A that reveal a class of nucleic acid-binding proteins with 11 PUM repeats arranged in an "L"-like shape. In contrast to classical PUF proteins, Puf-A forms sequence-independent interactions with DNA or RNA, mediated by conserved basic residues. We demonstrate that equivalent basic residues in yeast Puf6 are important for RNA binding, pre-rRNA processing, and mRNA localization. Thus, PUM repeats can be assembled into alternative folds that bind to structured nucleic acids in addition to forming canonical eight-repeat crescent-shaped RNA-binding domains found in classical PUF proteins.
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28
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Hammani K, Barkan A. An mTERF domain protein functions in group II intron splicing in maize chloroplasts. Nucleic Acids Res 2014; 42:5033-42. [PMID: 24500208 PMCID: PMC4005652 DOI: 10.1093/nar/gku112] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mitochondrial transcription termination factor (mTERF) proteins are nucleic acid binding proteins characterized by degenerate helical repeats of ∼30 amino acids. Metazoan genomes encode a small family of mTERF proteins whose members influence mitochondrial gene expression and DNA replication. The mTERF family in higher plants consists of roughly 30 members, which localize to mitochondria or chloroplasts. Effects of several mTERF proteins on plant development and physiology have been described, but molecular functions of mTERF proteins in plants are unknown. We show that a maize mTERF protein, Zm-mTERF4, promotes the splicing of group II introns in chloroplasts. Zm-mTERF4 coimmunoprecipitates with many chloroplast introns and the splicing of some of these introns is disrupted even in hypomorphic Zm-mterf4 mutants. Furthermore, Zm-mTERF4 is found in high molecular weight complexes that include known chloroplast splicing factors. The splicing of two transfer RNAs (trnI-GAU and trnA-UGC) and one ribosomal protein messenger RNA (rpl2) is particularly sensitive to the loss of Zm-mTERF4, accounting for the loss of plastid ribosomes in Zm-mTERF4 mutants. These findings extend the known functional repertoire of the mTERF family to include group II intron splicing and suggest that a conserved role in chloroplast RNA splicing underlies the physiological defects described for mutations in BSM/Rugosa2, the Zm-mTERF4 ortholog in Arabidopsis.
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Affiliation(s)
- Kamel Hammani
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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29
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Abstract
Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants, with more than 400 members in most species. Over the past decade, much has been learned about the molecular functions of these proteins, where they act in the cell, and what physiological roles they play during plant growth and development. A typical PPR protein is targeted to mitochondria or chloroplasts, binds one or several organellar transcripts, and influences their expression by altering RNA sequence, turnover, processing, or translation. Their combined action has profound effects on organelle biogenesis and function and, consequently, on photosynthesis, respiration, plant development, and environmental responses. Recent breakthroughs in understanding how PPR proteins recognize RNA sequences through modular base-specific contacts will help match proteins to potential binding sites and provide a pathway toward designing synthetic RNA-binding proteins aimed at desired targets.
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Affiliation(s)
- Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97405;
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30
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A pumilio homolog in Polycelis sp. Dev Genes Evol 2013; 224:53-6. [PMID: 24292205 DOI: 10.1007/s00427-013-0459-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 10/28/2013] [Indexed: 10/26/2022]
Abstract
Pumilio proteins (PUMs), members of the pumilio/fem-3 mRNA-binding factor (PUF) family, are eukaryote-specific RNA-binding proteins. We isolated a 2,048-basepair cDNA fragment of a pumilio homolog from the planarian flatworm Polycelis sp. This pumilio protein (PyPUM) contains a conserved pumilio homology domain (PUM-HD) consisting of eight repeats and two flanking half repeats. PyPUM shows high similarity to Dugesia japonica pumilio (DjPUM) from another planarian D. japonica, and their PUM-HD also shows high similarity to each other. Furthermore, our data showed that there is a flatworm-specific spacer between repeats 7 and 8. Phylogenetic analysis showed that PyPUM has a closer relationship to other PUM homologs from flatworms. These results provide a foundation for future functional studies of pumilio gene in Polycelis sp.
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31
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Mullins EA, Rubinson EH, Eichman BF. The substrate binding interface of alkylpurine DNA glycosylase AlkD. DNA Repair (Amst) 2013; 13:50-4. [PMID: 24286669 DOI: 10.1016/j.dnarep.2013.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 10/28/2013] [Accepted: 10/28/2013] [Indexed: 12/27/2022]
Abstract
Tandem helical repeats have emerged as an important DNA binding architecture. DNA glycosylase AlkD, which excises N3- and N7-alkylated nucleobases, uses repeating helical motifs to bind duplex DNA and to selectively pause at non-Watson-Crick base pairs. Remodeling of the DNA backbone promotes nucleotide flipping of the lesion and the complementary base into the solvent and toward the protein surface, respectively. The important features of this new DNA binding architecture that allow AlkD to distinguish between damaged and normal DNA without contacting the lesion are poorly understood. Here, we show through extensive mutational analysis that DNA binding and N3-methyladenine (3mA) and N7-methylguanine (7mG) excision are dependent upon each residue lining the DNA binding interface. Disrupting electrostatic or hydrophobic interactions with the DNA backbone substantially reduced binding affinity and catalytic activity. These results demonstrate that residues seemingly only involved in general DNA binding are important for catalytic activity and imply that base excision is driven by binding energy provided by the entire substrate interface of this novel DNA binding architecture.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Emily H Rubinson
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
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32
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Rubinson EH, Christov PP, Eichman BF. Depurination of N7-methylguanine by DNA glycosylase AlkD is dependent on the DNA backbone. Biochemistry 2013; 52:7363-5. [PMID: 24090276 DOI: 10.1021/bi401195r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA glycosylase AlkD excises N7-methylguanine (7mG) by a unique but unknown mechanism, in which the damaged nucleotide is positioned away from the protein and the phosphate backbone is distorted. Here, we show by methylphosphonate substitution that a phosphate proximal to the lesion has a significant effect on the rate enhancement of 7mG depurination by the enzyme. Thus, instead of a conventional mechanism whereby protein side chains participate in N-glycosidic bond cleavage, AlkD remodels the DNA into an active site composed exclusively of DNA functional groups that provide the necessary chemistry to catalyze depurination.
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Affiliation(s)
- Emily H Rubinson
- Department of Biological Sciences, Vanderbilt University , Nashville, Tennessee 37232, United States
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33
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The structure of TON1937 from archaeon Thermococcus onnurineus NA1 reveals a eukaryotic HEAT-like architecture. Int J Biol Macromol 2013; 61:433-8. [DOI: 10.1016/j.ijbiomac.2013.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 11/23/2022]
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34
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Small ID, Rackham O, Filipovska A. Organelle transcriptomes: products of a deconstructed genome. Curr Opin Microbiol 2013; 16:652-8. [DOI: 10.1016/j.mib.2013.07.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 07/15/2013] [Accepted: 07/16/2013] [Indexed: 11/25/2022]
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35
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Hammani K, Bonnard G, Bouchoucha A, Gobert A, Pinker F, Salinas T, Giegé P. Helical repeats modular proteins are major players for organelle gene expression. Biochimie 2013; 100:141-50. [PMID: 24021622 DOI: 10.1016/j.biochi.2013.08.031] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 08/30/2013] [Indexed: 11/18/2022]
Abstract
Mitochondria and chloroplasts are often described as semi-autonomous organelles because they have retained a genome. They thus require fully functional gene expression machineries. Many of the required processes going all the way from transcription to translation have specificities in organelles and arose during eukaryote history. Most factors involved in these RNA maturation steps have remained elusive for a long time. The recent identification of a number of novel protein families including pentatricopeptide repeat proteins, half-a-tetratricopeptide proteins, octotricopeptide repeat proteins and mitochondrial transcription termination factors has helped to settle long-standing questions regarding organelle gene expression. In particular, their functions have been related to replication, transcription, RNA processing, RNA editing, splicing, the control of RNA turnover and translation throughout eukaryotes. These families of proteins, although evolutionary independent, seem to share a common overall architecture. For all of them, proteins contain tandem arrays of repeated motifs. Each module is composed of two to three α-helices and their succession forms a super-helix. Here, we review the features characterising these protein families, in particular, their distribution, the identified functions and mode of action and propose that they might share similar substrate recognition mechanisms.
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36
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Backe PH, Simm R, Laerdahl JK, Dalhus B, Fagerlund A, Okstad OA, Rognes T, Alseth I, Kolstø AB, Bjørås M. A new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures. J Struct Biol 2013; 183:66-75. [PMID: 23623903 DOI: 10.1016/j.jsb.2013.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 04/09/2013] [Accepted: 04/16/2013] [Indexed: 12/27/2022]
Abstract
The recently discovered HEAT-like repeat (HLR) DNA glycosylase superfamily is widely distributed in all domains of life. The present bioinformatics and phylogenetic analysis shows that HLR DNA glycosylase superfamily members in the genus Bacillus form three subfamilies: AlkC, AlkD and AlkF/AlkG. The crystal structure of AlkF shows structural similarity with the DNA glycosylases AlkC and AlkD, however neither AlkF nor AlkG display any DNA glycosylase activity. Instead, both proteins have affinity to branched DNA structures such as three-way and Holliday junctions. A unique β-hairpin in the AlkF/AlkG subfamily is most likely inserted into the DNA major groove, and could be a structural determinant regulating DNA substrate affinity. We conclude that AlkF and AlkG represent a new family of HLR proteins with affinity for branched DNA structures.
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Affiliation(s)
- Paul H Backe
- Department of Microbiology, Oslo University Hospital and University of Oslo, P.O. Box 4950 Nydalen, 0424 Oslo, Norway
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37
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Yagi Y, Hayashi S, Kobayashi K, Hirayama T, Nakamura T. Elucidation of the RNA recognition code for pentatricopeptide repeat proteins involved in organelle RNA editing in plants. PLoS One 2013; 8:e57286. [PMID: 23472078 PMCID: PMC3589468 DOI: 10.1371/journal.pone.0057286] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 01/23/2013] [Indexed: 11/18/2022] Open
Abstract
Pentatricopeptide repeat (PPR) proteins are eukaryotic RNA-binding proteins that are commonly found in plants. Organelle transcript processing and stability are mediated by PPR proteins in a gene-specific manner through recognition by tandem arrays of degenerate 35-amino-acid repeating units, the PPR motifs. However, the sequence-specific RNA recognition mechanism of the PPR protein remains largely unknown. Here, we show the principle underlying RNA recognition for PPR proteins involved in RNA editing. The distance between the PPR-RNA alignment and the editable C was shown to be conserved. Amino acid variation at 3 particular positions within the motif determined recognition of a specific RNA in a programmable manner, with a 1-motif to 1-nucleotide correspondence, with no gap sequence. Data from the decoded nucleotide frequencies for these 3 amino acids were used to assign accurate interacting sites to several PPR proteins for RNA editing and to predict the target site for an uncharacterized PPR protein.
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Affiliation(s)
- Yusuke Yagi
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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38
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Brooks SC, Adhikary S, Rubinson EH, Eichman BF. Recent advances in the structural mechanisms of DNA glycosylases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:247-71. [PMID: 23076011 DOI: 10.1016/j.bbapap.2012.10.005] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 09/24/2012] [Accepted: 10/05/2012] [Indexed: 02/06/2023]
Abstract
DNA glycosylases safeguard the genome by locating and excising a diverse array of aberrant nucleobases created from oxidation, alkylation, and deamination of DNA. Since the discovery 28years ago that these enzymes employ a base flipping mechanism to trap their substrates, six different protein architectures have been identified to perform the same basic task. Work over the past several years has unraveled details for how the various DNA glycosylases survey DNA, detect damage within the duplex, select for the correct modification, and catalyze base excision. Here, we provide a broad overview of these latest advances in glycosylase mechanisms gleaned from structural enzymology, highlighting features common to all glycosylases as well as key differences that define their particular substrate specificities.
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Affiliation(s)
- Sonja C Brooks
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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39
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Yakubovskaya E, Guja KE, Mejia E, Castano S, Hambardjieva E, Choi WS, Garcia-Diaz M. Structure of the essential MTERF4:NSUN4 protein complex reveals how an MTERF protein collaborates to facilitate rRNA modification. Structure 2012; 20:1940-7. [PMID: 23022348 DOI: 10.1016/j.str.2012.08.027] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 11/15/2022]
Abstract
MTERF4 is the first MTERF family member shown to bind RNA and plays an essential role as a regulator of ribosomal biogenesis in mammalian mitochondria. It forms a complex with the rRNA methyltransferase NSUN4 and recruits it to the large ribosomal subunit. In this article, we characterize the interaction between both proteins, demonstrate that MTERF4 strongly stimulates the specificity of NSUN4 during in vitro methylation experiments, and present the 2.0 Å resolution crystal structure of the MTERF4:NSUN4 protein complex, lacking 48 residues of the MTERF4 C-terminal acidic tail, bound to S-adenosyl-L-methionine, thus revealing the nature of the interaction between both proteins and the structural conservation of the most divergent of the human MTERF family members. Moreover, the structure suggests a model for RNA binding by the MTERF4:NSUN4 complex, providing insight into the mechanism by which an MTERF family member facilitates rRNA methylation.
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Affiliation(s)
- Elena Yakubovskaya
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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40
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Mackereth CD, Sattler M. Dynamics in multi-domain protein recognition of RNA. Curr Opin Struct Biol 2012; 22:287-96. [DOI: 10.1016/j.sbi.2012.03.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/25/2012] [Indexed: 12/28/2022]
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41
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RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression. Proc Natl Acad Sci U S A 2012; 109:5651-6. [PMID: 22451905 DOI: 10.1073/pnas.1200318109] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The half-a-tetratricopeptide repeat (HAT) motif is a helical repeat motif found in proteins that influence various aspects of RNA metabolism, including rRNA biogenesis, RNA splicing, and polyadenylation. This functional association with RNA suggested that HAT repeat tracts might bind RNA. However, RNA binding activity has not been reported for any HAT repeat tract, and recent literature has emphasized a protein binding role. In this study, we show that a chloroplast-localized HAT protein, HCF107, is a sequence-specific RNA binding protein. HCF107 consists of 11 tandem HAT repeats and short flanking regions that are also predicted to form helical hairpins. The minimal HCF107 binding site spans ∼11 nt, consistent with the possibility that HAT repeats bind RNA through a modular one repeat-1 nt mechanism. Binding of HCF107 to its native RNA ligand in the psbH 5' UTR remodels local RNA structure and protects the adjacent RNA from exonucleases in vitro. These activities can account for the RNA stabilizing, RNA processing, and translational activation functions attributed to HCF107 based on genetic data. We suggest that analogous activities contribute to the functions of HAT domains found in ribonucleoprotein complexes in the nuclear-cytosolic compartment.
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