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Bommisetti P, Bandarian V. Insights into the Mechanism of Installation of 5-Carboxymethylaminomethyl Uridine Hypermodification by tRNA-Modifying Enzymes MnmE and MnmG. J Am Chem Soc 2023; 145:26947-26961. [PMID: 38050996 PMCID: PMC10723064 DOI: 10.1021/jacs.3c10182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG (and their homologues in Eukarya) install a 5-carboxymethylaminomethyl (cmnm5) or a 5-taurinomethyl (τm5) group onto wobble uridines of several tRNA species. The Escherichia coli MnmE binds guanosine-5'-triphosphate (GTP) and methylenetetrahydrofolate (CH2THF), while MnmG binds flavin adenine dinucleotide (FAD) and a reduced nicotinamide adenine dinucleotide (NADH). Together with glycine, MnmEG catalyzes the installation of cmnm5 in a reaction that also requires hydrolysis of GTP. In this letter, we investigated key steps of the MnmEG reaction using a combination of biochemical techniques. We show multiple lines of evidence supporting flavin-iminium FADH[N5═CH2]+ as a central intermediate in the MnmEG reaction. Using a synthetic FADH[N5═CD2]+ analogue, the intermediacy of the FAD in the transfer of the methylene group from CH2THF to the C5 position of U34 was unambiguously demonstrated. Further, MnmEG reactions containing the deuterated flavin-iminium intermediate and alternate nucleophiles such as taurine and ammonia also led to the formation of the anticipated U34-modified tRNAs, showing FAD[N5═CH2]+ as the universal intermediate for all MnmEG homologues. Additionally, an RNA-protein complex stable to urea-denaturing polyacrylamide gel electrophoresis was identified. Studies involving a series of nuclease (RNase T1) and protease (trypsin) digestions along with reverse transcription experiments suggest that the complex may be noncovalent. While the conserved MnmG cysteine C47 and C277 mutant variants were shown to reduce FAD, they were unable to promote the modified tRNA formation. Overall, this study provides critical insights into the biochemical mechanism underlying tRNA modification by the MnmEG.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
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2
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Kozlova MI, Shalaeva DN, Dibrova DV, Mulkidjanian AY. Common Patterns of Hydrolysis Initiation in P-loop Fold Nucleoside Triphosphatases. Biomolecules 2022; 12:biom12101345. [PMID: 36291554 PMCID: PMC9599529 DOI: 10.3390/biom12101345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/20/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
The P-loop fold nucleoside triphosphate (NTP) hydrolases (also known as Walker NTPases) function as ATPases, GTPases, and ATP synthases, are often of medical importance, and represent one of the largest and evolutionarily oldest families of enzymes. There is still no consensus on their catalytic mechanism. To clarify this, we performed the first comparative structural analysis of more than 3100 structures of P-loop NTPases that contain bound substrate Mg-NTPs or their analogues. We proceeded on the assumption that structural features common to these P-loop NTPases may be essential for catalysis. Our results are presented in two articles. Here, in the first, we consider the structural elements that stimulate hydrolysis. Upon interaction of P-loop NTPases with their cognate activating partners (RNA/DNA/protein domains), specific stimulatory moieties, usually Arg or Lys residues, are inserted into the catalytic site and initiate the cleavage of gamma phosphate. By analyzing a plethora of structures, we found that the only shared feature was the mechanistic interaction of stimulators with the oxygen atoms of gamma-phosphate group, capable of causing its rotation. One of the oxygen atoms of gamma phosphate coordinates the cofactor Mg ion. The rotation must pull this oxygen atom away from the Mg ion. This rearrangement should affect the properties of the other Mg ligands and may initiate hydrolysis according to the mechanism elaborated in the second article.
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Affiliation(s)
- Maria I. Kozlova
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Daria N. Shalaeva
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Daria V. Dibrova
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
| | - Armen Y. Mulkidjanian
- School of Physics, Osnabrueck University, D-49069 Osnabrueck, Germany
- Center of Cellular Nanoanalytics, Osnabrueck University, D-49069 Osnabrueck, Germany
- Correspondence: ; Tel.: +49-541-969-2698
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Peter MF, Tuukkanen AT, Heubach CA, Selsam A, Duthie FG, Svergun DI, Schiemann O, Hagelueken G. Studying Conformational Changes of the Yersinia Type-III-Secretion Effector YopO in Solution by Integrative Structural Biology. Structure 2019; 27:1416-1426.e3. [DOI: 10.1016/j.str.2019.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/08/2019] [Accepted: 06/18/2019] [Indexed: 10/26/2022]
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4
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Wauters L, Versées W, Kortholt A. Roco Proteins: GTPases with a Baroque Structure and Mechanism. Int J Mol Sci 2019; 20:ijms20010147. [PMID: 30609797 PMCID: PMC6337361 DOI: 10.3390/ijms20010147] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/21/2018] [Accepted: 12/25/2018] [Indexed: 01/05/2023] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are a common cause of genetically inherited Parkinson’s Disease (PD). LRRK2 is a large, multi-domain protein belonging to the Roco protein family, a family of GTPases characterized by a central RocCOR (Ras of complex proteins/C-terminal of Roc) domain tandem. Despite the progress in characterizing the GTPase function of Roco proteins, there is still an ongoing debate concerning the working mechanism of Roco proteins in general, and LRRK2 in particular. This review consists of two parts. First, an overview is given of the wide evolutionary range of Roco proteins, leading to a variety of physiological functions. The second part focusses on the GTPase function of the RocCOR domain tandem central to the action of all Roco proteins, and progress in the understanding of its structure and biochemistry is discussed and reviewed. Finally, based on the recent work of our and other labs, a new working hypothesis for the mechanism of Roco proteins is proposed.
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Affiliation(s)
- Lina Wauters
- VIB-VUB Center for Structural Biology, Pleinlaan 2, B-1050 Brussels, Belgium.
- Department of Cell Biochemistry, University of Groningen, NL-9747 AG Groningen, The Netherlands.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Pleinlaan 2, B-1050 Brussels, Belgium.
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, NL-9747 AG Groningen, The Netherlands.
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5
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Shalaeva DN, Cherepanov DA, Galperin MY, Golovin AV, Mulkidjanian AY. Evolution of cation binding in the active sites of P-loop nucleoside triphosphatases in relation to the basic catalytic mechanism. eLife 2018; 7:e37373. [PMID: 30526846 PMCID: PMC6310460 DOI: 10.7554/elife.37373] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/26/2018] [Indexed: 01/01/2023] Open
Abstract
The ubiquitous P-loop fold nucleoside triphosphatases (NTPases) are typically activated by an arginine or lysine 'finger'. Some of the apparently ancestral NTPases are, instead, activated by potassium ions. To clarify the activation mechanism, we combined comparative structure analysis with molecular dynamics (MD) simulations of Mg-ATP and Mg-GTP complexes in water and in the presence of potassium, sodium, or ammonium ions. In all analyzed structures of diverse P-loop NTPases, the conserved P-loop motif keeps the triphosphate chain of bound NTPs (or their analogs) in an extended, catalytically prone conformation, similar to that imposed on NTPs in water by potassium or ammonium ions. MD simulations of potassium-dependent GTPase MnmE showed that linking of alpha- and gamma phosphates by the activating potassium ion led to the rotation of the gamma-phosphate group yielding an almost eclipsed, catalytically productive conformation of the triphosphate chain, which could represent the basic mechanism of hydrolysis by P-loop NTPases.
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Affiliation(s)
- Daria N Shalaeva
- School of PhysicsUniversity of OsnabrückOsnabrückGermany
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Dmitry A Cherepanov
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- Semenov Institute of Chemical PhysicsRussian Academy of SciencesMoscowRussia
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Andrey V Golovin
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Armen Y Mulkidjanian
- School of PhysicsUniversity of OsnabrückOsnabrückGermany
- A.N. Belozersky Institute of Physico-Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
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6
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Ruiz-Partida R, Prado S, Villarroya M, Velázquez-Campoy A, Bravo J, Armengod ME. An Alternative Homodimerization Interface of MnmG Reveals a Conformational Dynamics that Is Essential for Its tRNA Modification Function. J Mol Biol 2018; 430:2822-2842. [PMID: 29870725 DOI: 10.1016/j.jmb.2018.05.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/25/2018] [Indexed: 01/28/2023]
Abstract
The Escherichia coli homodimeric proteins MnmE and MnmG form a functional complex, MnmEG, that modifies tRNAs using GTP, methylene-tetrahydrofolate, FAD, and glycine or ammonium. MnmE is a tetrahydrofolate- and GTP-binding protein, whereas MnmG is a FAD-binding protein with each protomer composed of the FAD-binding domain, two insertion domains, and the helical C-terminal domain. The detailed mechanism of the MnmEG-mediated reaction remains unclear partially due to incomplete structural information on the free- and substrate-bound forms of the complex. In this study, we show that MnmG can adopt in solution a dimer arrangement (form I) different from that currently considered as the only biologically active (form II). Normal mode analysis indicates that form I can oscillate in a range of open and closed conformations. Using isothermal titration calorimetry and native red electrophoresis, we show that a form-I open conformation, which can be stabilized in vitro by the formation of an interprotomer disulfide bond between the catalytic C277 residues, appears to be involved in the assembly of the MnmEG catalytic center. We also show that residues R196, D253, R436, R554 and E585 are important for the stabilization of form I and the tRNA modification function. We propose that the form I dynamics regulates the alternative access of MnmE and tRNA to the MnmG FAD active site. Finally, we show that the C-terminal region of MnmG contains a sterile alpha motif domain responsible for tRNA-protein and protein-protein interactions.
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Affiliation(s)
| | - Silvia Prado
- Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
| | | | - Adrián Velázquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, and Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, Zaragoza 50018, Spain; Aragon Institute for Health Research (IIS Aragon), Zaragoza, 50009, Spain; Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid 28029, Spain; Fundacion ARAID, Government of Aragon, Zaragoza 50018, Spain
| | - Jerónimo Bravo
- Instituto de Biomedicina de Valencia-CSIC, Valencia 46010, Spain
| | - M-Eugenia Armengod
- Centro de Investigación Príncipe Felipe, Valencia 46012, Spain; Biomedical Research Networking Centre for Rare Diseases (CIBERER, Node 721), Valencia, Spain.
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8
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Galazzo L, Maso L, De Rosa E, Bortolus M, Doni D, Acquasaliente L, De Filippis V, Costantini P, Carbonera D. Identifying conformational changes with site-directed spin labeling reveals that the GTPase domain of HydF is a molecular switch. Sci Rep 2017; 7:1714. [PMID: 28490758 PMCID: PMC5431965 DOI: 10.1038/s41598-017-01886-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/05/2017] [Indexed: 11/17/2022] Open
Abstract
[FeFe]-hydrogenases catalyse the reduction of protons to hydrogen at a complex 2Fe[4Fe4S] center called H-cluster. The assembly of this active site is a multistep process involving three proteins, HydE, HydF and HydG. According to the current models, HydF has the key double role of scaffold, upon which the final H-cluster precursor is assembled, and carrier to transfer it to the target hydrogenase. The X-ray structure of HydF indicates that the protein is a homodimer with both monomers carrying two functional domains: a C-terminal FeS cluster-binding domain, where the precursor is assembled, and a N-terminal GTPase domain, whose exact contribution to cluster biogenesis and hydrogenase activation is still elusive. We previously obtained several hints suggesting that the binding of GTP to HydF could be involved in the interactions of this scaffold protein with the other maturases and with the hydrogenase itself. In this work, by means of site directed spin labeling coupled to EPR/PELDOR spectroscopy, we explored the conformational changes induced in a recombinant HydF protein by GTP binding, and provide the first clue that the HydF GTPase domain could be involved in the H-cluster assembly working as a molecular switch similarly to other known small GTPases.
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Affiliation(s)
- Laura Galazzo
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy
| | - Lorenzo Maso
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Edith De Rosa
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy
| | - Davide Doni
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Vincenzo De Filippis
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131, Padova, Italy.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131, Padova, Italy.
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9
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Fislage M, Wauters L, Versées W. Invited review: MnmE, a GTPase that drives a complex tRNA modification reaction. Biopolymers 2017; 105:568-79. [PMID: 26832457 DOI: 10.1002/bip.22813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/19/2016] [Accepted: 01/27/2016] [Indexed: 01/30/2023]
Abstract
MnmE is a multi-domain GTPase that is conserved from bacteria to man. Together with its partner protein MnmG it is involved in the synthesis of a tRNA wobble uridine modification. The orthologues of these proteins in eukaryotes are targeted to mitochondria and mutations in the encoding genes are associated with severe mitochondrial diseases. While classical small GTP-binding proteins are regulated via auxiliary GEFs and GAPs, the GTPase activity of MnmE is activated via potassium-dependent homodimerization of its G domains. In this review we focus on the catalytic mechanism of GTP hydrolysis by MnmE and the large scale conformational changes that are triggered throughout the GTPase cycle. We also discuss how these conformational changes might be used to drive and tune the complex tRNA modification reaction. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 568-579, 2016.
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Affiliation(s)
- Marcus Fislage
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032.,Howard Hughes Medical Institute, Columbia University, New York, NY, 10032
| | - Lina Wauters
- Department of Cell Biochemistry, University of Groningen, Nijenborgh 7, Groningen, 9747 AG, Netherlands.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussel, 1050, Belgium.,Structural Biology Research Center, VIB, Pleinlaan 2, Brussel, 1050, Belgium
| | - Wim Versées
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussel, 1050, Belgium.,Structural Biology Research Center, VIB, Pleinlaan 2, Brussel, 1050, Belgium
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10
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Molecular Insights and Functional Implication of LRRK2 Dimerization. ADVANCES IN NEUROBIOLOGY 2017; 14:107-121. [DOI: 10.1007/978-3-319-49969-7_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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11
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Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods. Methods 2016; 118-119:146-162. [PMID: 27939506 DOI: 10.1016/j.ymeth.2016.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023] Open
Abstract
The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes.
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12
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A Structure-free Method for Quantifying Conformational Flexibility in proteins. Sci Rep 2016; 6:29040. [PMID: 27358108 PMCID: PMC4928179 DOI: 10.1038/srep29040] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/08/2016] [Indexed: 11/24/2022] Open
Abstract
All proteins sample a range of conformations at physiologic temperatures and this inherent flexibility enables them to carry out their prescribed functions. A comprehensive understanding of protein function therefore entails a characterization of protein flexibility. Here we describe a novel approach for quantifying a protein’s flexibility in solution using small-angle X-ray scattering (SAXS) data. The method calculates an effective entropy that quantifies the diversity of radii of gyration that a protein can adopt in solution and does not require the explicit generation of structural ensembles to garner insights into protein flexibility. Application of this structure-free approach to over 200 experimental datasets demonstrates that the methodology can quantify a protein’s disorder as well as the effects of ligand binding on protein flexibility. Such quantitative descriptions of protein flexibility form the basis of a rigorous taxonomy for the description and classification of protein structure.
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Shippy DC, Fadl AA. RNA modification enzymes encoded by the gid operon: Implications in biology and virulence of bacteria. Microb Pathog 2015; 89:100-7. [PMID: 26427881 DOI: 10.1016/j.micpath.2015.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/23/2015] [Indexed: 01/10/2023]
Abstract
Ribonucleic acid (RNA) molecules consist of numerous chemically modified nucleosides that are highly conserved in eukarya, archeae, and bacteria, while others are unique to each domain of life. In bacteria, hundreds of RNA modification enzymes have been identified and implicated in biological pathways associated with many cell processes. The glucose-inhibited division (gid) operon encodes genes for two RNA modification enzymes named GidA and GidB. Studies have shown GidA is essential for the proper biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) of bacterial transfer RNA (tRNA) with GidB responsible for the methylation of the 16S ribosomal RNA (rRNA). Furthermore, deletion of gidA and gidB has shown to alter numerous bacterial properties like virulence, stress response, morphology, growth, antibiotic susceptibility, and others. In this review, we discuss the present knowledge of the RNA modification enzymes GidA and GidB, and their potential role in the biology and virulence of bacteria.
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Affiliation(s)
- Daniel C Shippy
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amin A Fadl
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
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14
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Conformational heterogeneity of the Roc domains in C. tepidum Roc-COR and implications for human LRRK2 Parkinson mutations. Biosci Rep 2015; 35:BSR20150128. [PMID: 26310572 PMCID: PMC4721548 DOI: 10.1042/bsr20150128] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/10/2015] [Indexed: 12/30/2022] Open
Abstract
Ras of complex proteins (Roc) is a Ras-like GTP-binding domain that always occurs in tandem with the C-terminal of Roc (COR) domain and is found in bacteria, plants and animals. Recently, it has been shown that Roco proteins belong to the family of G-proteins activated by nucleotide (nt)-dependent dimerization (GADs). We investigated the RocCOR tandem from the bacteria Chlorobium tepidum with site-directed spin labelling and pulse EPR distance measurements to follow conformational changes during the Roco G-protein cycle. Our results confirm that the COR domains are a stable dimerization device serving as a scaffold for the Roc domains that, in contrast, are structurally heterogeneous and dynamic entities. Contrary to other GAD proteins, we observed only minor structural alterations upon binding and hydrolysis of GTP, indicating significant mechanistic variations within this protein class. Mutations in the most prominent member of the Roco family of proteins, leucine-rich repeat (LRR) kinase 2 (LRRK2), are the most frequent cause of late-onset Parkinson's disease (PD). Using a stable recombinant LRRK2 Roc-COR-kinase fragment we obtained detailed kinetic data for the G-protein cycle. Our data confirmed that dimerization is essential for efficient GTP hydrolysis and PD mutations in the Roc domain result in decreased GTPase activity. Previous data have shown that these LRRK2 PD-mutations are located in the interface between Roc and COR. Importantly, analogous mutations in the conserved C. tepidum Roc/COR interface significantly influence the structure and nt-induced conformational changes of the Roc domains.
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15
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Dunkel S, Pulagam LP, Steinhoff HJ, Klare JP. In vivo EPR on spin labeled colicin A reveals an oligomeric assembly of the pore-forming domain in E. coli membranes. Phys Chem Chem Phys 2015; 17:4875-8. [DOI: 10.1039/c4cp05638h] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
DEER distance measurements on intact Escherichia coli cells interacting with nitroxide spin-labeled ColA suggest that this bacteriocin forms dimers upon membrane insertion.
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Affiliation(s)
- S. Dunkel
- Department of Physics
- University of Osnabrück
- 49076 Osnabrück
- Germany
| | - L. P. Pulagam
- Department of Physics
- University of Osnabrück
- 49076 Osnabrück
- Germany
| | - H.-J. Steinhoff
- Department of Physics
- University of Osnabrück
- 49076 Osnabrück
- Germany
| | - J. P. Klare
- Department of Physics
- University of Osnabrück
- 49076 Osnabrück
- Germany
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16
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tRNA modification enzymes GidA and MnmE: potential role in virulence of bacterial pathogens. Int J Mol Sci 2014; 15:18267-80. [PMID: 25310651 PMCID: PMC4227215 DOI: 10.3390/ijms151018267] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/02/2014] [Accepted: 10/08/2014] [Indexed: 01/02/2023] Open
Abstract
Transfer RNA (tRNA) is an RNA molecule that carries amino acids to the ribosomes for protein synthesis. These tRNAs function at the peptidyl (P) and aminoacyl (A) binding sites of the ribosome during translation, with each codon being recognized by a specific tRNA. Due to this specificity, tRNA modification is essential for translational efficiency. Many enzymes have been implicated in the modification of bacterial tRNAs, and these enzymes may complex with one another or interact individually with the tRNA. Approximately, 100 tRNA modification enzymes have been identified with glucose-inhibited division (GidA) protein and MnmE being two of the enzymes studied. In Escherichia coli and Salmonella, GidA and MnmE bind together to form a functional complex responsible for the proper biosynthesis of 5-methylaminomethyl-2-thiouridine (mnm5s2U34) of tRNAs. Studies have implicated this pathway in a major pathogenic regulatory mechanism as deletion of gidA and/or mnmE has attenuated several bacterial pathogens like Salmonella enterica serovar Typhimurium, Pseudomonas syringae, Aeromonas hydrophila, and many others. In this review, we summarize the potential role of the GidA/MnmE tRNA modification pathway in bacterial virulence, interactions with the host, and potential therapeutic strategies resulting from a greater understanding of this regulatory mechanism.
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17
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Kuhle B, Ficner R. A monovalent cation acts as structural and catalytic cofactor in translational GTPases. EMBO J 2014; 33:2547-63. [PMID: 25225612 DOI: 10.15252/embj.201488517] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Translational GTPases are universally conserved GTP hydrolyzing enzymes, critical for fidelity and speed of ribosomal protein biosynthesis. Despite their central roles, the mechanisms of GTP-dependent conformational switching and GTP hydrolysis that govern the function of trGTPases remain poorly understood. Here, we provide biochemical and high-resolution structural evidence that eIF5B and aEF1A/EF-Tu bound to GTP or GTPγS coordinate a monovalent cation (M(+)) in their active site. Our data reveal that M(+) ions form constitutive components of the catalytic machinery in trGTPases acting as structural cofactor to stabilize the GTP-bound "on" state. Additionally, the M(+) ion provides a positive charge into the active site analogous to the arginine-finger in the Ras-RasGAP system indicating a similar role as catalytic element that stabilizes the transition state of the hydrolysis reaction. In sequence and structure, the coordination shell for the M(+) ion is, with exception of eIF2γ, highly conserved among trGTPases from bacteria to human. We therefore propose a universal mechanism of M(+)-dependent conformational switching and GTP hydrolysis among trGTPases with important consequences for the interpretation of available biochemical and structural data.
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Affiliation(s)
- Bernhard Kuhle
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik Göttinger Zentrum für Molekulare Biowissenschaften Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik Göttinger Zentrum für Molekulare Biowissenschaften Georg-August-Universität Göttingen, Göttingen, Germany
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18
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Vöpel T, Hengstenberg CS, Peulen TO, Ajaj Y, Seidel CAM, Herrmann C, Klare JP. Triphosphate induced dimerization of human guanylate binding protein 1 involves association of the C-terminal helices: a joint double electron-electron resonance and FRET study. Biochemistry 2014; 53:4590-600. [PMID: 24991938 DOI: 10.1021/bi500524u] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human guanylate binding protein 1 (hGBP1) is a member of the dynamin superfamily of large GTPases. During GTP hydrolysis, the protein undergoes structural changes leading to self-assembly. Previous studies have suggested dimerization of the protein by means of its large GTPase (LG) domain and significant conformational changes in helical regions near the LG domain and at its C-terminus. We used site-directed labeling and a combination of pulsed electron paramagnetic resonance and time-resolved fluorescence spectroscopy for structural investigations on hGBP1 dimerization and conformational changes of its C-terminal helix α13. Consistent distance measurements by double electron-electron resonance (DEER, also named pulse double electron resonance = PELDOR) spectroscopy and Förster resonance energy transfer (FRET) measurements using model-free analysis approaches revealed a close interaction of the two α13 helices in the hGBP1 dimer formed upon binding of the nonhydrolyzable nucleoside triphosphate derivate GppNHp. In molecular dynamics (MD) simulations, these two helices form a stable dimer in solution. Our data show that dimer formation of hGBP1 involves multiple spatially distant regions of the protein, namely, the N-terminal LG domain and the C-terminal helices α13. The contacts formed between the two α13 helices and the resulting juxtaposition are expected to be a key step for the physiological membrane localization of hGBP1 through the farnesyl groups attached to the end of α13.
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Affiliation(s)
- Tobias Vöpel
- Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum , Universitätsstrasse 150, 44780 Bochum, Germany
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19
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Gruian C, Boehme S, Simon S, Steinhoff HJ, Klare JP. Assembly and function of the tRNA-modifying GTPase MnmE adsorbed to surface functionalized bioactive glass. ACS APPLIED MATERIALS & INTERFACES 2014; 6:7615-7625. [PMID: 24785159 DOI: 10.1021/am500933e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Protein adsorption onto solid surfaces is a common phenomenon in tissue engineering related applications, and considerable progress was achieved in this field. However, there are still unanswered questions or contradictory opinions concerning details of the protein's structure, conformational changes, or aggregation once adsorbed onto solid surfaces. Electron paramagnetic resonance (EPR) spectroscopy and site-directed spin labeling (SDSL) were employed in this work to investigate the conformational changes and dynamics of the tRNA-modifying dimeric protein MnmE from E. coli, an ortholog of the human GTPBP3, upon adsorption on bioactive glass mimicking the composition of the classical 45S5 Bioglass. In addition, prior to protein attachment, the bioactive glass surface was modified with the protein coupling agent glutaraldehyde. Continuous wave EPR spectra of different spin labeled MnmE mutants were recorded to assess the dynamics of the attached spin labels before and after protein adsorption. The area of the continuous wave (cw)-EPR absorption spectrum was further used to determine the amount of the attached protein. Double electron-electron resonance (DEER) experiments were conducted to measure distances between the spin labels before and after adsorption. The results revealed that the contact regions between MnmE and the bioactive glass surface are located at the G domains and at the N-terminal domains. The low modulation depths of all DEER time traces recorded for the adsorbed single MnmE mutants, corroborated with the DEER measurements performed on MnmE double mutants, show that the adsorption process leads to dissociation of the dimer and alters the tertiary structure of MnmE, thereby abolishing its functionality. However, glutaraldehyde reduces the aggressiveness of the adsorption process and improves the stability of the protein attachment.
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Affiliation(s)
- C Gruian
- Faculty of Physics and Institute of Interdisciplinary Research in Bio-Nano-Sciences, Babes-Bolyai University , Cluj-Napoca, 400084, Romania
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20
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Fislage M, Brosens E, Deyaert E, Spilotros A, Pardon E, Loris R, Steyaert J, Garcia-Pino A, Versées W. SAXS analysis of the tRNA-modifying enzyme complex MnmE/MnmG reveals a novel interaction mode and GTP-induced oligomerization. Nucleic Acids Res 2014; 42:5978-92. [PMID: 24634441 PMCID: PMC4027165 DOI: 10.1093/nar/gku213] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/28/2014] [Accepted: 02/28/2014] [Indexed: 11/12/2022] Open
Abstract
Transfer ribonucleic acid (tRNA) modifications, especially at the wobble position, are crucial for proper and efficient protein translation. MnmE and MnmG form a protein complex that is implicated in the carboxymethylaminomethyl modification of wobble uridine (cmnm(5)U34) of certain tRNAs. MnmE is a G protein activated by dimerization (GAD), and active guanosine-5'-triphosphate (GTP) hydrolysis is required for the tRNA modification to occur. Although crystal structures of MnmE and MnmG are available, the structure of the MnmE/MnmG complex (MnmEG) and the nature of the nucleotide-induced conformational changes and their relevance for the tRNA modification reaction remain unknown. In this study, we mainly used small-angle X-ray scattering to characterize these conformational changes in solution and to unravel the mode of interaction between MnmE, MnmG and tRNA. In the nucleotide-free state MnmE and MnmG form an unanticipated asymmetric α2β2 complex. Unexpectedly, GTP binding promotes further oligomerization of the MnmEG complex leading to an α4β2 complex. The transition from the α2β2 to the α4β2 complex is fast, reversible and coupled to GTP binding and hydrolysis. We propose a model in which the nucleotide-induced changes in conformation and oligomerization of MnmEG form an integral part of the tRNA modification reaction cycle.
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Affiliation(s)
- Marcus Fislage
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Elke Brosens
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Egon Deyaert
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Alessandro Spilotros
- EMBL Hamburg outstation c/o DESY, Notkestrasse 85, Geb. 25A, 22603 Hamburg, Germany
| | - Els Pardon
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Remy Loris
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Jan Steyaert
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Abel Garcia-Pino
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Wim Versées
- Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussel, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
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21
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Lumme C, Altan-Martin H, Dastvan R, Sommer MS, Oreb M, Schuetz D, Hellenkamp B, Mirus O, Kretschmer J, Lyubenova S, Kügel W, Medelnik JP, Dehmer M, Michaelis J, Prisner TF, Hugel T, Schleiff E. Nucleotides and substrates trigger the dynamics of the Toc34 GTPase homodimer involved in chloroplast preprotein translocation. Structure 2014; 22:526-38. [PMID: 24631462 DOI: 10.1016/j.str.2014.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 01/29/2014] [Accepted: 02/01/2014] [Indexed: 12/13/2022]
Abstract
GTPases are molecular switches that control numerous crucial cellular processes. Unlike bona fide GTPases, which are regulated by intramolecular structural transitions, the less well studied GAD-GTPases are activated by nucleotide-dependent dimerization. A member of this family is the translocase of the outer envelope membrane of chloroplast Toc34 involved in regulation of preprotein import. The GTPase cycle of Toc34 is considered a major circuit of translocation regulation. Contrary to expectations, previous studies yielded only marginal structural changes of dimeric Toc34 in response to different nucleotide loads. Referencing PELDOR and FRET single-molecule and bulk experiments, we describe a nucleotide-dependent transition of the dimer flexibility from a tight GDP- to a flexible GTP-loaded state. Substrate binding induces an opening of the GDP-loaded dimer. Thus, the structural dynamics of bona fide GTPases induced by GTP hydrolysis is replaced by substrate-dependent dimer flexibility, which likely represents a general regulatory mode for dimerizing GTPases.
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Affiliation(s)
- Christina Lumme
- Physics Department E22 and IMETUM, Technical University Munich, 85748 Garching, Germany
| | - Hasret Altan-Martin
- Institute of Molecular Cell Biology of Plants, Goethe University, 60438 Frankfurt, Germany
| | - Reza Dastvan
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; Cluster of Excellence "Macromolecular Complexes", Goethe University, 60438 Frankfurt, Germany; Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany; Department of Molecular Physiology & Biophysics, Vanderbilt University, 741 Light Hall, 2215 Garland Avenue, Nashville, TN 37232, USA
| | - Maik S Sommer
- Institute of Molecular Cell Biology of Plants, Goethe University, 60438 Frankfurt, Germany
| | - Mislav Oreb
- Physics Department E22 and IMETUM, Technical University Munich, 85748 Garching, Germany
| | - Denise Schuetz
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; Cluster of Excellence "Macromolecular Complexes", Goethe University, 60438 Frankfurt, Germany; Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Björn Hellenkamp
- Physics Department E22 and IMETUM, Technical University Munich, 85748 Garching, Germany
| | - Oliver Mirus
- Institute of Molecular Cell Biology of Plants, Goethe University, 60438 Frankfurt, Germany
| | - Jens Kretschmer
- Institute of Molecular Cell Biology of Plants, Goethe University, 60438 Frankfurt, Germany
| | - Sevdalina Lyubenova
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; Cluster of Excellence "Macromolecular Complexes", Goethe University, 60438 Frankfurt, Germany; Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | | | - Jan P Medelnik
- Institute of Molecular Cell Biology of Plants, Goethe University, 60438 Frankfurt, Germany
| | - Manuela Dehmer
- Institute of Molecular Cell Biology of Plants, Goethe University, 60438 Frankfurt, Germany
| | | | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany; Cluster of Excellence "Macromolecular Complexes", Goethe University, 60438 Frankfurt, Germany; Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Thorsten Hugel
- Physics Department E22 and IMETUM, Technical University Munich, 85748 Garching, Germany
| | - Enrico Schleiff
- Institute of Molecular Cell Biology of Plants, Goethe University, 60438 Frankfurt, Germany; Cluster of Excellence "Macromolecular Complexes", Goethe University, 60438 Frankfurt, Germany; Center for Membrane Proteomics, Goethe University, 60438 Frankfurt, Germany.
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22
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Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland. ACTA ACUST UNITED AC 2013; 21:174-85. [PMID: 24315934 DOI: 10.1016/j.chembiol.2013.10.015] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 12/15/2022]
Abstract
Nature combines existing biochemical building blocks, at times with subtlety of purpose. RNA modifications are a prime example of this, where standard RNA nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. The result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. Here, we highlight several modifications that, because of their chemical intricacy, rely on seemingly unrelated pathways to provide cofactors for their synthesis. Besides their immediate role in affecting RNA function, modifications may act as sensors and transducers of information that connect a cell's metabolic state to its translational output, carefully orchestrating a delicate balance between metabolic rate and protein synthesis at a system's level.
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23
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Prado S, Villarroya M, Medina M, Armengod ME. The tRNA-modifying function of MnmE is controlled by post-hydrolysis steps of its GTPase cycle. Nucleic Acids Res 2013; 41:6190-208. [PMID: 23630314 PMCID: PMC3695501 DOI: 10.1093/nar/gkt320] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
MnmE is a homodimeric multi-domain GTPase involved in tRNA modification. This protein differs from Ras-like GTPases in its low affinity for guanine nucleotides and mechanism of activation, which occurs by a cis, nucleotide- and potassium-dependent dimerization of its G-domains. Moreover, MnmE requires GTP hydrolysis to be functionally active. However, how GTP hydrolysis drives tRNA modification and how the MnmE GTPase cycle is regulated remains unresolved. Here, the kinetics of the MnmE GTPase cycle was studied under single-turnover conditions using stopped- and quench-flow techniques. We found that the G-domain dissociation is the rate-limiting step of the overall reaction. Mutational analysis and fast kinetics assays revealed that GTP hydrolysis, G-domain dissociation and Pi release can be uncoupled and that G-domain dissociation is directly responsible for the ‘ON’ state of MnmE. Thus, MnmE provides a new paradigm of how the ON/OFF cycling of GTPases may regulate a cellular process. We also demonstrate that the MnmE GTPase cycle is negatively controlled by the reaction products GDP and Pi. This feedback mechanism may prevent inefficacious GTP hydrolysis in vivo. We propose a biological model whereby a conformational change triggered by tRNA binding is required to remove product inhibition and initiate a new GTPase/tRNA-modification cycle.
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Affiliation(s)
- Silvia Prado
- RNA Modification and Mitochondrial Diseases Laboratory, Centro de Investigación Príncipe Felipe, 46012-Valencia, Spain
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24
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Luo LF, Hou CC, Yang WX. Nuclear factors: roles related to mitochondrial deafness. Gene 2013; 520:79-89. [PMID: 23510774 DOI: 10.1016/j.gene.2013.03.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/08/2013] [Indexed: 12/16/2022]
Abstract
Hearing loss (HL) is a common disorder with mitochondrial dysfunction as one of the major causes leading to deafness. Mitochondrial dysfunction may be caused by either mutations in nuclear genes leading to defective nuclear-encoded proteins or mutations in mitochondrial genes leading to defective mitochondrial-encoded products. The specific nuclear genes involved in HL can be classified into two categories depending on whether mitochondrial gene mutations co-exist (modifier genes) or not (deafness-causing genes). TFB1M, MTO1, GTPBP3, and TRMU are modifier genes. A mutation in any of these modifier genes may lead to a deafness phenotype when accompanied by the mitochondrial gene mutation. OPA1, TIMM8A, SMAC/DIABLO, MPV17, PDSS1, BCS1L, SUCLA2, C10ORF2, COX10, PLOG1and RRM2B are deafness-causing genes. A mutation in any of these deafness-causing genes will directly induce variable phenotypic HL.
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Affiliation(s)
- Ling-Feng Luo
- Institute of Cell and Developmental Biology, Zhejiang University, Hangzhou 310058, China
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25
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El Yacoubi B, Bailly M, de Crécy-Lagard V. Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs. Annu Rev Genet 2012; 46:69-95. [DOI: 10.1146/annurev-genet-110711-155641] [Citation(s) in RCA: 380] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Basma El Yacoubi
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Marc Bailly
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
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26
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Klare JP, Ortiz de Orué Lucana D. Conformational changes in the novel redox sensor protein HbpS studied by site-directed spin labeling and its turnover in dependence on the catalase-peroxidase CpeB. Antioxid Redox Signal 2012; 16:639-48. [PMID: 21846213 PMCID: PMC3277929 DOI: 10.1089/ars.2011.4080] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS To establish conditions to study the oligomeric assembly of heme-binding protein (HbpS) in solution by applying the tools of site-directed spin labeling combined with pulse electron paramagnetic resonance (SDSL EPR) spectroscopy, as well as to analyze redox stress-based conformational changes in HbpS subunits within the oligomer in solution. In vivo elucidation of molecular mechanisms that control the downregulation of the novel redox-system HbpS-SenS-SenR. RESULTS Using a set of specifically generated HbpS mutants, and SDSL EPR spectroscopy, we show the octomeric assembly of HbpS in solution, and demonstrate that iron-mediated stress induces conformational changes in HbpS subunits within the octamer. We further demonstrate that the catalase-peroxidase CpeB protects HbpS from hydrogen peroxide (H(2)O(2))-mediated oxidative attack in vivo. Moreover, chromosomal inactivation of cpeB results in an enhanced sensitivity of the mutant to redox-cycling compounds. INNOVATION SDSL EPR has been used in this work for the first time to monitor redox-mediated conformational changes in a redox-sensing protein in solution. This work substantially explains redox-dependent dynamics in HbpS at the atomic level, and presents novel molecular mechanisms supporting downregulation of a signaling cascade. CONCLUSION Iron-mediated stress induces movements of subunits within the HbpS octomeric assembly. We suggest a motion of the C-terminal α-helix toward the preceding helical segment. These events upregulate the activity of the HbpS-SenS-SenR system, in which HbpS acts as an accessory element. The mycelia-associated CpeB, under the control of HbpS-SenS-SenR, protects the extracellular HbpS from oxidation in vivo. Thus, de novo synthesized HbpS proteins downregulate the HbpS-SenS-SenR signaling cascade.
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Affiliation(s)
- Johann P Klare
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
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27
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Armengod ME, Moukadiri I, Prado S, Ruiz-Partida R, Benítez-Páez A, Villarroya M, Lomas R, Garzón MJ, Martínez-Zamora A, Meseguer S, Navarro-González C. Enzymology of tRNA modification in the bacterial MnmEG pathway. Biochimie 2012; 94:1510-20. [PMID: 22386868 DOI: 10.1016/j.biochi.2012.02.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
Abstract
Among all RNAs, tRNA exhibits the largest number and the widest variety of post-transcriptional modifications. Modifications within the anticodon stem loop, mainly at the wobble position and purine-37, collectively contribute to stabilize the codon-anticodon pairing, maintain the translational reading frame, facilitate the engagement of the ribosomal decoding site and enable translocation of tRNA from the A-site to the P-site of the ribosome. Modifications at the wobble uridine (U34) of tRNAs reading two degenerate codons ending in purine are complex and result from the activity of two multi-enzyme pathways, the IscS-MnmA and MnmEG pathways, which independently work on positions 2 and 5 of the U34 pyrimidine ring, respectively, and from a third pathway, controlled by TrmL (YibK), that modifies the 2'-hydroxyl group of the ribose. MnmEG is the only common pathway to all the mentioned tRNAs, and involves the GTP- and FAD-dependent activity of the MnmEG complex and, in some cases, the activity of the bifunctional enzyme MnmC. The Escherichia coli MnmEG complex catalyzes the incorporation of an aminomethyl group into the C5 atom of U34 using methylene-tetrahydrofolate and glycine or ammonium as donors. The reaction requires GTP hydrolysis, probably to assemble the active site of the enzyme or to carry out substrate recognition. Inactivation of the evolutionarily conserved MnmEG pathway produces a pleiotropic phenotype in bacteria and mitochondrial dysfunction in human cell lines. While the IscS-MnmA pathway and the MnmA-mediated thiouridylation reaction are relatively well understood, we have limited information on the reactions mediated by the MnmEG, MnmC and TrmL enzymes and on the precise role of proteins MnmE and MnmG in the MnmEG complex activity. This review summarizes the present state of knowledge on these pathways and what we still need to know, with special emphasis on the MnmEG pathway.
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Affiliation(s)
- M-Eugenia Armengod
- Laboratorio de Genética Molecular, Centro de Investigación Príncipe Felipe, Molecular Genetics, Avenida Autopista del Saler, 16-3, 46012-Valencia, Spain.
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28
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Abstract
Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated soluble proteins can be measured by the DEER technique. The number of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystallization and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, experimental protocols were optimized and techniques for artifact suppression were introduced. Data analysis programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small number of distance constraints. The present scope and limitations of the technique are illustrated.
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Affiliation(s)
- Gunnar Jeschke
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Switzerland.
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29
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The universally conserved prokaryotic GTPases. Microbiol Mol Biol Rev 2012; 75:507-42, second and third pages of table of contents. [PMID: 21885683 DOI: 10.1128/mmbr.00009-11] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Members of the large superclass of P-loop GTPases share a core domain with a conserved three-dimensional structure. In eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. As targets of mutation and toxins, GTPases are involved in the pathogenesis of cancer and infectious diseases. In prokaryotes also, it is hard to overestimate the importance of GTPases in cell physiology. Numerous papers have shed new light on the role of bacterial GTPases in cell cycle regulation, ribosome assembly, the stress response, and other cellular processes. Moreover, bacterial GTPases have been identified as high-potential drug targets. A key paper published over 2 decades ago stated that, "It may never again be possible to capture [GTPases] in a family portrait" (H. R. Bourne, D. A. Sanders, and F. McCormick, Nature 348:125-132, 1990) and indeed, the last 20 years have seen a tremendous increase in publications on the subject. Sequence analysis identified 13 bacterial GTPases that are conserved in at least 75% of all bacterial species. We here provide an overview of these 13 protein subfamilies, covering their cellular functions as well as cellular localization and expression levels, three-dimensional structures, biochemical properties, and gene organization. Conserved roles in eukaryotic homologs will be discussed as well. A comprehensive overview summarizing current knowledge on prokaryotic GTPases will aid in further elucidating the function of these important proteins.
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30
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Wittinghofer A, Vetter IR. Structure-function relationships of the G domain, a canonical switch motif. Annu Rev Biochem 2011; 80:943-71. [PMID: 21675921 DOI: 10.1146/annurev-biochem-062708-134043] [Citation(s) in RCA: 333] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
GTP-binding (G) proteins constitute a class of P-loop (phosphate-binding loop) proteins that work as molecular switches between the GDP-bound OFF and the GTP-bound ON state. The common principle is the 160-180-residue G domain with an α,β topology that is responsible for nucleotide-dependent conformational changes and drives many biological functions. Although the G domain uses a universally conserved switching mechanism, its structure, function, and GTPase reaction are modified for many different pathways and processes.
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31
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Atomic structure of a nanobody-trapped domain-swapped dimer of an amyloidogenic beta2-microglobulin variant. Proc Natl Acad Sci U S A 2011; 108:1314-9. [PMID: 21220305 DOI: 10.1073/pnas.1008560108] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atomic-level structural investigation of the key conformational intermediates of amyloidogenesis remains a challenge. Here we demonstrate the utility of nanobodies to trap and characterize intermediates of β2-microglobulin (β2m) amyloidogenesis by X-ray crystallography. For this purpose, we selected five single domain antibodies that block the fibrillogenesis of a proteolytic amyloidogenic fragment of β2m (ΔN6β2m). The crystal structure of ΔN6β2m in complex with one of these nanobodies (Nb24) identifies domain swapping as a plausible mechanism of self-association of this amyloidogenic protein. In the swapped dimer, two extended hinge loops--corresponding to the heptapetide NHVTLSQ that forms amyloid in isolation--are unmasked and fold into a new two-stranded antiparallel β-sheet. The β-strands of this sheet are prone to self-associate and stack perpendicular to the direction of the strands to build large intermolecular β-sheets that run parallel to the axis of growing oligomers, providing an elongation mechanism by self-templated growth.
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Lee HH, Suh SW. Overexpression, crystallization and preliminary X-ray crystallographic analysis of Pseudomonas aeruginosa MnmE, a GTPase involved in tRNA modification. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:905-8. [PMID: 20693664 DOI: 10.1107/s1744309110018750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 05/19/2010] [Indexed: 11/10/2022]
Abstract
MnmE, an evolutionarily conserved GTPase, is involved in modification of the uridine base (U34) at the wobble position of certain tRNAs. Previous crystal structures of MnmE suggest that it is a dimer with considerable conformational flexibility. To facilitate structural comparisons among MnmE proteins, structural analysis of MnmE from Pseudomonas aeruginosa encoded by the PA5567 gene was initiated. It was overexpressed in Escherichia coli and crystallized at 297 K using a reservoir solution consisting of 100 mM sodium ADA pH 6.5, 12%(w/v) polyethylene glycol 4000, 100 mM lithium sulfate, 2%(v/v) 2-propanol and 2.5 mM dithiothreitol. X-ray diffraction data were collected to 2.69 A resolution. The crystals belonged to the orthorhombic space group C222(1), with unit-cell parameters a=96.74, b=204.66, c=120.90 A. Two monomers were present in the asymmetric unit, resulting in a crystal volume per protein mass (VM) of 2.99 A3 Da(-1) and a solvent content of 58.8%.
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Affiliation(s)
- Hyung Ho Lee
- Department of Bio and Nano Chemistry, Kookmin University, Seoul 136-702, Republic of Korea.
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Transient tether between the SRP RNA and SRP receptor ensures efficient cargo delivery during cotranslational protein targeting. Proc Natl Acad Sci U S A 2010; 107:7698-703. [PMID: 20385832 DOI: 10.1073/pnas.1002968107] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinetic control of macromolecular interactions plays key roles in biological regulation. An example of such control occurs in cotranslational protein targeting by the signal recognition particle (SRP), during which the SRP RNA and the cargo both accelerate complex assembly between the SRP and SRP receptor FtsY 10(2)-fold. The molecular mechanism underlying these rate accelerations was unclear. Here we show that a highly conserved basic residue, Lys399, on the lateral surface of FtsY provides a novel RNA tetraloop receptor to mediate the SRP RNA- and cargo-induced acceleration of SRP-FtsY complex assembly. We propose that the SRP RNA, by using its tetraloop to interact with FtsY-Lys399, provides a transient tether to stabilize the early stage and transition state of complex formation; this accelerates the assembly of a stable SRP-FtsY complex and allows the loading of cargo to be efficiently coupled to its membrane delivery. The use of a transient tether to increase the lifetime of collisional intermediates and reduce the dimension of diffusional search represents a novel and effective mechanism to accelerate macromolecular interactions.
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Böhme S, Meyer S, Krüger A, Steinhoff HJ, Wittinghofer A, Klare JP. Stabilization of G domain conformations in the tRNA-modifying MnmE-GidA complex observed with double electron electron resonance spectroscopy. J Biol Chem 2010; 285:16991-7000. [PMID: 20353943 DOI: 10.1074/jbc.m109.096131] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MnmE is a GTP-binding protein conserved between bacteria and eukarya. It is a dimeric three-domain protein where the two G domains have to approach each other for activation of the potassium-stimulated GTPase reaction. Together with GidA, in a heterotetrameric alpha(2)beta(2) complex, it is involved in the modification of the wobble uridine base U34 of the first anticodon position of particular tRNAs. Here we show, using various spin-labeled MnmE mutants and EPR spectroscopy, that GidA binding induces large conformational and dynamic changes in MnmE. It stimulates the GTPase reaction by stabilizing the GTP-bound conformation in a potassium-independent manner. Surprisingly, GidA binding influences not only the GTP- but also the GDP-bound conformation. Thus GidA is a new type of regulator for a G protein activated by dimerization.
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Affiliation(s)
- Sabine Böhme
- Department of Physics, University of Osnabrück, Barbarastrasse 7, D-49076 Osnabrück, Germany
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