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Loveland AB, Bah E, Madireddy R, Zhang Y, Brilot AF, Grigorieff N, Korostelev AA. Ribosome•RelA structures reveal the mechanism of stringent response activation. eLife 2016; 5. [PMID: 27434674 PMCID: PMC4974054 DOI: 10.7554/elife.17029] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/18/2016] [Indexed: 12/18/2022] Open
Abstract
Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding.
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Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry, Brandeis University, Waltham, United States.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
| | - Eugene Bah
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Rohini Madireddy
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Ying Zhang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Axel F Brilot
- Department of Biochemistry, Brandeis University, Waltham, United States.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
| | - Nikolaus Grigorieff
- Department of Biochemistry, Brandeis University, Waltham, United States.,Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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Biochemical studies on Francisella tularensis RelA in (p)ppGpp biosynthesis. Biosci Rep 2015; 35:BSR20150229. [PMID: 26450927 PMCID: PMC4708007 DOI: 10.1042/bsr20150229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/16/2015] [Indexed: 12/19/2022] Open
Abstract
Francisella tularensis RelA shows significant sequence differences from other members of the RelA family of enzymes. In the present study, we describe the functional similarities and differences between F. tularensis RelA and the model RelA from Escherichia coli. The bacterial stringent response is induced by nutrient deprivation and is mediated by enzymes of the RSH (RelA/SpoT homologue; RelA, (p)ppGpp synthetase I; SpoT, (p)ppGpp synthetase II) superfamily that control concentrations of the ‘alarmones’ (p)ppGpp (guanosine penta- or tetra-phosphate). This regulatory pathway is present in the vast majority of pathogens and has been proposed as a potential anti-bacterial target. Current understanding of RelA-mediated responses is based on biochemical studies using Escherichia coli as a model. In comparison, the Francisella tularensis RelA sequence contains a truncated regulatory C-terminal region and an unusual synthetase motif (EXSD). Biochemical analysis of F. tularensis RelA showed the similarities and differences of this enzyme compared with the model RelA from Escherichia coli. Purification of the enzyme yielded a stable dimer capable of reaching concentrations of 10 mg/ml. In contrast with other enzymes from the RelA/SpoT homologue superfamily, activity assays with F. tularensis RelA demonstrate a high degree of specificity for GTP as a pyrophosphate acceptor, with no measurable turnover for GDP. Steady state kinetic analysis of F. tularensis RelA gave saturation activity curves that best fitted a sigmoidal function. This kinetic profile can result from allosteric regulation and further measurements with potential allosteric regulators demonstrated activation by ppGpp (5′,3′-dibisphosphate guanosine) with an EC50 of 60±1.9 μM. Activation of F. tularensis RelA by stalled ribosomal complexes formed with ribosomes purified from E. coli MRE600 was observed, but interestingly, significantly weaker activation with ribosomes isolated from Francisella philomiragia.
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Metabolic adaptations of Azospirillum brasilense to oxygen stress by cell-to-cell clumping and flocculation. Appl Environ Microbiol 2015; 81:8346-57. [PMID: 26407887 DOI: 10.1128/aem.02782-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/18/2015] [Indexed: 11/20/2022] Open
Abstract
The ability of bacteria to monitor their metabolism and adjust their behavior accordingly is critical to maintain competitiveness in the environment. The motile microaerophilic bacterium Azospirillum brasilense navigates oxygen gradients by aerotaxis in order to locate low oxygen concentrations that can support metabolism. When cells are exposed to elevated levels of oxygen in their surroundings, motile A. brasilense cells implement an alternative response to aerotaxis and form transient clumps by cell-to-cell interactions. Clumping was suggested to represent a behavior protecting motile cells from transiently elevated levels of aeration. Using the proteomics of wild-type and mutant strains affected in the extent of their clumping abilities, we show that cell-to-cell clumping represents a metabolic scavenging strategy that likely prepares the cells for further metabolic stresses. Analysis of mutants affected in carbon or nitrogen metabolism confirmed this assumption. The metabolic changes experienced as clumping progresses prime cells for flocculation, a morphological and metabolic shift of cells triggered under elevated-aeration conditions and nitrogen limitation. The analysis of various mutants during clumping and flocculation characterized an ordered set of changes in cell envelope properties accompanying the metabolic changes. These data also identify clumping and early flocculation to be behaviors compatible with the expression of nitrogen fixation genes, despite the elevated-aeration conditions. Cell-to-cell clumping may thus license diazotrophy to microaerophilic A. brasilense cells under elevated oxygen conditions and prime them for long-term survival via flocculation if metabolic stress persists.
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Mazzoleni M, Figuet S, Martin-Laffon J, Mininno M, Gilgen A, Leroux M, Brugière S, Tardif M, Alban C, Ravanel S. Dual Targeting of the Protein Methyltransferase PrmA Contributes to Both Chloroplastic and Mitochondrial Ribosomal Protein L11 Methylation in Arabidopsis. PLANT & CELL PHYSIOLOGY 2015; 56:1697-710. [PMID: 26116422 DOI: 10.1093/pcp/pcv098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/22/2015] [Indexed: 05/09/2023]
Abstract
Methylation of ribosomal proteins has long been described in prokaryotes and eukaryotes, but our knowledge about the enzymes responsible for these modifications in plants is scarce. The bacterial protein methyltransferase PrmA catalyzes the trimethylation of ribosomal protein L11 (RPL11) at three distinct sites. The role of these modifications is still unknown. Here, we show that PrmA from Arabidopsis thaliana (AtPrmA) is dually targeted to chloroplasts and mitochondria. Mass spectrometry and enzymatic assays indicated that the enzyme methylates RPL11 in plasto- and mitoribosomes in vivo. We determined that the Arabidopsis and Escherichia coli PrmA enzymes share similar product specificity, making trimethylated residues, but, despite an evolutionary relationship, display a difference in substrate site specificity. In contrast to the bacterial enzyme that trimethylates the ε-amino group of two lysine residues and the N-terminal α-amino group, AtPrmA methylates only one lysine in the MAFCK(D/E)(F/Y)NA motif of plastidial and mitochondrial RPL11. The plant enzyme possibly methylates the N-terminus of plastidial RPL11, whereas mitochondrial RPL11 is N-α-acetylated by an unknown acetyltransferase. Lastly, we found that an Arabidopsis prma-null mutant is viable in standard environmental conditions and no molecular defect could be associated with a lack of RPL11 methylation in leaf chloroplasts or mitochondria. However, the conservation of PrmA during the evolution of photosynthetic eukaryotes together with the location of methylated residues at the binding site of translation factors to ribosomes suggests that RPL11 methylation in plant organelles could be involved, in combination with other post-translational modifications, in optimizing ribosome function.
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Affiliation(s)
- Meryl Mazzoleni
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Sylvie Figuet
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Jacqueline Martin-Laffon
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Morgane Mininno
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Annabelle Gilgen
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Mélanie Leroux
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Sabine Brugière
- Université Grenoble Alpes, F-38041 Grenoble, France CEA, iRTSV, Biologie à Grande Echelle, F-38054 Grenoble, France INSERM, U1038, F-38054 Grenoble, France
| | - Marianne Tardif
- Université Grenoble Alpes, F-38041 Grenoble, France CEA, iRTSV, Biologie à Grande Echelle, F-38054 Grenoble, France INSERM, U1038, F-38054 Grenoble, France
| | - Claude Alban
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
| | - Stéphane Ravanel
- Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, F-38054 Grenoble, France INRA, USC1359, F-38054 Grenoble, France
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Mitroshin I, Garber M, Gabdulkhakov A. Crystallographic analysis of archaeal ribosomal protein L11. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1083-7. [PMID: 26249704 DOI: 10.1107/s2053230x15011395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/12/2015] [Indexed: 11/10/2022]
Abstract
Ribosomal protein L11 is an important part of the GTPase-associated centre in ribosomes of all organisms. L11 is a highly conserved two-domain ribosomal protein. The C-terminal domain of L11 is an RNA-binding domain that binds to a fragment of 23S rRNA and stabilizes its structure. The complex between L11 and 23S rRNA is involved in the GTPase activity of the translation elongation and release factors. Bacterial and archaeal L11-rRNA complexes are targets for peptide antibiotics of the thiazole class. To date, there is no complete structure of archaeal L11 owing to the mobility of the N-terminal domain of the protein. Here, the crystallization and X-ray analysis of the ribosomal protein L11 from Methanococcus jannaschii are reported. Crystals of the native protein and its selenomethionine derivative belonged to the orthorhombic space group I222 and were suitable for structural studies. Native and single-wavelength anomalous dispersion data sets have been collected and determination of the structure is in progress.
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Affiliation(s)
- Ivan Mitroshin
- Laboratory for Structural Studies of the Translation Apparatus, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Maria Garber
- Laboratory for Structural Studies of the Translation Apparatus, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
| | - Azat Gabdulkhakov
- Laboratory for Structural Studies of the Translation Apparatus, Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russian Federation
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6
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Positive allosteric feedback regulation of the stringent response enzyme RelA by its product. EMBO Rep 2012; 13:835-9. [PMID: 22814757 DOI: 10.1038/embor.2012.106] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 06/23/2012] [Accepted: 07/02/2012] [Indexed: 11/08/2022] Open
Abstract
During the stringent response, Escherichia coli enzyme RelA produces the ppGpp alarmone, which in turn regulates transcription, translation and replication. We show that ppGpp dramatically increases the turnover rate of its own ribosome-dependent synthesis by RelA, resulting in direct positive regulation of an enzyme by its product. Positive allosteric regulation therefore constitutes a new mechanism of enzyme activation. By integrating the output of individual RelA molecules and ppGpp degradation pathways, this regulatory circuit contributes to a fast and coordinated transition to stringency.
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Stringent response of Escherichia coli: revisiting the bibliome using literature mining. MICROBIAL INFORMATICS AND EXPERIMENTATION 2011; 1:14. [PMID: 22587779 PMCID: PMC3372295 DOI: 10.1186/2042-5783-1-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 12/30/2011] [Indexed: 12/11/2022]
Abstract
Background Understanding the mechanisms responsible for cellular responses depends on the systematic collection and analysis of information on the main biological concepts involved. Indeed, the identification of biologically relevant concepts in free text, namely genes, tRNAs, mRNAs, gene products and small molecules, is crucial to capture the structure and functioning of different responses. Results In this work, we review literature reports on the study of the stringent response in Escherichia coli. Rather than undertaking the development of a highly specialised literature mining approach, we investigate the suitability of concept recognition and statistical analysis of concept occurrence as means to highlight the concepts that are most likely to be biologically engaged during this response. The co-occurrence analysis of core concepts in this stringent response, i.e. the (p)ppGpp nucleotides with gene products was also inspected and suggest that besides the enzymes RelA and SpoT that control the basal levels of (p)ppGpp nucleotides, many other proteins have a key role in this response. Functional enrichment analysis revealed that basic cellular processes such as metabolism, transcriptional and translational regulation are central, but other stress-associated responses might be elicited during the stringent response. In addition, the identification of less annotated concepts revealed that some (p)ppGpp-induced functional activities are still overlooked in most reviews. Conclusions In this paper we applied a literature mining approach that offers a more comprehensive analysis of the stringent response in E. coli. The compilation of relevant biological entities to this stress response and the assessment of their functional roles provided a more systematic understanding of this cellular response. Overlooked regulatory entities, such as transcriptional regulators, were found to play a role in this stress response. Moreover, the involvement of other stress-associated concepts demonstrates the complexity of this cellular response.
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Stallings CL, Chu L, Li LX, Glickman MS. Catalytic and non-catalytic roles for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response. PLoS One 2011; 6:e21807. [PMID: 21789183 PMCID: PMC3138739 DOI: 10.1371/journal.pone.0021807] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/07/2011] [Indexed: 01/28/2023] Open
Abstract
Recent evidence indicates that the mycobacterial response to DNA double strand breaks (DSBs) differs substantially from previously characterized bacteria. These differences include the use of three DSB repair pathways (HR, NHEJ, SSA), and the CarD pathway, which integrates DNA damage with transcription. Here we identify a role for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response. Arr is transcriptionally induced following DNA damage and cellular stress. Although Arr is not required for induction of a core set of DNA repair genes, Arr is necessary for suppression of a set of ribosomal protein genes and rRNA during DNA damage, placing Arr in a similar pathway as CarD. Surprisingly, the catalytic activity of Arr is not required for this function, as catalytically inactive Arr was still able to suppress ribosomal protein and rRNA expression during DNA damage. In contrast, Arr substrate binding and catalytic activities were required for regulation of a small subset of other DNA damage responsive genes, indicating that Arr has both catalytic and noncatalytic roles in the DNA damage response. Our findings establish an endogenous cellular function for a mono-ADP-ribosyltransferase apart from its role in mediating Rifampin resistance.
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Affiliation(s)
- Christina L. Stallings
- Department of Molecular Microbiology Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Linda Chu
- Immunology program, Sloan Kettering Institute, New York, New York, United States of America
| | - Lucy X. Li
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Summer Undergraduate Research Program, New York, New York, United States of America
| | - Michael S. Glickman
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Immunology program, Sloan Kettering Institute, New York, New York, United States of America
- * E-mail:
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Boutte CC, Crosson S. The complex logic of stringent response regulation in Caulobacter crescentus: starvation signalling in an oligotrophic environment. Mol Microbiol 2011; 80:695-714. [PMID: 21338423 DOI: 10.1111/j.1365-2958.2011.07602.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Bacteria rapidly adapt to nutritional changes via the stringent response, which entails starvation-induced synthesis of the small molecule, ppGpp, by RelA/SpoT homologue (Rsh) enzymes. Binding of ppGpp to RNA polymerase modulates the transcription of hundreds of genes and remodels the physiology of the cell. Studies of the stringent response have primarily focused on copiotrophic bacteria such as Escherichia coli; little is known about how stringent signalling is regulated in species that live in consistently nutrient-limited (i.e. oligotrophic) environments. Here we define the input logic and transcriptional output of the stringent response in the oligotroph, Caulobacter crescentus. The sole Rsh protein, SpoT(CC), binds to and is regulated by the ribosome, and exhibits AND-type control logic in which amino acid starvation is a necessary but insufficient signal for activation of ppGpp synthesis. While both glucose and ammonium starvation upregulate the synthesis of ppGpp, SpoT(CC) detects these starvation signals by two independent mechanisms. Although the logic of stringent response control in C. crescentus differs from E. coli, the global transcriptional effects of elevated ppGpp are similar, with the exception of 16S rRNA transcription, which is controlled independently of spoT(CC). This study highlights how the regulatory logic controlling the stringent response may be adapted to the nutritional niche of a bacterial species.
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Affiliation(s)
- Cara C Boutte
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
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