1
|
Alobaidallah MSA, García V, De Mets R, Wellner SM, Thomsen LE, Herrero-Fresno A, Olsen JE. Uncovering the Important Genetic Factors for Growth during Cefotaxime-Gentamicin Combination Treatment in blaCTX-M-1 Encoding Escherichia coli. Antibiotics (Basel) 2023; 12:993. [PMID: 37370312 DOI: 10.3390/antibiotics12060993] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Due to the rapid spread of CTX-M type ESBLs, the rate of resistance to third-generation cephalosporin has increased among Gram-negative bacteria, especially in Escherichia coli, and there is a need to find ways to re-sensitize ESBL E. coli to cephalosporin treatment. A previous study showed that genes involved in protein synthesis were significantly up-regulated in the presence of subinhibitory concentration of cefotaxime (CTX) in a CTX-M-1-producing E. coli. In this study, the interaction between CTX and gentamicin (GEN), targeting protein synthesis, was evaluated in MG1655/pTF2, and the MIC of CTX was strongly reduced (128-fold) in the presence of this combnation therapy. Since the underlying mechanism behind this synergy is not known, we constructed a saturated transposon mutant library in MG1655/pTF2::blaCTX-M-1 containing 315,925 unique transposon insertions to measure mutant depletion upon exposure to CTX, GEN, and combination treatment of CTX and GEN by Transposon Directed Insertion-site Sequencing (TraDIS). We identified 57 genes that were depleted (log2FC ≤ -2 and with q.value ≤ 0.01) during exposure to CTX, 18 for GEN, and 31 for combination treatment of CTX and GEN. For validation, we deleted eight genes that were either uniquely identified in combination treatment, overlapped with monotherapy of GEN, or were shared between combination treatment and monotherapy with CTX and GEN. Of these genes, we found that the inactivation of dnaK, mnmA, rsgA, and ybeD increased the efficacy of both CTX and GEN treatment, the inactivation of cpxR and yafN increased the efficacy of only CTX, and the inactivation of mnmA, rsgA, and ybeD resulted in increased synergy between CTX and GEN. Thus, the study points to putative targets for helper drugs that can restore susceptibility to these important drugs, and it indicates that genes involved in protein synthesis are essential for the synergy between these two drugs. In summary, the study identified mutants that sensitize ESBL-producing E. coli to CTX and a combination of CTX and GEN, and it increased our understanding of the mechanism behind synergy between β-lactam and aminoglycoside drugs. This forms a framework for developing new strategies to combat infections caused by resistant bacteria.
Collapse
Affiliation(s)
- Mosaed Saleh A Alobaidallah
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Jeddah 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah 22384, Saudi Arabia
| | - Vanesa García
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain
| | - Richard De Mets
- Department of Biomedical Sciences, Core Facility for Integrated Microscopy, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sandra M Wellner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Line E Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| |
Collapse
|
2
|
Maksimova E, Kravchenko O, Korepanov A, Stolboushkina E. Protein Assistants of Small Ribosomal Subunit Biogenesis in Bacteria. Microorganisms 2022; 10:microorganisms10040747. [PMID: 35456798 PMCID: PMC9032327 DOI: 10.3390/microorganisms10040747] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/16/2022] [Accepted: 03/26/2022] [Indexed: 01/27/2023] Open
Abstract
Ribosome biogenesis is a fundamental and multistage process. The basic steps of ribosome assembly are the transcription, processing, folding, and modification of rRNA; the translation, folding, and modification of r-proteins; and consecutive binding of ribosomal proteins to rRNAs. Ribosome maturation is facilitated by biogenesis factors that include a broad spectrum of proteins: GTPases, RNA helicases, endonucleases, modification enzymes, molecular chaperones, etc. The ribosome assembly factors assist proper rRNA folding and protein–RNA interactions and may sense the checkpoints during the assembly to ensure correct order of this process. Inactivation of these factors is accompanied by severe growth phenotypes and accumulation of immature ribosomal subunits containing unprocessed rRNA, which reduces overall translation efficiency and causes translational errors. In this review, we focus on the structural and biochemical analysis of the 30S ribosomal subunit assembly factors RbfA, YjeQ (RsgA), Era, KsgA (RsmA), RimJ, RimM, RimP, and Hfq, which take part in the decoding-center folding.
Collapse
Affiliation(s)
| | | | - Alexey Korepanov
- Correspondence: (A.K.); (E.S.); Tel.: +7-925-7180670 (A.K.); +7-915-4791359 (E.S.)
| | - Elena Stolboushkina
- Correspondence: (A.K.); (E.S.); Tel.: +7-925-7180670 (A.K.); +7-915-4791359 (E.S.)
| |
Collapse
|
3
|
Maksimova EM, Korepanov AP, Kravchenko OV, Baymukhametov TN, Myasnikov AG, Vassilenko KS, Afonina ZA, Stolboushkina EA. RbfA Is Involved in Two Important Stages of 30S Subunit Assembly: Formation of the Central Pseudoknot and Docking of Helix 44 to the Decoding Center. Int J Mol Sci 2021; 22:ijms22116140. [PMID: 34200244 PMCID: PMC8201178 DOI: 10.3390/ijms22116140] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
Ribosome biogenesis is a highly coordinated and complex process that requires numerous assembly factors that ensure prompt and flawless maturation of ribosomal subunits. Despite the increasing amount of data collected, the exact role of most assembly factors and mechanistic details of their operation remain unclear, mainly due to the shortage of high-resolution structural information. Here, using cryo-electron microscopy, we characterized 30S ribosomal particles isolated from an Escherichia coli strain with a deleted gene for the RbfA factor. The cryo-EM maps for pre-30S subunits were divided into six classes corresponding to consecutive assembly intermediates: from the particles with a completely unresolved head domain and unfolded central pseudoknot to almost mature 30S subunits with well-resolved body, platform, and head domains and partially distorted helix 44. The structures of two predominant 30S intermediates belonging to most populated classes obtained at 2.7 Å resolutions indicate that RbfA acts at two distinctive 30S assembly stages: early formation of the central pseudoknot including folding of the head, and positioning of helix 44 in the decoding center at a later stage. Additionally, it was shown that the formation of the central pseudoknot may promote stabilization of the head domain, likely through the RbfA-dependent maturation of the neck helix 28. An update to the model of factor-dependent 30S maturation is proposed, suggesting that RfbA is involved in most of the subunit assembly process.
Collapse
Affiliation(s)
- Elena M. Maksimova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Alexey P. Korepanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Olesya V. Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Timur N. Baymukhametov
- National Research Center, “Kurchatov Institute”, Akademika Kurchatova pl. 1, 123182 Moscow, Russia;
| | - Alexander G. Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC “Kurchatov Institute”, 188300 Gatchina, Russia;
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Konstantin S. Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
- Correspondence: (K.S.V.); (E.A.S.); Tel.: +7-903-6276710 (K.S.V.); +7-915-4791359 (E.A.S.)
| | - Zhanna A. Afonina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Elena A. Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
- Correspondence: (K.S.V.); (E.A.S.); Tel.: +7-903-6276710 (K.S.V.); +7-915-4791359 (E.A.S.)
| |
Collapse
|
4
|
Razi A, Davis JH, Hao Y, Jahagirdar D, Thurlow B, Basu K, Jain N, Gomez-Blanco J, Britton RA, Vargas J, Guarné A, Woodson SA, Williamson JR, Ortega J. Role of Era in assembly and homeostasis of the ribosomal small subunit. Nucleic Acids Res 2019; 47:8301-8317. [PMID: 31265110 PMCID: PMC6736133 DOI: 10.1093/nar/gkz571] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/11/2019] [Accepted: 06/27/2019] [Indexed: 01/23/2023] Open
Abstract
Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation factors. To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, high resolution cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it assembled and revealed that with the exception of key helices in the platform domain, all other 16S rRNA domains fold even in the absence of Era. Notably, the maturing particles did not stall while waiting for the platform domain to mature and instead re-routed their folding pathway to enable concerted maturation of other structural motifs spanning multiple rRNA domains. We also found that binding of Era to the mature 30S subunit destabilized helix 44 and the decoding center preventing binding of YjeQ, another assembly factor. This work establishes Era’s role in ribosome assembly and suggests new roles in maintaining ribosome homeostasis.
Collapse
Affiliation(s)
- Aida Razi
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Joseph H Davis
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yumeng Hao
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Brett Thurlow
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S4K1, Canada
| | - Kaustuv Basu
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Nikhil Jain
- Department of Molecular Virology and Microbiology, Baylor College of Medicine,Houston, TX 77030, USA.,Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Josue Gomez-Blanco
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine,Houston, TX 77030, USA.,Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - Javier Vargas
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Alba Guarné
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1 Canada
| | - Sarah A Woodson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - James R Williamson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| |
Collapse
|
5
|
López-Alonso JP, Kaminishi T, Kikuchi T, Hirata Y, Iturrioz I, Dhimole N, Schedlbauer A, Hase Y, Goto S, Kurita D, Muto A, Zhou S, Naoe C, Mills DJ, Gil-Carton D, Takemoto C, Himeno H, Fucini P, Connell SR. RsgA couples the maturation state of the 30S ribosomal decoding center to activation of its GTPase pocket. Nucleic Acids Res 2017; 45:6945-6959. [PMID: 28482099 PMCID: PMC5499641 DOI: 10.1093/nar/gkx324] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 04/19/2017] [Indexed: 01/18/2023] Open
Abstract
During 30S ribosomal subunit biogenesis, assembly factors are believed to prevent accumulation of misfolded intermediate states of low free energy that slowly convert into mature 30S subunits, namely, kinetically trapped particles. Among the assembly factors, the circularly permuted GTPase, RsgA, plays a crucial role in the maturation of the 30S decoding center. Here, directed hydroxyl radical probing and single particle cryo-EM are employed to elucidate RsgA΄s mechanism of action. Our results show that RsgA destabilizes the 30S structure, including late binding r-proteins, providing a structural basis for avoiding kinetically trapped assembly intermediates. Moreover, RsgA exploits its distinct GTPase pocket and specific interactions with the 30S to coordinate GTPase activation with the maturation state of the 30S subunit. This coordination validates the architecture of the decoding center and facilitates the timely release of RsgA to control the progression of 30S biogenesis.
Collapse
Affiliation(s)
- Jorge Pedro López-Alonso
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Tatsuya Kaminishi
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Takeshi Kikuchi
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuya Hirata
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Idoia Iturrioz
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Neha Dhimole
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Andreas Schedlbauer
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Yoichi Hase
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Simon Goto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Akira Muto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Shu Zhou
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Chieko Naoe
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Deryck J Mills
- Max Planck Institute of Biophysics, Department of Structural Biology, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - David Gil-Carton
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Paola Fucini
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Sean R Connell
- Molecular Recognition and Host-Pathogen Interactions, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| |
Collapse
|
6
|
|
7
|
Razi A, Britton RA, Ortega J. The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly. Nucleic Acids Res 2017; 45:1027-1040. [PMID: 28180306 PMCID: PMC5388408 DOI: 10.1093/nar/gkw1231] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/20/2016] [Accepted: 11/25/2016] [Indexed: 01/14/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) had played a central role in the study of ribosome structure and the process of translation in bacteria since the development of this technique in the mid 1980s. Until recently cryo-EM structures were limited to ∼10 Å in the best cases. However, the recent advent of direct electron detectors has greatly improved the resolution of cryo-EM structures to the point where atomic resolution is now achievable. This improved resolution will allow cryo-EM to make groundbreaking contributions in essential aspects of ribosome biology, including the assembly process. In this review, we summarize important insights that cryo-EM, in combination with chemical and genetic approaches, has already brought to our current understanding of the ribosomal assembly process in bacteria using previous detector technology. More importantly, we discuss how the higher resolution structures now attainable with direct electron detectors can be leveraged to propose precise testable models regarding this process. These structures will provide an effective platform to develop new antibiotics that target this fundamental cellular process.
Collapse
Affiliation(s)
- Aida Razi
- Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
| | - Robert A Britton
- Department of Molecular Virology and Microbiology and Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and M. G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
8
|
The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly. Proc Natl Acad Sci U S A 2017; 114:E3396-E3403. [PMID: 28396444 DOI: 10.1073/pnas.1618016114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading. This finding indicates that, along with acting as an assembly factor, YjeQ has a role as a checkpoint protein, consisting of testing the proofreading ability of the 30S subunit. The structure also informs the mechanism by which YjeQ implements the release from the 30S subunit of a second assembly factor, called RbfA. Finally, it reveals how the 30S subunit stimulates YjeQ GTPase activity and leads to release of the protein. Checkpoint functions have been described for eukaryotic ribosome assembly factors; however, this work describes an example of a bacterial assembly factor that tests a specific translation mechanism of the 30S subunit.
Collapse
|
9
|
Thurlow B, Davis JH, Leong V, Moraes TF, Williamson JR, Ortega J. Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit. Nucleic Acids Res 2016; 44:9918-9932. [PMID: 27382067 PMCID: PMC5175332 DOI: 10.1093/nar/gkw613] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 06/26/2016] [Accepted: 06/27/2016] [Indexed: 11/13/2022] Open
Abstract
Our understanding regarding the function of YjeQ (also called RsgA), RbfA, RimM and Era in ribosome biogenesis has been derived in part from the study of immature 30S particles that accumulate in null strains lacking one of these factors. However, their mechanistic details are still unknown. Here, we demonstrate that these immature particles are not dead-end products of assembly, but progress into mature 30S subunits. Mass spectrometry analysis revealed that in vivo the occupancy level of these factors in these immature 30S particles is below 10% and that the concentration of factors does not increase when immature particles accumulate in cells. We measured by microscale thermophoresis that YjeQ and Era binds to the mature 30S subunit with high affinity. However, the binding affinity of these factors to the immature particles and of RimM and RbfA to mature or immature particles was weak, suggesting that binding is not occurring at physiological concentrations. These results suggest that in the absence of these factors, the immature particles evolve into a thermodynamically stable intermediate that exhibits low affinity for the assembly factors. These results imply that the true substrates of YjeQ, RbfA, RimM and Era are immature particles that precede the ribosomal particles accumulating in the knockouts strains.
Collapse
Affiliation(s)
- Brett Thurlow
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Joseph H Davis
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Vivian Leong
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S1A8, Canada
| | - James R Williamson
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences and M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| |
Collapse
|
10
|
Stokes JM, Brown ED. Chemical modulators of ribosome biogenesis as biological probes. Nat Chem Biol 2015; 11:924-32. [PMID: 26575239 DOI: 10.1038/nchembio.1957] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 10/13/2015] [Indexed: 01/17/2023]
Abstract
Small-molecule inhibitors of protein biosynthesis have been instrumental in the dissection of the complexities of ribosome structure and function. Ribosome biogenesis, on the other hand, is a complex and largely enigmatic process for which there is a paucity of chemical probes. Indeed, ribosome biogenesis has been studied almost exclusively using genetic and biochemical approaches without the benefit of small-molecule inhibitors of this process. Here, we provide a perspective on the promise of chemical inhibitors of ribosome assembly for future research. We explore key obstacles that complicate the interpretation of studies aimed at perturbing ribosome biogenesis in vivo using genetic methods, and we argue that chemical inhibitors are especially powerful because they can be used to induce perturbations in a manner that obviates these difficulties. Thus, in combination with leading-edge biochemical and structural methods, chemical probes offer unique advantages toward elucidating the molecular events that define the assembly of ribosomes.
Collapse
Affiliation(s)
- Jonathan M Stokes
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
11
|
Jeganathan A, Razi A, Thurlow B, Ortega J. The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly. RNA (NEW YORK, N.Y.) 2015; 21:1203-1216. [PMID: 25904134 PMCID: PMC4436671 DOI: 10.1261/rna.049171.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/22/2015] [Indexed: 06/04/2023]
Abstract
YjeQ (also called RsgA) and RbfA proteins in Escherichia coli bind to immature 30S ribosome subunits at late stages of assembly to assist folding of the decoding center. A key step for the subunit to enter the pool of actively translating ribosomes is the release of these factors. YjeQ promotes dissociation of RbfA during the final stages of maturation; however, the mechanism implementing this functional interplay has not been elucidated. YjeQ features an amino-terminal oligonucleotide/oligosaccharide binding domain, a central GTPase module and a carboxy-terminal zinc-finger domain. We found that the zinc-finger domain is comprised of two functional motifs: the region coordinating the zinc ion and a carboxy-terminal α-helix. The first motif is essential for the anchoring of YjeQ to the 30S subunit and the carboxy-terminal α-helix facilitates the removal of RbfA once the 30S subunit reaches the mature state. Furthermore, the ability of the mature 30S subunit to stimulate YjeQ GTPase activity also depends on the carboxy-terminal α-helix. Our data are consistent with a model in which YjeQ uses this carboxy-terminal α-helix as a sensor to gauge the conformation of helix 44, an essential motif of the decoding center. According to this model, the mature conformation of helix 44 is sensed by the carboxy-terminal α-helix, which in turn stimulates the YjeQ GTPase activity. Hydrolysis of GTP is believed to assist the release of YjeQ from the mature 30S subunit through a still uncharacterized mechanism. These results identify the structural determinants in YjeQ that implement the functional interplay with RbfA.
Collapse
Affiliation(s)
- Ajitha Jeganathan
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Aida Razi
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Brett Thurlow
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada L8S 4K1
| |
Collapse
|
12
|
In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state. Proc Natl Acad Sci U S A 2015; 112:2425-30. [PMID: 25675474 DOI: 10.1073/pnas.1411514112] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
It was shown decades ago that purified 30S ribosome subunits readily interconvert between "active" and "inactive" conformations in a switch that involves changes in the functionally important neck and decoding regions. However, the physiological significance of this conformational change had remained unknown. In exponentially growing Escherichia coli cells, RNA SHAPE probing revealed that 16S rRNA largely adopts the inactive conformation in stably assembled, mature 30S subunits and the active conformation in translating (70S) ribosomes. Inactive 30S subunits bind mRNA as efficiently as active subunits but initiate translation more slowly. Mutations that inhibited interconversion between states compromised translation in vivo. Binding by the small antibiotic paromomycin induced the inactive-to-active conversion, consistent with a low-energy barrier between the two states. Despite the small energetic barrier between states, but consistent with slow translation initiation and a functional role in vivo, interconversion involved large-scale changes in structure in the neck region that likely propagate across the 30S body via helix 44. These findings suggest the inactive state is a biologically relevant alternate conformation that regulates ribosome function as a conformational switch.
Collapse
|
13
|
Bharat A, Brown ED. Phenotypic investigations of the depletion of EngA in Escherichia coli are consistent with a role in ribosome biogenesis. FEMS Microbiol Lett 2014; 353:26-32. [PMID: 24822275 DOI: 10.1111/1574-6968.12403] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The EngA protein is a conserved and essential bacterial GTPase of largely enigmatic function. While most investigations of EngA have suggested a role in ribosome assembly, the protein has also been implicated in diverse elements of physiology including chromosome segregation, cell division, and cell cycle control. Here, we have probed additional phenotypes related to ribosome biogenesis on depletion of EngA in Escherichia coli to better understand its role in the cell. Depletion of EngA resulted in cold-sensitive growth and stimulation of a ribosomal rRNA promoter, both phenotypes associated with the disruption of ribosome biogenesis in bacteria. Among antibiotics that inhibit translation, depletion of EngA resulted in sensitization to the aminoglycoside class of antibiotics. EngA bound the alarmone ppGpp with equally high affinity as it bound GDP. These data offer additional support for a role in ribosome biogenesis for EngA, possibly in maturation of the A-site of the 50S subunit.
Collapse
|
14
|
Sashital DG, Greeman CA, Lyumkis D, Potter CS, Carragher B, Williamson JR. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. eLife 2014; 3. [PMID: 25313868 PMCID: PMC4371863 DOI: 10.7554/elife.04491] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 10/13/2014] [Indexed: 12/13/2022] Open
Abstract
Ribosome assembly is a complex process involving the folding and processing of ribosomal RNAs (rRNAs), concomitant binding of ribosomal proteins (r-proteins), and participation of numerous accessory cofactors. Here, we use a quantitative mass spectrometry/electron microscopy hybrid approach to determine the r-protein composition and conformation of 30S ribosome assembly intermediates in Escherichia coli. The relative timing of assembly of the 3' domain and the formation of the central pseudoknot (PK) structure depends on the presence of the assembly factor RimP. The central PK is unstable in the absence of RimP, resulting in the accumulation of intermediates in which the 3'-domain is unanchored and the 5'-domain is depleted for r-proteins S5 and S12 that contact the central PK. Our results reveal the importance of the cofactor RimP in central PK formation, and introduce a broadly applicable method for characterizing macromolecular assembly in cells.
Collapse
Affiliation(s)
- Dipali G Sashital
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Candacia A Greeman
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Dmitry Lyumkis
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Clinton S Potter
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Bridget Carragher
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| |
Collapse
|
15
|
Grosjean H, Breton M, Sirand-Pugnet P, Tardy F, Thiaucourt F, Citti C, Barré A, Yoshizawa S, Fourmy D, de Crécy-Lagard V, Blanchard A. Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes. PLoS Genet 2014; 10:e1004363. [PMID: 24809820 PMCID: PMC4014445 DOI: 10.1371/journal.pgen.1004363] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 03/24/2014] [Indexed: 11/18/2022] Open
Abstract
Mollicutes is a class of parasitic bacteria that have evolved from a common Firmicutes ancestor mostly by massive genome reduction. With genomes under 1 Mbp in size, most Mollicutes species retain the capacity to replicate and grow autonomously. The major goal of this work was to identify the minimal set of proteins that can sustain ribosome biogenesis and translation of the genetic code in these bacteria. Using the experimentally validated genes from the model bacteria Escherichia coli and Bacillus subtilis as input, genes encoding proteins of the core translation machinery were predicted in 39 distinct Mollicutes species, 33 of which are culturable. The set of 260 input genes encodes proteins involved in ribosome biogenesis, tRNA maturation and aminoacylation, as well as proteins cofactors required for mRNA translation and RNA decay. A core set of 104 of these proteins is found in all species analyzed. Genes encoding proteins involved in post-translational modifications of ribosomal proteins and translation cofactors, post-transcriptional modifications of t+rRNA, in ribosome assembly and RNA degradation are the most frequently lost. As expected, genes coding for aminoacyl-tRNA synthetases, ribosomal proteins and initiation, elongation and termination factors are the most persistent (i.e. conserved in a majority of genomes). Enzymes introducing nucleotides modifications in the anticodon loop of tRNA, in helix 44 of 16S rRNA and in helices 69 and 80 of 23S rRNA, all essential for decoding and facilitating peptidyl transfer, are maintained in all species. Reconstruction of genome evolution in Mollicutes revealed that, beside many gene losses, occasional gains by horizontal gene transfer also occurred. This analysis not only showed that slightly different solutions for preserving a functional, albeit minimal, protein synthetizing machinery have emerged in these successive rounds of reductive evolution but also has broad implications in guiding the reconstruction of a minimal cell by synthetic biology approaches.
Collapse
Affiliation(s)
- Henri Grosjean
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Université Paris-Sud, FRC 3115, Gif-sur-Yvette, France
| | - Marc Breton
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Pascal Sirand-Pugnet
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Florence Tardy
- Anses, Laboratoire de Lyon, UMR Mycoplasmoses des Ruminants, Lyon, France
- Université de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, Marcy L'Etoile, France
| | - François Thiaucourt
- Centre International de Recherche en Agronomie pour le Développement, UMR CMAEE, Montpellier, France
| | - Christine Citti
- INRA, UMR1225, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
- Université de Toulouse, INP-ENVT, UMR1225, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Aurélien Barré
- Univ. Bordeaux, Centre de bioinformatique et de génomique fonctionnelle, CBiB, Bordeaux, France
| | - Satoko Yoshizawa
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Université Paris-Sud, FRC 3115, Gif-sur-Yvette, France
| | - Dominique Fourmy
- Centre de Génétique Moléculaire, UPR 3404, CNRS, Université Paris-Sud, FRC 3115, Gif-sur-Yvette, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University Florida, Gainesville, Florida, United States of America
| | - Alain Blanchard
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- * E-mail:
| |
Collapse
|
16
|
Leong V, Kent M, Jomaa A, Ortega J. Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement. RNA (NEW YORK, N.Y.) 2013; 19:789-802. [PMID: 23611982 PMCID: PMC3683913 DOI: 10.1261/rna.037523.112] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Assembly of the Escherichia coli 30S ribosomal subunits proceeds through multiple parallel pathways. The protein factors RimM, YjeQ, RbfA, and Era work in conjunction to assist at the late stages of the maturation process of the small subunit. However, it is unclear how the functional interplay between these factors occurs in the context of multiple parallel pathways. To understand how these factors work together, we have characterized the immature 30S subunits that accumulate in ΔrimM cells and compared them with immature 30S subunits from a ΔyjeQ strain. The cryo-EM maps obtained from these particles showed that the densities representing helices 44 and 45 in the rRNA were partially missing, suggesting mobility of these motifs. These 30S subunits were also partially depleted in all tertiary ribosomal proteins, particularly those binding in the head domain. Using image classification, we identified four subpopulations of ΔrimM immature 30S subunits differing in the amount of missing density for helices 44 and 45, as well as the amount of density existing in these maps for the underrepresented proteins. The structural defects found in these immature subunits resembled those of the 30S subunits that accumulate in the ΔyjeQ strain. These findings are consistent with an "early convergency model" in which multiple parallel assembly pathways of the 30S subunit converge into a late assembly intermediate, as opposed to the mature state. Functionally related factors will bind to this intermediate to catalyze the last steps of maturation leading to the mature 30S subunit.
Collapse
MESH Headings
- Binding Sites
- Cryoelectron Microscopy
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- GTP Phosphohydrolases/genetics
- GTP Phosphohydrolases/metabolism
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/metabolism
- Gene Deletion
- Genes, Bacterial
- Models, Molecular
- Nucleic Acid Conformation
- Phenotype
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small, Bacterial/genetics
- Ribosome Subunits, Small, Bacterial/metabolism
- Species Specificity
Collapse
|
17
|
Impairment of ribosome maturation or function confers salt resistance on Escherichia coli cells. PLoS One 2013; 8:e65747. [PMID: 23741511 PMCID: PMC3669203 DOI: 10.1371/journal.pone.0065747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 04/26/2013] [Indexed: 11/19/2022] Open
Abstract
We found that loss of integrity of the ribosome by removal of a putative ribosome maturation factor or a ribosomal protein conferred salt tolerance on Escherichia coli cells. Some protein synthesis inhibitors including kasugamycin and chloramphenicol also had a similar effect, although kasugamycin affected neither 16S rRNA maturation nor subunit association into a 70S ribosome. Thus, salt tolerance is a common feature of cells in which maturation or function of the ribosome is impaired. In these cells, premature induction of an alternative sigma factor, σ(E), by salt stress was observed. These results suggest the existence of a yet-unknown stress response pathway mediated by the bacterial ribosome.
Collapse
|
18
|
Abstract
The ribosome is an RNA- and protein-based macromolecule having multiple functional domains to facilitate protein synthesis, and it is synthesized through multiple steps including transcription, stepwise cleavages of the primary transcript, modifications of ribosomal proteins and RNAs and assemblies of ribosomal proteins with rRNAs. This process requires dozens of trans-acting factors including GTP- and ATP-binding proteins to overcome several energy-consuming steps. Despite accumulation of genetic, biochemical and structural data, the entire process of bacterial ribosome synthesis remains elusive. Here, we review GTPases involved in bacterial ribosome maturation.
Collapse
Affiliation(s)
- Simon Goto
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | | | | |
Collapse
|
19
|
Jakovljevic J, Ohmayer U, Gamalinda M, Talkish J, Alexander L, Linnemann J, Milkereit P, Woolford JL. Ribosomal proteins L7 and L8 function in concert with six A₃ assembly factors to propagate assembly of domains I and II of 25S rRNA in yeast 60S ribosomal subunits. RNA (NEW YORK, N.Y.) 2012; 18:1805-22. [PMID: 22893726 PMCID: PMC3446705 DOI: 10.1261/rna.032540.112] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 07/02/2012] [Indexed: 05/24/2023]
Abstract
Ribosome biogenesis is a complex multistep process that involves alternating steps of folding and processing of pre-rRNAs in concert with assembly of ribosomal proteins. Recently, there has been increased interest in the roles of ribosomal proteins in eukaryotic ribosome biogenesis in vivo, focusing primarily on their function in pre-rRNA processing. However, much less is known about participation of ribosomal proteins in the formation and rearrangement of preribosomal particles as they mature to functional subunits. We have studied ribosomal proteins L7 and L8, which are required for the same early steps in pre-rRNA processing during assembly of 60S subunits but are located in different domains within ribosomes. Depletion of either leads to defects in processing of 27SA(3) to 27SB pre-rRNA and turnover of pre-rRNAs destined for large ribosomal subunits. A specific subset of proteins is diminished from these residual assembly intermediates: six assembly factors required for processing of 27SA(3) pre-rRNA and four ribosomal proteins bound to domain I of 25S and 5.8S rRNAs surrounding the polypeptide exit tunnel. In addition, specific sets of ribosomal proteins are affected in each mutant: In the absence of L7, proteins bound to domain II, L6, L14, L20, and L33 are greatly diminished, while proteins L13, L15, and L36 that bind to domain I are affected in the absence of L8. Thus, L7 and L8 might establish RNP structures within assembling ribosomes necessary for the stable association and function of the A(3) assembly factors and for proper assembly of the neighborhoods containing domains I and II.
Collapse
MESH Headings
- Active Transport, Cell Nucleus/genetics
- Active Transport, Cell Nucleus/physiology
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Gene Expression Profiling
- Gene Expression Regulation, Fungal
- Microarray Analysis
- Organisms, Genetically Modified
- Protein Interaction Domains and Motifs/genetics
- Protein Interaction Domains and Motifs/physiology
- Protein Multimerization/genetics
- Protein Multimerization/physiology
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA Processing, Post-Transcriptional/physiology
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/physiology
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomal Proteins/physiology
- Ribosome Subunits, Large, Eukaryotic/chemistry
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae/ultrastructure
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Saccharomyces cerevisiae Proteins/physiology
- Yeasts/genetics
- Yeasts/metabolism
Collapse
Affiliation(s)
- Jelena Jakovljevic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Uli Ohmayer
- Institut für Biochemie III, Universität Regensburg, 93053 Regensburg, Germany
| | - Michael Gamalinda
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Jason Talkish
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Lisa Alexander
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Jan Linnemann
- Institut für Biochemie III, Universität Regensburg, 93053 Regensburg, Germany
| | - Philipp Milkereit
- Institut für Biochemie III, Universität Regensburg, 93053 Regensburg, Germany
| | - John L. Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| |
Collapse
|
20
|
Pompeo F, Freton C, Wicker-Planquart C, Grangeasse C, Jault JM, Galinier A. Phosphorylation of CpgA protein enhances both its GTPase activity and its affinity for ribosome and is crucial for Bacillus subtilis growth and morphology. J Biol Chem 2012; 287:20830-8. [PMID: 22544754 DOI: 10.1074/jbc.m112.340331] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In Bacillus subtilis, the ribosome-associated GTPase CpgA is crucial for growth and proper morphology and was shown to be phosphorylated in vitro by the Ser/Thr protein kinase PrkC. To further understand the function of the Escherichia coli RsgA ortholog, CpgA, we first demonstrated that its GTPase activity is stimulated by its association with the 30 S ribosomal subunit. Then the role of CpgA phosphorylation was analyzed. A single phosphorylated residue, threonine 166, was identified by mass spectrometry. Phosphoablative replacement of this residue in CpgA induces a decrease of both its affinity for the 30 S ribosomal subunit and its GTPase activity, whereas a phosphomimetic replacement has opposite effects. Furthermore, cells expressing a nonphosphorylatable CpgA protein present the morphological and growth defects similar to those of a cpgA-deleted strain. Altogether, our results suggest that CpgA phosphorylation on Thr-166 could modulate its ribosome-induced GTPase activity. Given the role of PrkC in B. subtilis spore germination, we propose that CpgA phosphorylation is a key regulatory process that is essential for B. subtilis development.
Collapse
Affiliation(s)
- Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, FR 3479, CNRS, Aix-Marseille Université, 13402 Marseille Cedex 20, France.
| | | | | | | | | | | |
Collapse
|
21
|
Boehringer D, O'Farrell HC, Rife JP, Ban N. Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis. J Biol Chem 2012; 287:10453-10459. [PMID: 22308031 DOI: 10.1074/jbc.m111.318121] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation.
Collapse
Affiliation(s)
- Daniel Boehringer
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland, and
| | - Heather C O'Farrell
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Jason P Rife
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia 23298.
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland, and.
| |
Collapse
|