1
|
K M K, N U, S K. Conformational dynamics and ribosomal interactions of Bacillus subtilis Obg in various nucleotide-bound states: Insights from molecular dynamics simulation. Int J Biol Macromol 2024; 279:135337. [PMID: 39241998 DOI: 10.1016/j.ijbiomac.2024.135337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/24/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Obg, a GTPase, binds to the premature 50S ribosomal subunit and facilitates recruitment of rproteins and rRNA processing to form the mature 50S subunit. This binding depends on nucleotide-induced conformational changes (GDP/GTP). However, the mechanism by which Obg undergoes conformational changes to associate with the premature 50S subunit is unknown. Therefore, 1000 ns molecular dynamics simulations were conducted to investigate this mechanism. Visualization of the simulated trajectory showed that in GDP and GTP-bound states, the C-domain moved towards the SwI region, while in GTP-Mg2+ and ppGpp-bound states, the C-domain shifted towards the N-tails. Further, positioning these conformations of Obg on the 50S subunit suggests possible mechanisms by which the GTP-Mg2+ bound state is responsible for recruiting rprotein, as well as the impact of the absence of Mg2+ in the GTP-bound state. Furthermore, the study provides insights into the conformational changes that may lead to the dissociation of the GDP-bound state from the 50S subunit and explores the potential role of the ppGpp-bound state in inhibiting 70S ribosome formation. Additionally, RMSF and community network analyses reveal how internal dynamics and intricate connections within Obg affect C-domain motion.
Collapse
Affiliation(s)
- Kavya K M
- Department of Studies in Physics, University of Mysore, Mysuru, India.
| | - Upendra N
- Center for Research and Innovations, Faculty of Natural Sciences, Adichunchanagiri University, B.G.Nagara, India.
| | - Krishnaveni S
- Department of Studies in Physics, University of Mysore, Mysuru, India.
| |
Collapse
|
2
|
Brischigliaro M, Sierra‐Magro A, Ahn A, Barrientos A. Mitochondrial ribosome biogenesis and redox sensing. FEBS Open Bio 2024; 14:1640-1655. [PMID: 38849194 PMCID: PMC11452305 DOI: 10.1002/2211-5463.13844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Mitoribosome biogenesis is a complex process involving RNA elements encoded in the mitochondrial genome and mitoribosomal proteins typically encoded in the nuclear genome. This process is orchestrated by extra-ribosomal proteins, nucleus-encoded assembly factors, which play roles across all assembly stages to coordinate ribosomal RNA processing and maturation with the sequential association of ribosomal proteins. Both biochemical studies and recent cryo-EM structures of mammalian mitoribosomes have provided insights into their assembly process. In this article, we will briefly outline the current understanding of mammalian mitoribosome biogenesis pathways and the factors involved. Special attention is devoted to the recent identification of iron-sulfur clusters as structural components of the mitoribosome and a small subunit assembly factor, the existence of redox-sensitive cysteines in mitoribosome proteins and assembly factors, and the role they may play as redox sensor units to regulate mitochondrial translation under stress.
Collapse
Affiliation(s)
| | - Ana Sierra‐Magro
- Department of NeurologyUniversity of Miami Miller School of MedicineFLUSA
| | - Ahram Ahn
- Department of Biochemistry and Molecular BiologyUniversity of Miami Miller School of MedicineFLUSA
| | - Antoni Barrientos
- Department of NeurologyUniversity of Miami Miller School of MedicineFLUSA
- Department of Biochemistry and Molecular BiologyUniversity of Miami Miller School of MedicineFLUSA
- Bruce W. Carter Department of Veterans Affairs VA Medical CenterMiamiFLUSA
| |
Collapse
|
3
|
Mrnjavac N, Martin WF. GTP before ATP: The energy currency at the origin of genes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1866:149514. [PMID: 39326542 DOI: 10.1016/j.bbabio.2024.149514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/08/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Life is an exergonic chemical reaction. Many individual reactions in metabolism entail slightly endergonic steps that are coupled to free energy release, typically as ATP hydrolysis, in order to go forward. ATP is almost always supplied by the rotor-stator ATP synthase, which harnesses chemiosmotic ion gradients. Because the ATP synthase is a protein, it arose after the ribosome did. What was the energy currency of metabolism before the origin of the ATP synthase and how (and why) did ATP come to be the universal energy currency? About 27 % of a cell's energy budget is consumed as GTP during translation. The universality of GTP-dependence in ribosome function indicates that GTP was the ancestral energy currency of protein synthesis. The use of GTP in translation and ATP in small molecule synthesis are conserved across all lineages, representing energetic compartments that arose in the last universal common ancestor, LUCA. And what came before GTP? Recent findings indicate that the energy supporting the origin of LUCA's metabolism stemmed from H2-dependent CO2 reduction along routes that strongly resemble the reactions and transition metal catalysts of the acetyl-CoA pathway.
Collapse
Affiliation(s)
- Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
| |
Collapse
|
4
|
Kapila R, Mehra U, Kaur J, Verma Y, Jakar S, Datta K. Insights into Mtg3-mitochondrial ribosome association in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2024; 737:150502. [PMID: 39180962 DOI: 10.1016/j.bbrc.2024.150502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024]
Abstract
Ribosome biogenesis is a highly regulated multistep process aided by energy-consuming auxiliary factors. GTPases form the largest class of auxiliary factors used by bacterial, cytosolic, and mitochondrial ribosomes for their maturation. Mtg3, a circularly permuted YqeH family of GTPase, is implicated in the mitoribosome small subunit biogenesis. However, its precise mechanistic role has yet to be characterized. Mtg3 is likely to bind precursor mitoribosome molecules during subunit maturation in vivo. However, this interaction has yet to be observed with mitoribosomes biochemically. In this study, we delineate the specific conditions necessary for preserving the association of Mtg3 with mitoribosomes on a sucrose density gradient. We show that the C-terminal domain of Mtg3 is required for robust binding to the mitoribosome. Furthermore, point mutants likely to abrogate GTP/GDP binding and GTPase activity compromise protein function in vivo. Surprisingly, the association with the mitoribosome was not compromised in mutants likely to be deficient for nucleotide binding/hydrolysis. Thus, our finding supports a model wherein Mtg3 binds to a precursor mitoribosome through its C-terminus to facilitate a conformational change or validate a folding intermediate driven by the GTP/GDP binding and hydrolysis cycle.
Collapse
Affiliation(s)
- Ritika Kapila
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Upasana Mehra
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Jaswinder Kaur
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Yash Verma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Shweta Jakar
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Kaustuv Datta
- Department of Genetics, University of Delhi South Campus, New Delhi, India.
| |
Collapse
|
5
|
Sun X, Singla-Rastogi M, Wang J, Zhao C, Wang X, Li P. The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids. Nucleic Acids Res 2024; 52:7893-7909. [PMID: 38686791 PMCID: PMC11260468 DOI: 10.1093/nar/gkae339] [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: 01/18/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
In plant chloroplasts, certain ribosomal proteins (RPs) and ribosome biogenesis factors (RBFs) are present in nucleoids, implying an association between nucleoids and ribosome biogenesis. In Arabidopsis, the YqeH-type GTPase Brassinazole-Insensitive Pale Green2 (BPG2) is a chloroplast nucleoid-associated RBF. Here, we investigated the relationship between nucleoids and BPG2-involved ribosome biogenesis steps by exploring how BPG2 targets ribosomes. Our findings demonstrate that BPG2 interacts with an essential plastid RP, uS10c, in chloroplast nucleoids in a ribosomal RNA (rRNA)-independent manner. We also discovered that uS10c is a haploinsufficient gene, as the heterozygous deletion of this gene leads to variegated shoots and chlorophyll aggregation. uS10c is integrated into 30S ribosomal particles when rRNA is relatively exposed and also exists in polysome fractions. In contrast, BPG2 exclusively associates with 30S ribosomal particles. Notably, the interaction between BPG2 and 30S particles is influenced by the absence of uS10c, resulting in BPG2 diffusing in chloroplasts instead of targeting nucleoids. Further, our results reveal that the loss of BPG2 function and the heterozygous deletion of uS10c impair the processing of 16S and 23S-4.5S rRNAs, reduce plastid protein accumulation, and trigger the plastid signaling response. Together, these findings indicate that the uS10c-BPG2 module mediates ribosome biogenesis in chloroplast nucleoids.
Collapse
Affiliation(s)
- Xueping Sun
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | | | - Jingwen Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Pengcheng Li
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
6
|
Hussain A. DEAD Box RNA Helicases: Biochemical Properties, Role in RNA Processing and Ribosome Biogenesis. Cell Biochem Biophys 2024; 82:427-434. [PMID: 38430409 DOI: 10.1007/s12013-024-01240-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/20/2024] [Indexed: 03/03/2024]
Abstract
DEAD box RNA helicases are a versatile group of ATP dependent enzymes that play an essential role in cellular processes like transcription, RNA processing, ribosome biogenesis and translation. These enzymes perform structural rearrangement of complex RNA molecules and enhance the productive folding of RNA and organization of macromolecular complexes. In this review article besides providing the outline about structural organization of helicases, an in-depth discussion will be done on the biochemical properties of RNA helicases like their substrate binding, binding and hydrolysis of ATP and related conformational changes that are important for functioning of the RNA helicase enzymes. I will extensively discuss the physiological role of RNA helicases in RNA processing and ribosome biogenesis.
Collapse
Affiliation(s)
- Ashaq Hussain
- Centre for Cellular and Molecular Biology, Hyderabad, India.
| |
Collapse
|
7
|
Schmid LM, Manavski N, Chi W, Meurer J. Chloroplast Ribosome Biogenesis Factors. PLANT & CELL PHYSIOLOGY 2024; 65:516-536. [PMID: 37498958 DOI: 10.1093/pcp/pcad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/13/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation and adaptation.
Collapse
Affiliation(s)
- Lisa-Marie Schmid
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| | - Wei Chi
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, Planegg-Martinsried 82152, Germany
| |
Collapse
|
8
|
Lejeune C, Cornu D, Sago L, Redeker V, Virolle MJ. The stringent response is strongly activated in the antibiotic producing strain, Streptomyces coelicolor. Res Microbiol 2024; 175:104177. [PMID: 38159786 DOI: 10.1016/j.resmic.2023.104177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
S. lividans and S. coelicolor are phylogenetically closely related strains with different abilities to produce the same specialized metabolites. Previous studies revealed that the strong antibiotic producer, S. coelicolor, had a lower ability to assimilate nitrogen and phosphate than the weak producer, Streptomyces lividans, and this resulted into a lower growth rate. A comparative proteomic dataset was used to establish the consequences of these nutritional stresses on the abundance of proteins of the translational apparatus of these strains, grown in low and high phosphate availability. Our study revealed that most proteins of the translational apparatus were less abundant in S. coelicolor than in S. lividans whereas it was the opposite for ET-Tu 3 and a TrmA-like methyltransferase. The expression of the latter being known to be under the positive control of the stringent response whereas that of the other ribosomal proteins is under its negative control, this indicated the occurrence of a strong activation of the stringent response in S. coelicolor. Furthermore, in S. lividans, ribosomal proteins were more abundant in phosphate proficiency than in phosphate limitation suggesting that a limitation in phosphate, that was also shown to trigger RelA expression, contributes to the induction of the stringent response.
Collapse
Affiliation(s)
- Clara Lejeune
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - David Cornu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Laila Sago
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Virginie Redeker
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France; Institut Francois Jacob, Molecular Imaging Center (MIRCen), Laboratory of Neurodegenerative Diseases, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique, Université Paris-Saclay, Fontenay-aux-Roses, France.
| | - Marie-Joelle Virolle
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| |
Collapse
|
9
|
Wang L, Hilander T, Liu X, Tsang HY, Eriksson O, Jackson CB, Varjosalo M, Zhao H. GTPBP8 is required for mitoribosomal biogenesis and mitochondrial translation. Cell Mol Life Sci 2023; 80:361. [PMID: 37971521 PMCID: PMC10654211 DOI: 10.1007/s00018-023-05014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Mitochondrial translation occurs on the mitochondrial ribosome, also known as the mitoribosome. The assembly of mitoribosomes is a highly coordinated process. During mitoribosome biogenesis, various assembly factors transiently associate with the nascent ribosome, facilitating the accurate and efficient construction of the mitoribosome. However, the specific factors involved in the assembly process, the precise mechanisms, and the cellular compartments involved in this vital process are not yet fully understood. In this study, we discovered a crucial role for GTP-binding protein 8 (GTPBP8) in the assembly of the mitoribosomal large subunit (mt-LSU) and mitochondrial translation. GTPBP8 is identified as a novel GTPase located in the matrix and peripherally bound to the inner mitochondrial membrane. Importantly, GTPBP8 is specifically associated with the mt-LSU during its assembly. Depletion of GTPBP8 leads to an abnormal accumulation of mt-LSU, indicating that GTPBP8 is critical for proper mt-LSU assembly. Furthermore, the absence of GTPBP8 results in reduced levels of fully assembled 55S monosomes. This impaired assembly leads to compromised mitochondrial translation and, consequently, impaired mitochondrial function. The identification of GTPBP8 as an important player in these processes provides new insights into the molecular mechanisms underlying mitochondrial protein synthesis and its regulation.
Collapse
Affiliation(s)
- Liang Wang
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, #1 Keyuan Road, Gaopeng Street, High-Tech Development Zone, West China, Chengdu, 610041, China
| | - Taru Hilander
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology and Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Hoi Ying Tsang
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Ove Eriksson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Christopher B Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology and Helsinki Institute of Life Science, University of Helsinki, 00014, Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
| |
Collapse
|
10
|
Upendra N, Kavya KM, Krishnaveni S. Molecular dynamics simulation study on Bacillus subtilis EngA: the presence of Mg 2+ at the active-sites promotes the functionally important conformation. J Biomol Struct Dyn 2023; 41:9219-9231. [PMID: 36444972 DOI: 10.1080/07391102.2022.2151513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/20/2022] [Indexed: 11/30/2022]
Abstract
EngA, a GTPase contains two GTP binding domains [GD1, GD2], and the C-terminal KH domain shown to be involved in the later stages of ribosome maturation. Association of EngA to the ribosomal subunit in the intermediate stage of maturation is essential for complete ribosome maturation. However, this association was shown to be dependent on the nucleotide bound combinations. This nucleotide dependent association tendency is attributed to the conformational changes that occur among different nucleotide bound combinations. Therefore, to explore the conformational changes, all-atom molecular dynamics simulations for Bacillus subtilis EngA in different nucleotide bound combinations along with the presence or absence of Mg2+ in the active-sites were carried out. The presence of Mg2+ along with the bound nucleotide at the GD2 active-site dictates the GD2-Sw-II mobility, but the GD1-Sw-II mobility has not shown any nucleotide or Mg2+ dependent movement. However, the GD1-Sw-II secondary conformations are shown to be influenced by the GD2 nucleotide bound state. This allosteric connection between the GD2 active-site and the GD1-Sw-II is also observed through the dynamic network analysis. Further, the exploration of the GD1-KH interface interactions exhibited a more attractive tendency when GD1 is bound to GTP-Mg2+. In addition, the presence of Mg2+ stabilizes active-site water and also increases the distances between the α- and γ- phosphates of the bound GTP. Curiously, three water molecules in the GD1 active-site and only one water molecule in the GD2 active-site are stabilized. This indicates that the probability of GTP hydrolysis is more in GD1 compared to GD2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- N Upendra
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | - K M Kavya
- Department of Studies in Physics, University of Mysore, Mysuru, India
| | - S Krishnaveni
- Department of Studies in Physics, University of Mysore, Mysuru, India
| |
Collapse
|
11
|
Gruffaz C, Smirnov A. GTPase Era at the heart of ribosome assembly. Front Mol Biosci 2023; 10:1263433. [PMID: 37860580 PMCID: PMC10582724 DOI: 10.3389/fmolb.2023.1263433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Ribosome biogenesis is a key process in all organisms. It relies on coordinated work of multiple proteins and RNAs, including an array of assembly factors. Among them, the GTPase Era stands out as an especially deeply conserved protein, critically required for the assembly of bacterial-type ribosomes from Escherichia coli to humans. In this review, we bring together and critically analyze a wealth of phylogenetic, biochemical, structural, genetic and physiological data about this extensively studied but still insufficiently understood factor. We do so using a comparative and, wherever possible, synthetic approach, by confronting observations from diverse groups of bacteria and eukaryotic organelles (mitochondria and chloroplasts). The emerging consensus posits that Era intervenes relatively early in the small subunit biogenesis and is essential for the proper shaping of the platform which, in its turn, is a prerequisite for efficient translation. The timing of Era action on the ribosome is defined by its interactions with guanosine nucleotides [GTP, GDP, (p)ppGpp], ribosomal RNA, and likely other factors that trigger or delay its GTPase activity. As a critical nexus of the small subunit biogenesis, Era is subject to sophisticated regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. Failure of these mechanisms or a deficiency in Era function entail dramatic generalized consequences for the protein synthesis and far-reaching, pleiotropic effects on the organism physiology, such as the Perrault syndrome in humans.
Collapse
Affiliation(s)
- Christelle Gruffaz
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
| | - Alexandre Smirnov
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
| |
Collapse
|
12
|
Wei YM, Wang BH, Shao DJ, Yan RY, Wu JW, Zheng GM, Zhao YJ, Zhang XS, Zhao XY. Defective kernel 66 encodes a GTPase essential for kernel development in maize. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5694-5708. [PMID: 37490479 PMCID: PMC10540730 DOI: 10.1093/jxb/erad289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023]
Abstract
The mitochondrion is a semi-autonomous organelle that provides energy for cell activities through oxidative phosphorylation. In this study, we identified a defective kernel 66 (dek66)-mutant maize with defective kernels. We characterized a candidate gene, DEK66, encoding a ribosomal assembly factor located in mitochondria and possessing GTPase activity (which belongs to the ribosome biogenesis GTPase A family). In the dek66 mutant, impairment of mitochondrial structure and function led to the accumulation of reactive oxygen species and promoted programmed cell death in endosperm cells. Furthermore, the transcript levels of most of the key genes associated with nutrient storage, mitochondrial respiratory chain complex, and mitochondrial ribosomes in the dek66 mutant were significantly altered. Collectively, the results suggest that DEK66 is essential for the development of maize kernels by affecting mitochondrial function. This study provides a reference for understanding the impact of a mitochondrial ribosomal assembly factor in maize kernel development.
Collapse
Affiliation(s)
- Yi Ming Wei
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Bo Hui Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Dong Jie Shao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Ru Yu Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jia Wen Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Guang Ming Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Ya Jie Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| |
Collapse
|
13
|
Sheng K, Li N, Rabuck-Gibbons JN, Dong X, Lyumkis D, Williamson JR. Assembly landscape for the bacterial large ribosomal subunit. Nat Commun 2023; 14:5220. [PMID: 37633970 PMCID: PMC10460392 DOI: 10.1038/s41467-023-40859-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
Assembly of ribosomes in bacteria is highly efficient, taking ~2-3 min, but this makes the abundance of assembly intermediates very low, which is a challenge for mechanistic understanding. Genetic perturbations of the assembly process create bottlenecks where intermediates accumulate, facilitating structural characterization. We use cryo-electron microscopy, with iterative subclassification to identify intermediates in the assembly of the 50S ribosomal subunit from E. coli. The analysis of the ensemble of intermediates that spans the entire biogenesis pathway for the 50 S subunit was facilitated by a dimensionality reduction and cluster picking approach using PCA-UMAP-HDBSCAN. The identity of the cooperative folding units in the RNA with associated proteins is revealed, and the hierarchy of these units reveals a complete assembly map for all RNA and protein components. The assembly generally proceeds co-transcriptionally, with some flexibility in the landscape to ensure efficiency for this central cellular process under a variety of growth conditions.
Collapse
Affiliation(s)
- Kai Sheng
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ning Li
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jessica N Rabuck-Gibbons
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Xiyu Dong
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dmitry Lyumkis
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| |
Collapse
|
14
|
Gor K, Duss O. Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly. Biomolecules 2023; 13:866. [PMID: 37238735 PMCID: PMC10216711 DOI: 10.3390/biom13050866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Ribosome assembly is one of the most fundamental processes of gene expression and has served as a playground for investigating the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. A bacterial ribosome is composed of around 50 ribosomal proteins, several of which are co-transcriptionally assembled on a ~4500-nucleotide-long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 min in vivo and being assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades, resulting in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs in prokaryotes and eukaryotes. Here, we review biochemical, structural, and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of the complex and intricate molecular process of bacterial ribosome assembly. We also discuss emerging, cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors, and the native cellular environment shape ribosome assembly and RNP assembly at large.
Collapse
Affiliation(s)
- Kavan Gor
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69117 Heidelberg, Germany
| | - Olivier Duss
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
| |
Collapse
|
15
|
Harper NJ, Burnside C, Klinge S. Principles of mitoribosomal small subunit assembly in eukaryotes. Nature 2023; 614:175-181. [PMID: 36482135 PMCID: PMC9892005 DOI: 10.1038/s41586-022-05621-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is essential for ATP production and cellular metabolism1. Here we used cryo-electron microscopy to determine nine structures of native yeast and human mitoribosomal small subunit assembly intermediates, illuminating the mechanistic basis for how GTPases are used to control early steps of decoding centre formation, how initial rRNA folding and processing events are mediated, and how mitoribosomal proteins have active roles during assembly. Furthermore, this series of intermediates from two species with divergent mitoribosomal architecture uncovers both conserved principles and species-specific adaptations that govern the maturation of mitoribosomal small subunits in eukaryotes. By revealing the dynamic interplay between assembly factors, mitoribosomal proteins and rRNA that are required to generate functional subunits, our structural analysis provides a vignette for how molecular complexity and diversity can evolve in large ribonucleoprotein assemblies.
Collapse
Affiliation(s)
- Nathan J Harper
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, NY, USA
| | - Chloe Burnside
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY, USA
- Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, NY, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
16
|
Bikmullin AG, Fatkhullin B, Stetsenko A, Gabdulkhakov A, Garaeva N, Nurullina L, Klochkova E, Golubev A, Khusainov I, Trachtmann N, Blokhin D, Guskov A, Validov S, Usachev K, Yusupov M. Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from S. aureus. Int J Mol Sci 2023; 24:ijms24032118. [PMID: 36768442 PMCID: PMC9917171 DOI: 10.3390/ijms24032118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and proteins' folding, modification and binding, with the involvement of numerous RNAses, helicases, GTPases, chaperones, RNA, protein-modifying enzymes, and assembly factors. One such assembly factor involved in bacterial 30S subunit maturation is ribosomal binding factor A (RbfA). In this study, we present the crystal (determined at 2.2 Å resolution) and NMR structures of RbfA as well as the 2.9 Å resolution cryo-EM reconstruction of the 30S-RbfA complex from Staphylococcus aureus (S. aureus). Additionally, we show that the manner of RbfA action on the small ribosomal subunit during its maturation is shared between bacteria and mitochondria. The obtained results clarify the function of RbfA in the 30S maturation process and its role in ribosome functioning in general. Furthermore, given that S. aureus is a serious human pathogen, this study provides an additional prospect to develop antimicrobials targeting bacterial pathogens.
Collapse
Affiliation(s)
- Aydar G. Bikmullin
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | - Bulat Fatkhullin
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, 67400 Illkirch, France
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Artem Stetsenko
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9700 AB Groningen, The Netherlands
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Natalia Garaeva
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | - Liliia Nurullina
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, 67400 Illkirch, France
| | - Evelina Klochkova
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | - Alexander Golubev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
| | | | - Natalie Trachtmann
- Institute of Microbiology, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Dmitriy Blokhin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, 420008 Kazan, Russia
| | - Albert Guskov
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9700 AB Groningen, The Netherlands
| | - Shamil Validov
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
- Federal Research Center “Kazan Scientific Center of Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Konstantin Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
- Federal Research Center “Kazan Scientific Center of Russian Academy of Sciences”, 420111 Kazan, Russia
| | - Marat Yusupov
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, 67400 Illkirch, France
- Correspondence:
| |
Collapse
|
17
|
Conor Moran J, Del'Olio S, Choi A, Zhong H, Barrientos A. Mitoribosome Biogenesis. Methods Mol Biol 2023; 2661:23-51. [PMID: 37166630 PMCID: PMC10639111 DOI: 10.1007/978-1-0716-3171-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Mitoribosome biogenesis is a complex and energetically costly process that involves RNA elements encoded in the mitochondrial genome and mitoribosomal proteins most frequently encoded in the nuclear genome. The process is catalyzed by extra-ribosomal proteins, nucleus-encoded assembly factors that act in all stages of the assembly process to coordinate the processing and maturation of ribosomal RNAs with the hierarchical association of ribosomal proteins. Biochemical studies and recent cryo-EM structures of mammalian mitoribosomes have provided hints regarding their assembly. In this general concept chapter, we will briefly describe the current knowledge, mainly regarding the mammalian mitoribosome biogenesis pathway and factors involved, and will emphasize the biological sources and approaches that have been applied to advance the field.
Collapse
Affiliation(s)
- J Conor Moran
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Samuel Del'Olio
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Austin Choi
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Hui Zhong
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Antoni Barrientos
- Department of Neurology and Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL, USA.
| |
Collapse
|
18
|
Stoll J, Zegarra V, Bange G, Graumann PL. Single-molecule dynamics suggest that ribosomes assemble at sites of translation in Bacillus subtilis. Front Microbiol 2022; 13:999176. [PMID: 36406443 PMCID: PMC9670183 DOI: 10.3389/fmicb.2022.999176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 04/07/2024] Open
Abstract
Eukaryotic cells transcribe ribosomal RNA and largely assemble ribosomes in a structure called the nucleolus, where chromosomal regions containing rRNA operons are clustered. In bacteria, many rRNA operons cluster close to the origin regions that are positioned on the outer borders of nucleoids, close to polar areas, where translating 70S ribosomes are located. Because outer regions of the nucleoids contain the highest accumulation of RNA polymerase, it has been hypothesized that bacteria contain "nucleolus-like" structures. However, ribosome subunits freely diffuse through the entire cells, and could thus be assembled and matured throughout the non-compartmentalized cell. By tracking single molecules of two GTPases that play an essential role in ribosomal folding and processing in Bacillus subtilis, we show that this process takes place at sites of translation, i.e., predominantly at the cell poles. Induction of the stringent response led to a change in the population of GTPases assumed to be active in maturation, but did not abolish nucleoid occlusion of ribosomes or of GTPases. Our findings strongly support the idea of the conceptualization of nucleolus-like structures in bacteria, i.e., rRNA synthesis, ribosomal protein synthesis and subunit assembly occurring in close proximity at the cell poles, facilitating the efficiency of ribosome maturation even under conditions of transient nutrient deprivation.
Collapse
Affiliation(s)
| | | | | | - Peter L. Graumann
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| |
Collapse
|
19
|
Li Q, Chen X, Lin L, Zhang L, Wang L, Bao J, Zhang D. Transcriptomic Dynamics of Active and Inactive States of Rho GTPase MoRho3 in Magnaporthe oryzae. J Fungi (Basel) 2022; 8:jof8101060. [PMID: 36294629 PMCID: PMC9605073 DOI: 10.3390/jof8101060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022] Open
Abstract
The small Rho GTPase acts as a molecular switch in eukaryotic signal transduction, which plays a critical role in polar cell growth and vesicle trafficking. Previous studies demonstrated that constitutively active (CA) mutant strains, of MoRho3-CA were defective in appressorium formation. While dominant-negative (DN) mutant strains MoRho3-DN shows defects in polar growth. However, the molecular dynamics of MoRho3-mediated regulatory networks in the pathogenesis of Magnaporthe oryzae still needs to be uncovered. Here, we perform comparative transcriptomic profiling of MoRho3-CA and MoRho3-DN mutant strains using a high-throughput RNA sequencing approach. We find that genetic manipulation of MoRho3 significantly disrupts the expression of 28 homologs of Saccharomyces cerevisiae Rho3-interacting proteins, including EXO70, BNI1, and BNI2 in the MoRho3 CA, DN mutant strains. Functional enrichment analyses of up-regulated DEGs reveal a significant enrichment of genes associated with ribosome biogenesis in the MoRho3-CA mutant strain. Down-regulated DEGs in the MoRho3-CA mutant strains shows significant enrichment in starch/sucrose metabolism and the ABC transporter pathway. Moreover, analyses of down-regulated DEGs in the in MoRho3-DN reveals an over-representation of genes enriched in metabolic pathways. In addition, we observe a significant suppression in the expression levels of secreted proteins suppressed in both MoRho3-CA and DN mutant strains. Together, our results uncover expression dynamics mediated by two states of the small GTPase MoRho3, demonstrating its crucial roles in regulating the expression of ribosome biogenesis and secreted proteins.
Collapse
Affiliation(s)
- Qian Li
- Meishan Vocational Technical College, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Q.L.); (D.Z.)
| | - Xi Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianyu Lin
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianhu Zhang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Li Wang
- Meishan Vocational Technical College, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiandong Bao
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Zhang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Q.L.); (D.Z.)
| |
Collapse
|
20
|
Naganathan A, Culver GM. Interdependency and Redundancy Add Complexity and Resilience to Biogenesis of Bacterial Ribosomes. Annu Rev Microbiol 2022; 76:193-210. [PMID: 35609945 DOI: 10.1146/annurev-micro-041020-121806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pace and efficiency of ribosomal subunit production directly impact the fitness of bacteria. Biogenesis demands more than just the union of ribosomal components, including RNA and proteins, to form this functional ribonucleoprotein particle. Extra-ribosomal protein factors play a fundamental role in the efficiency and efficacy of ribosomal subunit biogenesis. A paucity of data on intermediate steps, multiple and overlapping pathways, and the puzzling number of functions that extra-ribosomal proteins appear to play in vivo make unraveling the formation of this macromolecular assemblage difficult. In this review, we outline with examples the multinodal landscape of factor-assisted mechanisms that influence ribosome synthesis in bacteria. We discuss in detail late-stage events that mediate correct ribosome formation and the transition to translation initiation and thereby ensure high-fidelity protein synthesis.
Collapse
Affiliation(s)
- Anusha Naganathan
- Department of Biology, University of Rochester, Rochester, New York, USA; ,
| | - Gloria M Culver
- Department of Biology, University of Rochester, Rochester, New York, USA; ,
- Center for RNA Biology and Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York, USA
| |
Collapse
|
21
|
Chakraborty A, Halder S, Kishore P, Saha D, Saha S, Sikder K, Basu A. The structure-function analysis of Obg-like GTPase proteins along the evolutionary tree from bacteria to humans. Genes Cells 2022; 27:469-481. [PMID: 35610748 PMCID: PMC9545696 DOI: 10.1111/gtc.12942] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/12/2022] [Accepted: 04/17/2022] [Indexed: 11/28/2022]
Abstract
Obg proteins belong to P-loop guanine triphosphatase (GTPase) that are conserved from bacteria to humans. Like other GTPases, Obg cycles between guanine triphosphate (GTP) bound "on" state and guanine diphosphate (GDP)-bound "off" state, thereby controlling various cellular processes. Different members of this group have unique structural characteristics; a conserved glycine-rich N-terminal domain known as obg fold, a central conserved nucleotide binding domain, and a less conserved C-terminal domain of other functions. Obg is a ribosome dependent GTPase helps in ribosome maturation by interacting with several proteins of the 50S subunit of the ribosome. Obg proteins have been widely considered as a regulator of cellular functions, helping in DNA replication, cell division. Apart from that, this protein also takes part in various stress adaptation pathways like a stringent response, sporulation, and general stress response. In this particular review, the structural features of ObgE have been highlighted and how the structure plays important role in interacting with regulators like GTP, ppGpp that are crucial for executing biological function has been orchestrated. In particular, we believe that Obg-like proteins can provide a link between different global pathways that are necessary for fine-tuning cellular processes to maintain the cellular energy status.
Collapse
Affiliation(s)
- Asmita Chakraborty
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sheta Halder
- Department of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Purvi Kishore
- Department of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Disha Saha
- Department of Biotechnology, Amity University Kolkata, Kolkata, India
| | - Sujata Saha
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Kunal Sikder
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Arnab Basu
- JIVAN, Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| |
Collapse
|
22
|
Babu VMP, Sankari S, Ghosal A, Walker GC. A Mutant Era GTPase Suppresses Phenotypes Caused by Loss of Highly Conserved YbeY Protein in Escherichia coli. Front Microbiol 2022; 13:896075. [PMID: 35663862 PMCID: PMC9159920 DOI: 10.3389/fmicb.2022.896075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 12/03/2022] Open
Abstract
Ribosome assembly is a complex fundamental cellular process that involves assembling multiple ribosomal proteins and several ribosomal RNA species in a highly coordinated yet flexible and resilient manner. The highly conserved YbeY protein is a single-strand specific endoribonuclease, important for ribosome assembly, 16S rRNA processing, and ribosome quality control. In Escherichia coli, ybeY deletion results in pleiotropic phenotypes including slow growth, temperature sensitivity, accumulation of precursors of 16S rRNA, and impaired formation of fully assembled 70S subunits. Era, an essential highly conserved GTPase protein, interacts with many ribosomal proteins, and its depletion results in ribosome assembly defects. YbeY has been shown to interact with Era together with ribosomal protein S11. In this study, we have analyzed a suppressor mutation, era(T99I), that can partially suppress a subset of the multiple phenotypes of ybeY deletion. The era(T99I) allele was able to improve 16S rRNA processing and ribosome assembly at 37°C. However, it failed to suppress the temperature sensitivity and did not improve 16S rRNA stability. The era(T99I) allele was also unable to improve the 16S rRNA processing defects caused by the loss of ribosome maturation factors. We also show that era(T99I) increases the GroEL levels in the 30S ribosome fractions independent of YbeY. We propose that the mechanism of suppression is that the changes in Era's structure caused by the era(T99I) mutation affect its GTP/GDP cycle in a way that increases the half-life of RNA binding to Era, thereby facilitating alternative processing of the 16S RNA precursor. Taken together, this study offers insights into the role of Era and YbeY in ribosome assembly and 16S rRNA processing events.
Collapse
Affiliation(s)
| | | | | | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
23
|
Abstract
In all living cells, the ribosome translates the genetic information carried by messenger RNAs (mRNAs) into proteins. The process of ribosome recycling, a key step during protein synthesis that ensures ribosomal subunits remain available for new rounds of translation, has been largely overlooked. Despite being essential to the survival of the cell, several mechanistic aspects of ribosome recycling remain unclear. In eubacteria and mitochondria, recycling of the ribosome into subunits requires the concerted action of the ribosome recycling factor (RRF) and elongation factor G (EF-G). Recently, the conserved protein HflX was identified in bacteria as an alternative factor that recycles the ribosome under stress growth conditions. The homologue of HflX, the GTP-binding protein 6 (GTPBP6), has a dual role in mitochondrial translation by facilitating ribosome recycling and biogenesis. In this review, mechanisms of ribosome recycling in eubacteria and mitochondria are described based on structural studies of ribosome complexes.
Collapse
Affiliation(s)
- Savannah M Seely
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA
| | - Matthieu G Gagnon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1019, USA.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas 77555, USA
| |
Collapse
|
24
|
Lahry K, Gopal A, Kumar Sahu A, Nora Marbaniang C, Ahmad Shah R, Mehta A, Varshney U. An alternative role of RluD in the fidelity of translation initiation in Escherichia coli. J Mol Biol 2022; 434:167588. [DOI: 10.1016/j.jmb.2022.167588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/21/2022] [Accepted: 04/10/2022] [Indexed: 10/18/2022]
|
25
|
How to save a bacterial ribosome in times of stress. Semin Cell Dev Biol 2022; 136:3-12. [PMID: 35331628 DOI: 10.1016/j.semcdb.2022.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/01/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022]
Abstract
Biogenesis of ribosomes is one of the most cost- and resource-intensive processes in all living cells. In bacteria, ribosome biogenesis is rate-limiting for growth and must be tightly coordinated to yield maximum fitness of the cells. Since bacteria are continuously facing environmental changes and stress conditions, they have developed sophisticated systems to sense and regulate their nutritional status. Amino acid starvation leads to the synthesis and accumulation of the nucleotide-based second messengers ppGpp and pppGpp [(p)ppGpp], which in turn function as central players of a pleiotropic metabolic adaptation mechanism named the stringent response. Here, we review our current knowledge on the multiple roles of (p)ppGpp in the stress-related modulation of the prokaryotic protein biosynthesis machinery with the ribosome as its core constituent. The alarmones ppGpp/pppGpp act as competitors of their GDP/GTP counterparts, to affect a multitude of ribosome-associated P-loop GTPases involved in the translation cycle, ribosome biogenesis and hibernation. A similar mode of inhibition has been found for the GTPases of the proteins involved in the SRP-dependent membrane-targeting machinery present in the periphery of the ribosome. In this sense, during stringent conditions, binding of (p)ppGpp restricts the membrane insertion and secretion of proteins. Altogether, we highlight the enormously resource-intensive stages of ribosome biogenesis as a critical regulatory hub of the stringent response that ultimately tunes the protein synthesis capacity and consequently the survival of the cell.
Collapse
|
26
|
Leroux M, Soubry N, Reyes-Lamothe R. Dynamics of Proteins and Macromolecular Machines in Escherichia coli. EcoSal Plus 2021; 9:eESP00112020. [PMID: 34060908 PMCID: PMC11163846 DOI: 10.1128/ecosalplus.esp-0011-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/16/2021] [Indexed: 11/20/2022]
Abstract
Proteins are major contributors to the composition and the functions in the cell. They often assemble into larger structures, macromolecular machines, to carry out intricate essential functions. Although huge progress in understanding how macromolecular machines function has been made by reconstituting them in vitro, the role of the intracellular environment is still emerging. The development of fluorescence microscopy techniques in the last 2 decades has allowed us to obtain an increased understanding of proteins and macromolecular machines in cells. Here, we describe how proteins move by diffusion, how they search for their targets, and how they are affected by the intracellular environment. We also describe how proteins assemble into macromolecular machines and provide examples of how frequent subunit turnover is used for them to function and to respond to changes in the intracellular conditions. This review emphasizes the constant movement of molecules in cells, the stochastic nature of reactions, and the dynamic nature of macromolecular machines.
Collapse
Affiliation(s)
- Maxime Leroux
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Nicolas Soubry
- Department of Biology, McGill University, Montreal, QC, Canada
| | | |
Collapse
|
27
|
Upendra N, Krishnaveni S. Conformational exploration of RbgA using molecular dynamics: Possible implications in ribosome maturation and GTPase activity in different nucleotide bound states. J Mol Graph Model 2021; 111:108087. [PMID: 34864321 DOI: 10.1016/j.jmgm.2021.108087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/30/2021] [Accepted: 11/21/2021] [Indexed: 11/26/2022]
Abstract
Ribosome biogenesis GTPase A (RbgA) is involved in the late steps of the 50S ribosomal subunit maturation by binding into the 45S pre-ribosomal subunit. The association of RbgA to the 45S intermediate subunit depends on its bound nucleotide (GTP/GDP), probably because of the conformational shifts that occur between the GTP and GDP bound states. However, the available crystal structures of Staphylococcus aureus RbgA (SaRbgA) do not show any significant variations between different nucleotide bound states. Therefore, conformational exploration of SaRbgA in different nucleotide bound states was carried out using all-atom molecular dynamics (MD) simulations. Exploration of conformational distribution using cluster analysis and principal component analysis (PCA) revealed that GDP and pppGpp bound systems exhibit a larger distribution. This is majorly due to the fluctuations of the C-terminal tail (C-tail) as a result of the unwinding of α-helical secondary conformations into loop conformations which are observed from RMSF and DSSP analyses. Further investigation of the network of interactions revealed that the GTP and GMPPNP bound systems hold the C-tail in an α-helical form through stronger interactions between the active-site and C-tail. We also find that the presence of Mg2+ positions Sw-I loop away from the bound nucleotide and stabilizes the active-site water molecules. This seems to assist SaRbgA GTPase activity. In addition, mutations at the C-terminal and Sw-II conserved residues exhibit a larger conformational distribution majorly due to the C-tail fluctuations suggesting that the C-tail of SaRbgA probably interacts with the rRNA or rprotein in the process of ribosome biogenesis.
Collapse
Affiliation(s)
- N Upendra
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysuru, 570006, India
| | - S Krishnaveni
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysuru, 570006, India.
| |
Collapse
|
28
|
Anderson BW, Fung DK, Wang JD. Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria. Annu Rev Genet 2021; 55:115-133. [PMID: 34416118 DOI: 10.1146/annurev-genet-021821-025827] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacterial stress-signaling alarmones are important components of a protective network against diverse stresses such as nutrient starvation and antibiotic assault. pppGpp and ppGpp, collectively (p)ppGpp, have well-documented regulatory roles in gene expression and protein translation. Recent work has highlighted another key function of (p)ppGpp: inducing rapid and coordinated changes in cellular metabolism by regulating enzymatic activities, especially those involved in purine nucleotide synthesis. Failure of metabolic regulation by (p)ppGpp results in the loss of coordination between metabolic and macromolecular processes, leading to cellular toxicity. In this review, we document how (p)ppGpp and newly characterized nucleotides pGpp and (p)ppApp directly regulate these enzymatic targets for metabolic remodeling. We examine targets' common determinants for alarmone interaction as well as their evolutionary diversification. We highlight classical and emerging themes in nucleotide signaling, including oligomerization and allostery along with metabolic interconversion and crosstalk, illustrating how they allow optimized bacterial adaptation to their environmental niches.
Collapse
Affiliation(s)
- Brent W Anderson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , ,
| | - Danny K Fung
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , ,
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , ,
| |
Collapse
|
29
|
The Stringent Response Inhibits 70S Ribosome Formation in Staphylococcus aureus by Impeding GTPase-Ribosome Interactions. mBio 2021; 12:e0267921. [PMID: 34749534 PMCID: PMC8579695 DOI: 10.1128/mbio.02679-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
During nutrient limitation, bacteria produce the alarmones (p)ppGpp as effectors of a stress signaling network termed the stringent response. RsgA, RbgA, Era, and HflX are four ribosome-associated GTPases (RA-GTPases) that bind to (p)ppGpp in Staphylococcus aureus. These enzymes are cofactors in ribosome assembly, where they cycle between the ON (GTP-bound) and OFF (GDP-bound) ribosome-associated states. Entry into the OFF state occurs upon hydrolysis of GTP, with GTPase activity increasing substantially upon ribosome association. When bound to (p)ppGpp, GTPase activity is inhibited, reducing 70S ribosome assembly and growth. Here, we determine how (p)ppGpp impacts RA-GTPase-ribosome interactions. We show that RA-GTPases preferentially bind to 5′-diphosphate-containing nucleotides GDP and ppGpp over GTP, which is likely exploited as a regulatory mechanism within the cell to shut down ribosome biogenesis during stress. Stopped-flow fluorescence and association assays reveal that when bound to (p)ppGpp, the association of RA-GTPases to ribosomal subunits is destabilized, both in vitro and within bacterial cells. Consistently, structural analysis of the ppGpp-bound RA-GTPase RsgA reveals an OFF-state conformation similar to the GDP-bound state, with the G2/switch I loop adopting a conformation incompatible with ribosome association. Altogether, we highlight (p)ppGpp-mediated inhibition of RA-GTPases as a major mechanism of stringent response-mediated ribosome assembly and growth control.
Collapse
|
30
|
Chandrasekaran V, Desai N, Burton NO, Yang H, Price J, Miska EA, Ramakrishnan V. Visualizing formation of the active site in the mitochondrial ribosome. eLife 2021; 10:e68806. [PMID: 34609277 PMCID: PMC8492066 DOI: 10.7554/elife.68806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome assembly is an essential and conserved process that is regulated at each step by specific factors. Using cryo-electron microscopy (cryo-EM), we visualize the formation of the conserved peptidyl transferase center (PTC) of the human mitochondrial ribosome. The conserved GTPase GTPBP7 regulates the correct folding of 16S ribosomal RNA (rRNA) helices and ensures 2'-O-methylation of the PTC base U3039. GTPBP7 binds the RNA methyltransferase NSUN4 and MTERF4, which sequester H68-71 of the 16S rRNA and allow biogenesis factors to access the maturing PTC. Mutations that disrupt binding of their Caenorhabditis elegans orthologs to the large subunit potently activate mitochondrial stress and cause viability, development, and sterility defects. Next-generation RNA sequencing reveals widespread gene expression changes in these mutant animals that are indicative of mitochondrial stress response activation. We also answer the long-standing question of why NSUN4, but not its enzymatic activity, is indispensable for mitochondrial protein synthesis.
Collapse
Affiliation(s)
| | - Nirupa Desai
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Hanting Yang
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Jon Price
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Eric A Miska
- Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - V Ramakrishnan
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| |
Collapse
|
31
|
Naganathan A, Keltz R, Lyon H, Culver GM. Uncovering a delicate balance between endonuclease RNase III and ribosomal protein S15 in E. coli ribosome assembly. Biochimie 2021; 191:104-117. [PMID: 34508826 DOI: 10.1016/j.biochi.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 12/01/2022]
Abstract
The bacterial ribosomal protein S15 is located in the platform, a functional region of the 30S ribosomal subunit. While S15 is critical for in vitro formation of E. coli small subunits (SSUs), it is dispensable for in vivo biogenesis and growth. In this work, a novel synergistic interaction between rpsO, the gene that encodes S15, and rnc (the gene that encodes RNase III), was uncovered in E. coli. RNase III catalyzes processing of precursor ribosomal RNA (rRNA) transcripts and thus is involved in functional ribosome subunit maturation. Strains lacking S15 (ΔrpsO), RNase III (Δrnc) or both genes were examined to understand the relationship between these two factors and the impact of this double deletion on rRNA processing and SSU maturation. The double deletion of rpsO and rnc partially alleviates the observed cold sensitivity of ΔrpsO alone. A novel 16S rRNA precursor (17S∗ rRNA) that is detected in free 30S subunits of Δrnc is incorporated in 70S-like ribosomes in the double deletion. The stable accumulation of 17S∗ rRNA suggests that timing of processing events is closely coupled with SSU formation events in vivo. The double deletion has a suppressive effect on the cell elongation phenotype of ΔrpsO. The alteration of the phenotypes associated with S15 loss, due to the absence of RNase III, indicates that pre-rRNA processing and improvement of growth, relative to that observed for ΔrpsO, are connected. The characterization of the functional link between the two factors illustrates that there are redundancies and compensatory pathways for SSU maturation.
Collapse
Affiliation(s)
| | - Roxanne Keltz
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Hiram Lyon
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Gloria M Culver
- Department of Biology, University of Rochester, Rochester, NY, USA; Center for RNA Biology, University of Rochester, Rochester, NY, USA; Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, USA.
| |
Collapse
|
32
|
HflX is a GTPase that controls hypoxia-induced replication arrest in slow-growing mycobacteria. Proc Natl Acad Sci U S A 2021; 118:2006717118. [PMID: 33723035 DOI: 10.1073/pnas.2006717118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
GTPase high frequency of lysogenization X (HflX) is highly conserved in prokaryotes and acts as a ribosome-splitting factor as part of the heat shock response in Escherichia coli. Here we report that HflX produced by slow-growing Mycobacterium bovis bacillus Calmette-Guérin (BCG) is a GTPase that plays a critical role in the pathogen's transition to a nonreplicating, drug-tolerant state in response to hypoxia. Indeed, HflX-deficient M. bovis BCG (KO) replicated markedly faster in the microaerophilic phase of a hypoxia model that resulted in premature entry into dormancy. The KO mutant displayed hallmarks of nonreplicating mycobacteria, including phenotypic drug resistance, altered morphology, low intracellular ATP levels, and overexpression of Dormancy (Dos) regulon proteins. Mice nasally infected with HflX KO mutant displayed increased bacterial burden in the lungs, spleen, and lymph nodes during the chronic phase of infection, consistent with the higher replication rate observed in vitro in microaerophilic conditions. Unlike fast growing mycobacteria, M. bovis BCG HlfX was not involved in antibiotic resistance under aerobic growth. Proteomics, pull-down, and ribo-sequencing approaches supported that mycobacterial HflX is a ribosome-binding protein that controls translational activity of the cell. With HflX fully conserved between M. bovis BCG and M. tuberculosis, our work provides further insights into the molecular mechanisms deployed by pathogenic mycobacteria to adapt to their hypoxic microenvironment.
Collapse
|
33
|
Bange G, Bedrunka P. Physiology of guanosine-based second messenger signaling in Bacillus subtilis. Biol Chem 2021; 401:1307-1322. [PMID: 32881708 DOI: 10.1515/hsz-2020-0241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/22/2020] [Indexed: 12/19/2022]
Abstract
The guanosine-based second messengers (p)ppGpp and c-di-GMP are key players of the physiological regulation of the Gram-positive model organism Bacillus subtilis. Their regulatory spectrum ranges from key metabolic processes over motility to biofilm formation. Here we review our mechanistic knowledge on their synthesis and degradation in response to environmental and stress signals as well as what is known on their cellular effectors and targets. Moreover, we discuss open questions and our gaps in knowledge on these two important second messengers.
Collapse
Affiliation(s)
- Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 6, C07, Marburg, D-35043,Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 6, C07, Marburg, D-35043,Germany
| |
Collapse
|
34
|
Cipullo M, Pearce SF, Lopez Sanchez IG, Gopalakrishna S, Krüger A, Schober F, Busch JD, Li X, Wredenberg A, Atanassov I, Rorbach J. Human GTPBP5 is involved in the late stage of mitoribosome large subunit assembly. Nucleic Acids Res 2021; 49:354-370. [PMID: 33283228 PMCID: PMC7797037 DOI: 10.1093/nar/gkaa1131] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Human mitoribosomes are macromolecular complexes essential for translation of 11 mitochondrial mRNAs. The large and the small mitoribosomal subunits undergo a multistep maturation process that requires the involvement of several factors. Among these factors, GTP-binding proteins (GTPBPs) play an important role as GTP hydrolysis can provide energy throughout the assembly stages. In bacteria, many GTPBPs are needed for the maturation of ribosome subunits and, of particular interest for this study, ObgE has been shown to assist in the 50S subunit assembly. Here, we characterize the role of a related human Obg-family member, GTPBP5. We show that GTPBP5 interacts specifically with the large mitoribosomal subunit (mt-LSU) proteins and several late-stage mitoribosome assembly factors, including MTERF4:NSUN4 complex, MRM2 methyltransferase, MALSU1 and MTG1. Interestingly, we find that interaction of GTPBP5 with the mt-LSU is compromised in the presence of a non-hydrolysable analogue of GTP, implying a different mechanism of action of this protein in contrast to that of other Obg-family GTPBPs. GTPBP5 ablation leads to severe impairment in the oxidative phosphorylation system, concurrent with a decrease in mitochondrial translation and reduced monosome formation. Overall, our data indicate an important role of GTPBP5 in mitochondrial function and suggest its involvement in the late-stage of mt-LSU maturation.
Collapse
Affiliation(s)
- Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Sarah F Pearce
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Isabel G Lopez Sanchez
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, 32 Gisborne Street, East Melbourne, 3002 Victoria, Australia
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Annika Krüger
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Florian Schober
- Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Solna (L1:00), 171 76 Stockholm, Sweden
| | - Jakob D Busch
- Department of Mitochondrial Biology, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Xinping Li
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max-Planck-Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden.,Max Planck Institute Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
35
|
The Yersinia pestis GTPase BipA Promotes Pathogenesis of Primary Pneumonic Plague. Infect Immun 2021; 89:IAI.00673-20. [PMID: 33257531 PMCID: PMC7822129 DOI: 10.1128/iai.00673-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/11/2020] [Indexed: 12/27/2022] Open
Abstract
Yersinia pestis is a highly virulent pathogen and the causative agent of bubonic, septicemic, and pneumonic plague. Primary pneumonic plague caused by inhalation of respiratory droplets contaminated with Y. pestis is nearly 100% lethal within 4 to 7 days without antibiotic intervention. Pneumonic plague progresses in two phases, beginning with extensive bacterial replication in the lung with minimal host responsiveness, followed by the abrupt onset of a lethal proinflammatory response. The precise mechanisms by which Y. pestis is able to colonize the lung and survive two very distinct disease phases remain largely unknown. To date, a few bacterial virulence factors, including the Ysc type 3 secretion system, are known to contribute to the pathogenesis of primary pneumonic plague. The bacterial GTPase BipA has been shown to regulate expression of virulence factors in a number of Gram-negative bacteria, including Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica serovar Typhi. However, the role of BipA in Y. pestis has yet to be investigated. Here, we show that BipA is a Y. pestis virulence factor that promotes defense against early neutrophil-mediated bacterial killing in the lung. This work identifies a novel Y. pestis virulence factor and highlights the importance of early bacterial/neutrophil interactions in the lung during primary pneumonic plague.
Collapse
|
36
|
Role of GTPases in Driving Mitoribosome Assembly. Trends Cell Biol 2021; 31:284-297. [PMID: 33419649 DOI: 10.1016/j.tcb.2020.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 01/08/2023]
Abstract
Mitoribosomes catalyze essential protein synthesis within mitochondria. Mitoribosome biogenesis is assisted by an increasing number of assembly factors, among which guanosine triphosphate hydrolases (GTPases) are the most abundant class. Here, we review recent progress in our understanding of mitoribosome assembly GTPases. We describe their shared and specific features and mechanisms of action, compare them with their bacterial counterparts, and discuss their possible roles in the assembly of small or large mitoribosomal subunits and the formation of the monosome by establishing quality-control checkpoints during these processes. Furthermore, following the recent unification of the nomenclature for the mitoribosomal proteins, we also propose a unified nomenclature for mitoribosome assembly GTPases.
Collapse
|
37
|
Ferrari A, Del'Olio S, Barrientos A. The Diseased Mitoribosome. FEBS Lett 2020; 595:1025-1061. [PMID: 33314036 DOI: 10.1002/1873-3468.14024] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/17/2022]
Abstract
Mitochondria control life and death in eukaryotic cells. Harboring a unique circular genome, a by-product of an ancient endosymbiotic event, mitochondria maintains a specialized and evolutionary divergent protein synthesis machinery, the mitoribosome. Mitoribosome biogenesis depends on elements encoded in both the mitochondrial genome (the RNA components) and the nuclear genome (all ribosomal proteins and assembly factors). Recent cryo-EM structures of mammalian mitoribosomes have illuminated their composition and provided hints regarding their assembly and elusive mitochondrial translation mechanisms. A growing body of literature involves the mitoribosome in inherited primary mitochondrial disorders. Mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors impede mitoribosome biogenesis, causing protein synthesis defects that lead to respiratory chain failure and mitochondrial disorders such as encephalo- and cardiomyopathy, deafness, neuropathy, and developmental delays. In this article, we review the current fundamental understanding of mitoribosome assembly and function, and the clinical landscape of mitochondrial disorders driven by mutations in mitoribosome components and assembly factors, to portray how basic and clinical studies combined help us better understand both mitochondrial biology and medicine.
Collapse
Affiliation(s)
- Alberto Ferrari
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
| | - Samuel Del'Olio
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, FL, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, FL, USA
| |
Collapse
|
38
|
Overproduction of a Dominant Mutant of the Conserved Era GTPase Inhibits Cell Division in Escherichia coli. J Bacteriol 2020; 202:JB.00342-20. [PMID: 32817092 DOI: 10.1128/jb.00342-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/07/2020] [Indexed: 12/24/2022] Open
Abstract
Cell growth and division are coordinated, ensuring homeostasis under any given growth condition, with division occurring as cell mass doubles. The signals and controlling circuit(s) between growth and division are not well understood; however, it is known in Escherichia coli that the essential GTPase Era, which is growth rate regulated, coordinates the two functions and may be a checkpoint regulator of both. We have isolated a mutant of Era that separates its effect on growth and division. When overproduced, the mutant protein Era647 is dominant to wild-type Era and blocks division, causing cells to filament. Multicopy suppressors that prevent the filamentation phenotype of Era647 either increase the expression of FtsZ or decrease the expression of the Era647 protein. Excess Era647 induces complete delocalization of Z rings, providing an explanation for why Era647 induces filamentation, but this effect is probably not due to direct interaction between Era647 and FtsZ. The hypermorphic ftsZ* allele at the native locus can suppress the effects of Era647 overproduction, indicating that extra FtsZ is not required for the suppression, but another hypermorphic allele that accelerates cell division through periplasmic signaling, ftsL*, cannot. Together, these results suggest that Era647 blocks cell division by destabilizing the Z ring.IMPORTANCE All cells need to coordinate their growth and division, and small GTPases that are conserved throughout life play a key role in this regulation. One of these, Era, provides an essential function in the assembly of the 30S ribosomal subunit in Escherichia coli, but its role in regulating E. coli cell division is much less well understood. Here, we characterize a novel dominant negative mutant of Era (Era647) that uncouples these two activities when overproduced; it inhibits cell division by disrupting assembly of the Z ring, without significantly affecting ribosome production. The unique properties of this mutant should help to elucidate how Era regulates cell division and coordinates this process with ribosome biogenesis.
Collapse
|
39
|
N U, S K. Molecular dynamics simulation study on Thermotoga maritima EngA: GTP/GDP bound state of the second G-domain influences the domain-domain interface interactions. J Biomol Struct Dyn 2020; 40:1387-1399. [PMID: 33016853 DOI: 10.1080/07391102.2020.1826359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
EngA, a GTPase involved in the late steps of ribosome maturation, consists of two GTP binding domains (G-domains) [GD1, GD2] and a C-terminal domain. The combination of GTP/GDP in G-domains dictates its binding to the ribosomal subunits by altering its conformation. Studies and comparisons on the available structures of EngA enable us to understand the correlation between nucleotide bound states and its conformation. Using all-atom molecular dynamics (MD) simulations, we have explored the conformational behavior of EngA from Thermotoga maritima (TmDer) upon binding the various combinations of GTP and GDP. Analyses of Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Root Mean Square Fluctuation (RMSF) emphasize the importance of the second G-domain nucleotide bound state. RMSD and Rg exhibit slightly lower values when GTP is embedded in GD2 compared to GDP. These lower values are due to Sw-II of GD2, which has been observed from RMSF plot. Further investigation on the effects of GD2 nucleotide bound state using Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analysis manifests an allosteric connection between GD2 nucleotide bound state and the GD1-KH interface. This is further validated by extracting electrostatic interactions and H-bonds at the GD1-KH interface. In silico mutations at the GD1 interface of KH domain affect the Sw-II mobility of GD2 by showing inverted behavior. This suggests using the second G-domain as an antibacterial target and further simulation studies on different species of EngA are to be explored.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Upendra N
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysuru, India
| | - Krishnaveni S
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysuru, India
| |
Collapse
|
40
|
Maiti P, Antonicka H, Gingras AC, Shoubridge EA, Barrientos A. Human GTPBP5 (MTG2) fuels mitoribosome large subunit maturation by facilitating 16S rRNA methylation. Nucleic Acids Res 2020; 48:7924-7943. [PMID: 32652011 PMCID: PMC7430652 DOI: 10.1093/nar/gkaa592] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 12/30/2022] Open
Abstract
Biogenesis of mammalian mitochondrial ribosomes (mitoribosomes) involves several conserved small GTPases. Here, we report that the Obg family protein GTPBP5 or MTG2 is a mitochondrial protein whose absence in a TALEN-induced HEK293T knockout (KO) cell line leads to severely decreased levels of the 55S monosome and attenuated mitochondrial protein synthesis. We show that a fraction of GTPBP5 co-sediments with the large mitoribosome subunit (mtLSU), and crosslinks specifically with the 16S rRNA, and several mtLSU proteins and assembly factors. Notably, the latter group includes MTERF4, involved in monosome assembly, and MRM2, the methyltransferase that catalyzes the modification of the 16S mt-rRNA A-loop U1369 residue. The GTPBP5 interaction with MRM2 was also detected using the proximity-dependent biotinylation (BioID) assay. In GTPBP5-KO mitochondria, the mtLSU lacks bL36m, accumulates an excess of the assembly factors MTG1, GTPBP10, MALSU1 and MTERF4, and contains hypomethylated 16S rRNA. We propose that GTPBP5 primarily fuels proper mtLSU maturation by securing efficient methylation of two 16S rRNA residues, and ultimately serves to coordinate subunit joining through the release of late-stage mtLSU assembly factors. In this way, GTPBP5 provides an ultimate quality control checkpoint function during mtLSU assembly that minimizes premature subunit joining to ensure the assembly of the mature 55S monosome.
Collapse
MESH Headings
- Cell Line
- GTP Phosphohydrolases/metabolism
- HEK293 Cells
- Humans
- Methylation
- Methyltransferases/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- Mitochondrial Proteins/metabolism
- Mitochondrial Proteins/physiology
- Mitochondrial Ribosomes/enzymology
- Mitochondrial Ribosomes/metabolism
- Monomeric GTP-Binding Proteins/metabolism
- Monomeric GTP-Binding Proteins/physiology
- Oxidative Phosphorylation
- Protein Biosynthesis
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- Ribosome Subunits, Large, Eukaryotic/chemistry
- Ribosome Subunits, Large, Eukaryotic/enzymology
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Transcription Factors/metabolism
Collapse
Affiliation(s)
- Priyanka Maiti
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Hana Antonicka
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eric A Shoubridge
- Montreal Neurological Institute and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| |
Collapse
|
41
|
Ueta M, Wada C, Wada A. YkgM and YkgO maintain translation by replacing their paralogs, zinc‐binding ribosomal proteins L31 and L36, with identical activities. Genes Cells 2020; 25:562-581. [DOI: 10.1111/gtc.12796] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/08/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022]
Affiliation(s)
| | | | - Akira Wada
- Yoshida Biological Laboratory Kyoto Japan
| |
Collapse
|
42
|
Jaskolowski M, Ramrath DJF, Bieri P, Niemann M, Mattei S, Calderaro S, Leibundgut M, Horn EK, Boehringer D, Schneider A, Ban N. Structural Insights into the Mechanism of Mitoribosomal Large Subunit Biogenesis. Mol Cell 2020; 79:629-644.e4. [PMID: 32679035 DOI: 10.1016/j.molcel.2020.06.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/04/2020] [Accepted: 06/11/2020] [Indexed: 12/19/2022]
Abstract
In contrast to the bacterial translation machinery, mitoribosomes and mitochondrial translation factors are highly divergent in terms of composition and architecture. There is increasing evidence that the biogenesis of mitoribosomes is an intricate pathway, involving many assembly factors. To better understand this process, we investigated native assembly intermediates of the mitoribosomal large subunit from the human parasite Trypanosoma brucei using cryo-electron microscopy. We identify 28 assembly factors, 6 of which are homologous to bacterial and eukaryotic ribosome assembly factors. They interact with the partially folded rRNA by specifically recognizing functionally important regions such as the peptidyltransferase center. The architectural and compositional comparison of the assembly intermediates indicates a stepwise modular assembly process, during which the rRNA folds toward its mature state. During the process, several conserved GTPases and a helicase form highly intertwined interaction networks that stabilize distinct assembly intermediates. The presented structures provide general insights into mitoribosomal maturation.
Collapse
Affiliation(s)
| | | | - Philipp Bieri
- Department of Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Moritz Niemann
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | - Simone Mattei
- Department of Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Salvatore Calderaro
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | | | - Elke K Horn
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | | | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland.
| | - Nenad Ban
- Department of Biology, ETH Zurich, Zurich 8093, Switzerland.
| |
Collapse
|
43
|
Loss of a single methylation in 23S rRNA delays 50S assembly at multiple late stages and impairs translation initiation and elongation. Proc Natl Acad Sci U S A 2020; 117:15609-15619. [PMID: 32571953 DOI: 10.1073/pnas.1914323117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ribosome biogenesis is a complex process, and dozens of factors are required to facilitate and regulate the subunit assembly in bacteria. The 2'-O-methylation of U2552 in 23S rRNA by methyltransferase RrmJ is a crucial step in late-stage assembly of the 50S subunit. Its absence results in severe growth defect and marked accumulation of pre50S assembly intermediates. In the present work, we employed cryoelectron microscopy to characterize a set of late-stage pre50S particles isolated from an Escherichia coli ΔrrmJ strain. These assembly intermediates (solved at 3.2 to 3.8 Å resolution) define a collection of late-stage particles on a progressive assembly pathway. Apart from the absence of L16, L35, and L36, major structural differences between these intermediates and the mature 50S subunit are clustered near the peptidyl transferase center, such as H38, H68-71, and H89-93. In addition, the ribosomal A-loop of the mature 50S subunit from ΔrrmJ strain displays large local flexibility on nucleotides next to unmethylated U2552. Fast kinetics-based biochemical assays demonstrate that the ΔrrmJ 50S subunit is only 50% active and two times slower than the WT 50S subunit in rapid subunit association. While the ΔrrmJ 70S ribosomes show no defect in peptide bond formation, peptide release, and ribosome recycling, they translocate with 20% slower rate than the WT ribosomes in each round of elongation. These defects amplify during synthesis of the full-length proteins and cause overall defect in protein synthesis. In conclusion, our data reveal the molecular roles of U2552 methylation in both ribosome biogenesis and protein translation.
Collapse
|
44
|
Sharma H, Anand B. Ribosome assembly defects subvert initiation Factor3 mediated scrutiny of bona fide start signal. Nucleic Acids Res 2020; 47:11368-11386. [PMID: 31586395 PMCID: PMC6868393 DOI: 10.1093/nar/gkz825] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/17/2019] [Accepted: 10/03/2019] [Indexed: 12/02/2022] Open
Abstract
In bacteria, the assembly factors tightly orchestrate the maturation of ribosomes whose competency for protein synthesis is validated by translation machinery at various stages of translation cycle. However, what transpires to the quality control measures when the ribosomes are produced with assembly defects remains enigmatic. In Escherichia coli, we show that 30S ribosomes that harbour assembly defects due to the lack of assembly factors such as RbfA and KsgA display suboptimal initiation codon recognition and bypass the critical codon–anticodon proofreading steps during translation initiation. These premature ribosomes on entering the translation cycle compromise the fidelity of decoding that gives rise to errors during initiation and elongation. We show that the assembly defects compromise the binding of initiation factor 3 (IF3), which in turn appears to license the rapid transition of 30S (pre) initiation complex to 70S initiation complex by tempering the validation of codon–anticodon interaction during translation initiation. This suggests that the premature ribosomes harbouring the assembly defects subvert the IF3 mediated proofreading of cognate initiation codon to enter the translation cycle.
Collapse
Affiliation(s)
- Himanshu Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - B Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| |
Collapse
|
45
|
Abstract
This article describes 20 years of research that investigated a second novel target for ribosomal antibiotics, the biogenesis of the two subunits. Over that period, we have examined the effect of 52 different antibiotics on ribosomal subunit formation in six different microorganisms. Most of the antimicrobials we have studied are specific, preventing the formation of only the subunit to which they bind. A few interesting exceptions have also been observed. Forty-one research publications and a book chapter have resulted from this investigation. This review will describe the methodology we used and the fit of our results to a hypothetical model. The model predicts that inhibition of subunit assembly and translation are equivalent targets for most of the antibiotics we have investigated.
Collapse
Affiliation(s)
- W Scott Champney
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
| |
Collapse
|
46
|
Gray MW, Burger G, Derelle R, Klimeš V, Leger MM, Sarrasin M, Vlček Č, Roger AJ, Eliáš M, Lang BF. The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome. BMC Biol 2020; 18:22. [PMID: 32122349 PMCID: PMC7050145 DOI: 10.1186/s12915-020-0741-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/21/2020] [Indexed: 01/02/2023] Open
Abstract
Background Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date. Results In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids. Conclusions As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.
Collapse
Affiliation(s)
- Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Gertraud Burger
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Romain Derelle
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Michelle M Leger
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada.,Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Matt Sarrasin
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Čestmír Vlček
- Current address: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - B Franz Lang
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| |
Collapse
|
47
|
Gupta A, Gupta K, Habib S. YihA GTPases localize to the apicoplast and mitochondrion of the malaria parasite and interact with LSU of organellar ribosomes. Mol Biochem Parasitol 2020; 236:111265. [PMID: 32057832 DOI: 10.1016/j.molbiopara.2020.111265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/06/2020] [Accepted: 02/08/2020] [Indexed: 11/29/2022]
Abstract
The YihA TRAFAC GTPases are critical for late-stage assembly of the ribosomal large subunit (LSU). In order to explore biogenesis of the reduced organellar ribosomes of the malaria parasite, we identified three nuclear-encoded homologs of YihA in Plasmodium falciparum. PfYihA1 targeted to the parasite apicoplast, PfYihA2 to the mitochondrion, and PfYihA3 was found in both the apicoplast and cytosol. The three PfYihA, expressed as recombinant proteins, were active GTPases and interacted with surrogate E. coli ribosomes in a nucleotide-independent manner. In vivo complexation of PfYihA with parasite organellar and/or cytosolic LSU was confirmed by co-immunoprecipitation using specific antibodies. Mitochondrial PfYihA2 carries a large C-ter extension with a strongly positively charged stretch. We hypothesise that this is important in compensating for the absence of helices of the central protuberance in the fragmented rRNA of Plasmodium mitoribosomes and may provide additional contact sites to aid in complex assembly. Combined with previous reports, our results indicate that P. falciparum mitochondria are likely to assemble ribosomes with the aid of PfEngA, PfObg1 and PfYihA2 GTPases while apicoplast ribosomes might use PfYihA1 and 3 in combination with other factors.
Collapse
Affiliation(s)
- Ankit Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Kirti Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| |
Collapse
|
48
|
Brandi A, Piersimoni L, Feto NA, Spurio R, Alix JH, Schmidt F, Gualerzi CO. Translation initiation factor IF2 contributes to ribosome assembly and maturation during cold adaptation. Nucleic Acids Res 2019; 47:4652-4662. [PMID: 30916323 PMCID: PMC6511846 DOI: 10.1093/nar/gkz188] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/07/2019] [Accepted: 03/22/2019] [Indexed: 01/13/2023] Open
Abstract
Cold-stress in Escherichia coli induces de novo synthesis of translation initiation factors IF1, IF2 and IF3 while ribosome synthesis and assembly slow down. Consequently, the IFs/ribosome stoichiometric ratio increases about 3-fold during the first hours of cold adaptation. The IF1 and IF3 increase plays a role in translation regulation at low temperature (cold-shock-induced translational bias) but so far no specific role could be attributed to the extra copies of IF2. In this work, we show that the extra-copies of IF2 made after cold stress are associated with immature ribosomal subunits together with at least another nine proteins involved in assembly and/or maturation of ribosomal subunits. This finding, coupled with evidence that IF2 is endowed with GTPase-associated chaperone activity that promotes refolding of denatured GFP, and the finding that two cold-sensitive IF2 mutations cause the accumulation of immature ribosomal particles, indicate that IF2 is yet another GTPase protein that participates in ribosome assembly/maturation, especially at low temperatures. Overall, these findings are instrumental in redefining the functional role of IF2, which cannot be regarded as being restricted to its well documented functions in translation initiation of bacterial mRNA.
Collapse
Affiliation(s)
- Anna Brandi
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| | - Lolita Piersimoni
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Naser Aliye Feto
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| | - Roberto Spurio
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| | - Jean-Hervé Alix
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Claudio O Gualerzi
- Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy
| |
Collapse
|
49
|
Ishiguro K, Arai T, Suzuki T. Depletion of S-adenosylmethionine impacts on ribosome biogenesis through hypomodification of a single rRNA methylation. Nucleic Acids Res 2019; 47:4226-4239. [PMID: 30799486 PMCID: PMC6486555 DOI: 10.1093/nar/gkz111] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/18/2019] [Indexed: 11/14/2022] Open
Abstract
S-adenosylmethionine (SAM) is an essential metabolite and a methyl group donor in all living organisms. The intracellular SAM concentration is tightly regulated, and depletion causes hypomethylation of substrates, growth defects and pathological consequences. In the emerging field of epitranscriptomics, SAM-dependent RNA methylations play a critical role in gene expression. Herein, we analyzed the methylation status of ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) in Escherichia coli Δmtn strain in which cellular SAM was down-regulated, and found hypomodification of several methylation sites, including 2′-O-methylation at position 2552 (Um2552) of 23S rRNA. We observed severe growth defect of the Δmtn strain with significant accumulation of 45S ribosomal precursor harboring 23S rRNA with hypomodified Um2552. Strikingly, the growth defect was partially restored by overexpression of rlmE encoding the SAM-dependent methyltransferase responsible for Um2552. Although SAM is involved not only in rRNA methylation but also in various cellular processes, effects on ribosome biogenesis contribute substantially to the observed defects on cell proliferation.
Collapse
Affiliation(s)
- Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Taiga Arai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
50
|
Bennison DJ, Irving SE, Corrigan RM. The Impact of the Stringent Response on TRAFAC GTPases and Prokaryotic Ribosome Assembly. Cells 2019; 8:cells8111313. [PMID: 31653044 PMCID: PMC6912228 DOI: 10.3390/cells8111313] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/24/2022] Open
Abstract
Many facets of ribosome biogenesis and function, including ribosomal RNA (rRNA) transcription, 70S assembly and protein translation, are negatively impacted upon induction of a nutrient stress-sensing signalling pathway termed the stringent response. This stress response is mediated by the alarmones guanosine tetra- and penta-phosphate ((p)ppGpp), the accumulation of which leads to a massive cellular response that slows growth and aids survival. The 70S bacterial ribosome is an intricate structure, with assembly both complex and highly modular. Presiding over the assembly process is a group of P-loop GTPases within the TRAFAC (Translation Factor Association) superclass that are crucial for correct positioning of both early and late stage ribosomal proteins (r-proteins) onto the rRNA. Often described as 'molecular switches', members of this GTPase superfamily readily bind and hydrolyse GTP to GDP in a cyclic manner that alters the propensity of the GTPase to carry out a function. TRAFAC GTPases are considered to act as checkpoints to ribosome assembly, involved in binding to immature sections in the GTP-bound state, preventing further r-protein association until maturation is complete. Here we review our current understanding of the impact of the stringent response and (p)ppGpp production on ribosome maturation in prokaryotic cells, focusing on the inhibition of (p)ppGpp on GTPase-mediated subunit assembly, but also touching upon the inhibition of rRNA transcription and protein translation.
Collapse
Affiliation(s)
- Daniel J Bennison
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Sophie E Irving
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Rebecca M Corrigan
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| |
Collapse
|