1
|
Maksimova E, Kravchenko O, Korepanov A, Stolboushkina E. Protein Assistants of Small Ribosomal Subunit Biogenesis in Bacteria. Microorganisms 2022; 10:microorganisms10040747. [PMID: 35456798 PMCID: PMC9032327 DOI: 10.3390/microorganisms10040747] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/16/2022] [Accepted: 03/26/2022] [Indexed: 01/27/2023] Open
Abstract
Ribosome biogenesis is a fundamental and multistage process. The basic steps of ribosome assembly are the transcription, processing, folding, and modification of rRNA; the translation, folding, and modification of r-proteins; and consecutive binding of ribosomal proteins to rRNAs. Ribosome maturation is facilitated by biogenesis factors that include a broad spectrum of proteins: GTPases, RNA helicases, endonucleases, modification enzymes, molecular chaperones, etc. The ribosome assembly factors assist proper rRNA folding and protein–RNA interactions and may sense the checkpoints during the assembly to ensure correct order of this process. Inactivation of these factors is accompanied by severe growth phenotypes and accumulation of immature ribosomal subunits containing unprocessed rRNA, which reduces overall translation efficiency and causes translational errors. In this review, we focus on the structural and biochemical analysis of the 30S ribosomal subunit assembly factors RbfA, YjeQ (RsgA), Era, KsgA (RsmA), RimJ, RimM, RimP, and Hfq, which take part in the decoding-center folding.
Collapse
Affiliation(s)
| | | | - Alexey Korepanov
- Correspondence: (A.K.); (E.S.); Tel.: +7-925-7180670 (A.K.); +7-915-4791359 (E.S.)
| | - Elena Stolboushkina
- Correspondence: (A.K.); (E.S.); Tel.: +7-925-7180670 (A.K.); +7-915-4791359 (E.S.)
| |
Collapse
|
2
|
Maksimova EM, Korepanov AP, Kravchenko OV, Baymukhametov TN, Myasnikov AG, Vassilenko KS, Afonina ZA, Stolboushkina EA. RbfA Is Involved in Two Important Stages of 30S Subunit Assembly: Formation of the Central Pseudoknot and Docking of Helix 44 to the Decoding Center. Int J Mol Sci 2021; 22:ijms22116140. [PMID: 34200244 PMCID: PMC8201178 DOI: 10.3390/ijms22116140] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
Ribosome biogenesis is a highly coordinated and complex process that requires numerous assembly factors that ensure prompt and flawless maturation of ribosomal subunits. Despite the increasing amount of data collected, the exact role of most assembly factors and mechanistic details of their operation remain unclear, mainly due to the shortage of high-resolution structural information. Here, using cryo-electron microscopy, we characterized 30S ribosomal particles isolated from an Escherichia coli strain with a deleted gene for the RbfA factor. The cryo-EM maps for pre-30S subunits were divided into six classes corresponding to consecutive assembly intermediates: from the particles with a completely unresolved head domain and unfolded central pseudoknot to almost mature 30S subunits with well-resolved body, platform, and head domains and partially distorted helix 44. The structures of two predominant 30S intermediates belonging to most populated classes obtained at 2.7 Å resolutions indicate that RbfA acts at two distinctive 30S assembly stages: early formation of the central pseudoknot including folding of the head, and positioning of helix 44 in the decoding center at a later stage. Additionally, it was shown that the formation of the central pseudoknot may promote stabilization of the head domain, likely through the RbfA-dependent maturation of the neck helix 28. An update to the model of factor-dependent 30S maturation is proposed, suggesting that RfbA is involved in most of the subunit assembly process.
Collapse
Affiliation(s)
- Elena M. Maksimova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Alexey P. Korepanov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Olesya V. Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Timur N. Baymukhametov
- National Research Center, “Kurchatov Institute”, Akademika Kurchatova pl. 1, 123182 Moscow, Russia;
| | - Alexander G. Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC “Kurchatov Institute”, 188300 Gatchina, Russia;
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Konstantin S. Vassilenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
- Correspondence: (K.S.V.); (E.A.S.); Tel.: +7-903-6276710 (K.S.V.); +7-915-4791359 (E.A.S.)
| | - Zhanna A. Afonina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
| | - Elena A. Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.M.); (A.P.K.); (O.V.K.); (Z.A.A.)
- Correspondence: (K.S.V.); (E.A.S.); Tel.: +7-903-6276710 (K.S.V.); +7-915-4791359 (E.A.S.)
| |
Collapse
|
3
|
The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
Collapse
|
4
|
Clatterbuck Soper SF, Dator RP, Limbach PA, Woodson SA. In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent remodeling of late assembly intermediates. Mol Cell 2013; 52:506-16. [PMID: 24207057 DOI: 10.1016/j.molcel.2013.09.020] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 08/20/2013] [Accepted: 09/19/2013] [Indexed: 12/27/2022]
Abstract
Assembly of 30S ribosomal subunits from their protein and RNA components requires extensive refolding of the 16S rRNA and is assisted by 10-20 assembly factors in bacteria. We probed the structures of 30S assembly intermediates in E. coli cells, using a synchrotron X-ray beam to generate hydroxyl radical in the cytoplasm. Widespread differences between mature and pre-30S complexes in the absence of assembly factors RbfA and RimM revealed global reorganization of RNA-protein interactions prior to maturation of the 16S rRNA and showed how RimM reduces misfolding of the 16S 3' domain during transcription in vivo. Quantitative (14)N/(15)N mass spectrometry of affinity-purified pre-30S complexes confirmed the absence of tertiary assembly proteins and showed that N-terminal acetylation of proteins S18 and S5 correlates with correct folding of the platform and central pseudoknot. Our results indicate that cellular factors delay specific RNA folding steps to ensure the quality of assembly.
Collapse
Affiliation(s)
- Sarah F Clatterbuck Soper
- Cell, Molecular, and Developmental Biology and Biophysics Program, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218-2685, USA
| | | | | | | |
Collapse
|
5
|
Vetting MW, Bareich DC, Yu M, Blanchard JS. Crystal structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for N(alpha)-acetylation of ribosomal protein S18. Protein Sci 2008; 17:1781-90. [PMID: 18596200 DOI: 10.1110/ps.035899.108] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The three ribosomal proteins L7, S5, and S18 are included in the rare subset of prokaryotic proteins that are known to be N(alpha)-acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N(alpha)-acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimI(ST)), overexpressed, and purified to homogeneity. Steady-state kinetic parameters for RimI(ST) were determined for AcCoA and a peptide substrate consisting of the first six amino acids of the target protein S18. The crystal structure of RimI(ST) was determined in complex with CoA, AcCoA, and a CoA-S-acetyl-ARYFRR bisubstrate inhibitor. The structures are consistent with a direct nucleophilic addition-elimination mechanism with Glu103 and Tyr115 acting as the catalytic base and acid, respectively. The RimI(ST)-bisubstrate complex suggests that several residues change conformation upon interacting with the N terminus of S18, including Glu103, the proposed active site base, facilitating proton exchange and catalysis.
Collapse
Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | | |
Collapse
|
6
|
Brinsmade SR, Escalante-Semerena JC. In vivo and in vitro analyses of single-amino acid variants of the Salmonella enterica phosphotransacetylase enzyme provide insights into the function of its N-terminal domain. J Biol Chem 2007; 282:12629-40. [PMID: 17339319 DOI: 10.1074/jbc.m611439200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The function of the N-terminal domain ( approximately 350 residues) of the Pta (phosphotransacetylase) enzyme of Salmonella enterica is unclear. Results from in vivo genetic and in vitro studies suggest that the N-terminal domain of Pta is a sensor for NADH and pyruvate. We isolated 10 single-amino acid variants of Pta that, unlike the wild-type protein, supported growth of a strain of S. enterica devoid of Acs (acetyl-CoA synthetase; AMP-forming) activity on 10 mm acetate. All mutations were mapped within the N-terminal domain of the protein. Kinetic analyses of the wild type and three variant Pta proteins showed that two of the variant proteins were faster enzymes (k(cat) 2.5-3-fold > k(cat) Pta(WT). Results from sedimentation equilibrium experiments are consistent with Pta(WT) being a trimer. Pta variants formed more hexamer than the Pta(WT) protein. NADH inhibited Pta(WT) activity by inducing a conformational change detectable by limited trypsin proteolysis; NADH did not inhibit variant protein Pta(R252H). Pyruvate stimulated Pta(WT) activity, and its effect was potentiated in the variants, being most pronounced on Pta(R252H).
Collapse
Affiliation(s)
- Shaun R Brinsmade
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
| | | |
Collapse
|
7
|
Odintsova TI, Müller EC, Ivanov AV, Egorov TA, Bienert R, Vladimirov SN, Kostka S, Otto A, Wittmann-Liebold B, Karpova GG. Characterization and analysis of posttranslational modifications of the human large cytoplasmic ribosomal subunit proteins by mass spectrometry and Edman sequencing. JOURNAL OF PROTEIN CHEMISTRY 2003; 22:249-58. [PMID: 12962325 DOI: 10.1023/a:1025068419698] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The 60S ribosomal proteins were isolated from ribosomes of human placenta and separated by reversed phase HPLC. The fractions obtained were subjected to trypsin and Glu-C digestion and analyzed by mass fingerprinting (MALDI-TOF), MS/MS (ESI), and Edman sequencing. Forty-six large subunit proteins were found, 22 of which showed masses in accordance with the SwissProt database (June 2002) masses (proteins L6, L7, L9, L13, L15, L17, L18, L21, L22, L24, L26, L27, L30, L32, L34, L35, L36, L37, L37A, L38, L39, L41). Eleven (proteins L7, L10A, L11, L12, L13A, L23, L23A, L27A, L28, L29, and P0) resulted in mass changes that are consistent with N-terminal loss of methionine, acetylation, internal methylation, or hydroxylation. A loss of methionine without acetylation was found for protein L8 and L17. For nine proteins (L3, L4, L5, L7A, L10, L14, L19, L31, and L40), the molecular masses could not be determined. Proteins P1 and protein L3-like were not identified by the methods applied.
Collapse
Affiliation(s)
- Tatyana I Odintsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation
| | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Poot RA, van den Worm SH, Pleij CW, van Duin J. Base complementarity in helix 2 of the central pseudoknot in 16S rRNA is essential for ribosome functioning. Nucleic Acids Res 1998; 26:549-53. [PMID: 9421514 PMCID: PMC147307 DOI: 10.1093/nar/26.2.549] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Helix 2 of the central pseudoknot structure in Escherichia coli 16S rRNA is formed by a long-distance interaction between nt 17-19 and 918-916, resulting in three base pairs: U17-A918, C18-G917and A19-U916. Previous work has shown that disruption of the central base pair abolishes ribosomal activity. We have mutated the first and last base pairs and tested the mutants for their translational activity in vivo , using a specialized ribosome system. Mutations that disrupt Watson-Crick base pairing result in strongly impaired translational activity. An exception is the mutation U916-->G, creating an A.G pair, which shows almost no decrease in activity. Mutations that maintain base complementarity have little or no impact on translational efficiency. Some of the introduced base pair substitutions substantially alter the stability of helix 2, but this does not influence ribosome functioning, neither at 42 nor at 28 degrees C. Therefore, our results do not support models in which the pseudoknot is periodically disrupted. Rather, the central pseudoknot structure is suggested to function as a permanent structural element necessary for proper organization in the center of the 30S subunit.
Collapse
Affiliation(s)
- R A Poot
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | | | | | | |
Collapse
|
9
|
Triman KL, Peister A, Goel RA. Expanded versions of the 16S and 23S ribosomal RNA mutation databases (16SMDBexp and 23SMDBexp). Nucleic Acids Res 1998; 26:280-4. [PMID: 9399853 PMCID: PMC147214 DOI: 10.1093/nar/26.1.280] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Expanded versions of the Ribosomal RNA Mutation Databases provide lists of mutated positions in 16S and 16S-like ribosomal RNA (16SMDBexp) and 23S and 23S-like ribosomal RNA (23SMDBexp) and the identity of each alteration. Alterations from organisms other than Escherichia coli are reported at positions according to the E.coli numbering system. Information provided for each mutation includes: (i) a brief description of the phenotype(s) associated with each mutation, (ii) whether a mutant phenotype has been detected by in vivo or in vitro methods, and (iii) relevant literature citations. The databases are available via ftp and on the World Wide Web at the following URL: http: //www.fandm.edu/Departments/Biology/Databases/RNA.h tml
Collapse
Affiliation(s)
- K L Triman
- Department of Biology, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA.
| | | | | |
Collapse
|