1
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Zivkovic I, Gruic-Sovulj I. Exploring mechanisms of mupirocin resistance and hyper-resistance. Biochem Soc Trans 2024; 52:1109-1120. [PMID: 38884776 DOI: 10.1042/bst20230581] [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: 04/30/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
Mupirocin is a broad-spectrum antibiotic that acts predominantly against Gram-positive bacteria. It is produced by Pseudomonas fluorescens NCIMB 10586 and has been clinically used to treat primary and secondary skin infections and to eradicate nasal colonisation of methicillin-resistant Staphylococcus aureus strains. Mupirocin inhibits protein synthesis by blocking the active site of isoleucyl-tRNA synthetase (IleRS), which prevents the enzyme from binding isoleucine and ATP for Ile-tRNAIle synthesis. Two types of IleRS are found in bacteria - while IleRS1 is susceptible to mupirocin inhibition, IleRS2 provides resistance to cells. These two types belong to distinct evolutionary clades which likely emerged from an early gene duplication in bacteria. Resistance in IleRS2 is based on the loss of interactions that govern mupirocin binding to IleRS1, such as hydrogen bonding to the carboxylate moiety of mupirocin. IleRS2 enzymes with Ki in the millimolar range have recently been discovered. These hyper-resistant IleRS2 variants surprisingly have a non-canonical version of the catalytic motif, which serves as a signature motif of class I aminoacyl-tRNA synthetases to which IleRS belongs. The non-canonical motif, in which the 1st and 3rd positions are swapped, is key for hyper-resistance and can be accommodated without abolishing enzyme activity in IleRS2 but not in IleRS1. Clinical use of mupirocin led to the emergence of resistance in S. aureus. Low-level resistance arises by mutations of the housekeeping IleRS1, while high-level resistance develops by the acquisition of the resistant IleRS2 on a plasmid. There is no evidence that hyper-resistant variants have been found in clinical isolates.
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Affiliation(s)
- Igor Zivkovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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2
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Ević V, Rokov-Plavec J. Interplay between mistranslation and oxidative stress in Escherichia coli. Arh Hig Rada Toksikol 2024; 75:147-154. [PMID: 38963138 PMCID: PMC11223507 DOI: 10.2478/aiht-2024-75-3834] [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: 03/01/2024] [Revised: 03/01/2024] [Accepted: 05/01/2024] [Indexed: 07/05/2024] Open
Abstract
Mistakes in translation are mostly associated with toxic effects in the cell due to the production of functionally aberrant and misfolded proteins. However, under certain circumstances mistranslation can have beneficial effects and enable cells to preadapt to other stress conditions. Mistranslation may be caused by mistakes made by aminoacyl-tRNA synthetases, essential enzymes that link amino acids to cognate tRNAs. There is an Escherichia coli strain expressing isoleucyl-tRNA synthetase mutant variant with inactivated editing domain which produces mistranslated proteomes where valine (Val) and norvaline (Nva) are misincorporated into proteins instead of isoleucine. We compared this strain with the wild-type to determine the effects of such mistranslation on bacterial growth in oxidative stress conditions. When the cells were pre-incubated with 0.75 mmol/L Nva or 1.5 mmol/L Val or Nva and exposed to hydrogen peroxide, no beneficial effect of mistranslation was observed. However, when the editing-deficient strain was cultivated in medium supplemented with 0.75 mmol/L Val up to the early or mid-exponential phase of growth and then exposed to oxidative stress, it slightly outgrew the wild-type grown in the same conditions. Our results therefore show a modest adaptive effect of isoleucine mistranslation on bacterial growth in oxidative stress, but only in specific conditions. This points to a delicate balance between deleterious and beneficial effects of mistranslation.
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Affiliation(s)
- Valentina Ević
- University of Zagreb Faculty of Science, Department of Chemistry, Zagreb, Croatia
| | - Jasmina Rokov-Plavec
- University of Zagreb Faculty of Science, Department of Chemistry, Zagreb, Croatia
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3
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Rybak MY, Gagnon MG. Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance. Nat Struct Mol Biol 2024; 31:810-816. [PMID: 38538914 DOI: 10.1038/s41594-024-01236-3] [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: 02/28/2023] [Accepted: 01/31/2024] [Indexed: 04/18/2024]
Abstract
The frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 104 codons. In the universal genetic code, the AUN codon box specifies two amino acids, isoleucine and methionine. In bacteria and archaea, decoding specificity of the AUA and AUG codons relies on the wobble avoidance strategy that requires modification of C34 in the anticodon loop of isoleucine transfer RNAIleCAU (tRNAIleCAU). Bacterial tRNAIleCAU with 2-lysylcytidine (lysidine) at the wobble position deciphers AUA while avoiding AUG. Here we report cryo-electron microscopy structures of the Escherichia coli 70S ribosome complexed with elongation factor thermo unstable (EF-Tu) and isoleucine-tRNAIleLAU in the process of decoding AUA and AUG. Lysidine in tRNAIleLAU excludes AUG by promoting the formation of an unusual Hoogsteen purine-pyrimidine nucleobase geometry at the third position of the codon, weakening the interactions with the mRNA and destabilizing the EF-Tu ternary complex. Our findings elucidate the molecular mechanism by which tRNAIleLAU specifically decodes AUA over AUG.
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MESH Headings
- Peptide Elongation Factor Tu/metabolism
- Peptide Elongation Factor Tu/chemistry
- Peptide Elongation Factor Tu/genetics
- Cryoelectron Microscopy
- Escherichia coli/metabolism
- Escherichia coli/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Ribosomes/chemistry
- RNA, Transfer, Ile/metabolism
- RNA, Transfer, Ile/chemistry
- RNA, Transfer, Ile/genetics
- Models, Molecular
- Codon/metabolism
- Codon/genetics
- Anticodon/chemistry
- Anticodon/metabolism
- Nucleic Acid Conformation
- Isoleucine/metabolism
- Isoleucine/chemistry
- RNA, Messenger/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- Lysine/analogs & derivatives
- Pyrimidine Nucleosides
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Affiliation(s)
- Mariia Yu Rybak
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Matthieu G Gagnon
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
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4
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Chen X, Guo Y, Shi J, Wang Y, Guo X, Wu G, Li S, Zhang T. Structural basis for substrate and antibiotic recognition by Helicobacter pylori isoleucyl-tRNA synthetase. FEBS Lett 2024; 598:521-536. [PMID: 38246751 DOI: 10.1002/1873-3468.14805] [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: 10/28/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024]
Abstract
Helicobacter pylori infection is a global health concern, affecting over half of the world's population. Acquiring structural information on pharmacological targets is crucial to facilitate inhibitor design. Here, we have determined the crystal structures of H. pylori isoleucyl-tRNA synthetase (HpIleRS) in apo form as well as in complex with various substrates (Ile, Ile-AMP, Val, and Val-AMP) or an inhibitor (mupirocin). Our results provide valuable insights into substrate specificity, recognition, and the mechanism by which HpIleRS is inhibited by an antibiotic. Moreover, we identified Asp641 as a prospective regulatory site and conducted biochemical analyses to investigate its regulatory mechanism. The detailed structural information acquired from this research holds promise for the development of highly selective and effective inhibitors against H. pylori infection.
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Affiliation(s)
- Xiaobao Chen
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Yu Guo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiawen Shi
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Yilun Wang
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Xinyi Guo
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Guihua Wu
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
| | - Sheng Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, China
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Tianlong Zhang
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, 500 Yonghe Road, Nantong, China
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5
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Dulic M, Krpan N, Gruic-Sovulj I. Gly56 in the synthetic site of isoleucyl-tRNA synthetase confers specificity and maintains communication with the editing site. FEBS Lett 2023; 597:3114-3124. [PMID: 38015921 DOI: 10.1002/1873-3468.14780] [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: 08/07/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023]
Abstract
Isoleucyl-tRNA synthetase (IleRS) links isoleucine to cognate tRNA via the Ile-AMP intermediate. Non-cognate valine is often mistakenly recognized as the IleRS substrate; therefore, to maintain the accuracy of translation, IleRS hydrolyzes Val-AMP within the synthetic site (pre-transfer editing). As this activity is not efficient enough, Val-tRNAIle is formed and hydrolyzed in the distant post-transfer editing site. A strictly conserved synthetic site residue Gly56 was previously shown to safeguard Ile-to-Val discrimination during aminoacyl (aa)-AMP formation. Here, we show that the Gly56Ala variant lost its specificity in pre-transfer editing, confirming that this residue ensures the selectivity of all synthetic site reactions. Moreover, we found that the Gly56Ala mutation affects IleRS interaction with aa-tRNA likely by disturbing tRNA-dependent communication between the two active sites.
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Affiliation(s)
- Morana Dulic
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
| | - Nina Krpan
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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6
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Brkic A, Leibundgut M, Jablonska J, Zanki V, Car Z, Petrovic Perokovic V, Marsavelski A, Ban N, Gruic-Sovulj I. Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif. Nat Commun 2023; 14:5498. [PMID: 37679387 PMCID: PMC10485003 DOI: 10.1038/s41467-023-41244-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Antibiotics target key biological processes that include protein synthesis. Bacteria respond by developing resistance, which increases rapidly due to antibiotics overuse. Mupirocin, a clinically used natural antibiotic, inhibits isoleucyl-tRNA synthetase (IleRS), an enzyme that links isoleucine to its tRNAIle for protein synthesis. Two IleRSs, mupirocin-sensitive IleRS1 and resistant IleRS2, coexist in bacteria. The latter may also be found in resistant Staphylococcus aureus clinical isolates. Here, we describe the structural basis of mupirocin resistance and unravel a mechanism of hyper-resistance evolved by some IleRS2 proteins. We surprisingly find that an up to 103-fold increase in resistance originates from alteration of the HIGH motif, a signature motif of the class I aminoacyl-tRNA synthetases to which IleRSs belong. The structural analysis demonstrates how an altered HIGH motif could be adopted in IleRS2 but not IleRS1, providing insight into an elegant mechanism for coevolution of the key catalytic motif and associated antibiotic resistance.
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Affiliation(s)
- A Brkic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - M Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
| | - J Jablonska
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - V Zanki
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Z Car
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - V Petrovic Perokovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - A Marsavelski
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - N Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland.
| | - I Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia.
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7
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Hauth F, Funck D, Hartig JS. A standalone editing protein deacylates mischarged canavanyl-tRNAArg to prevent canavanine incorporation into proteins. Nucleic Acids Res 2023; 51:2001-2010. [PMID: 36626933 PMCID: PMC10018355 DOI: 10.1093/nar/gkac1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
Error-free translation of the genetic code into proteins is vitally important for all organisms. Therefore, it is crucial that the correct amino acids are loaded onto their corresponding tRNAs. This process is highly challenging when aminoacyl-tRNA-synthetases encounter structural analogues to the native substrate like the arginine antimetabolite canavanine. To circumvent deleterious incorporation due to tRNA mischarging, editing mechanisms have evolved. However, only for half of the tRNA synthetases, editing activity is known and only few specific standalone editing proteins have been described. Understanding the diverse mechanisms resulting in error-free protein synthesis is of great importance. Here, we report the discovery of a protein that is upregulated upon canavanine stimulation in bacteria that live associated with canavanine-producing plants. We demonstrate that it acts as standalone editing protein specifically deacylating canavanylated tRNAArg. We therefore propose canavanyl-tRNAArgdeacylase (CtdA) as systematic name. Knockout strains show severe growth defects in canavanine-containing media and incorporate high amounts of canavanine into the proteome. CtdA is frequently found under control of guanidine riboswitches, revealing a functional connection of canavanine and guanidine metabolisms. Our results are the first to show editing activity towards mischarged tRNAArg and add to the puzzle of how faithful translation is ensured in nature.
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Affiliation(s)
- Franziskus Hauth
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Dietmar Funck
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- To whom correspondence should be addressed. Tel: +49 7531 88 4575;
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8
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Zanki V, Bozic B, Mocibob M, Ban N, Gruic-Sovulj I. A pair of isoleucyl-tRNA synthetases in Bacilli fulfills complementary roles to keep fast translation and provide antibiotic resistance. Protein Sci 2022; 31:e4418. [PMID: 36757682 PMCID: PMC9909778 DOI: 10.1002/pro.4418] [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: 02/09/2022] [Revised: 07/05/2022] [Accepted: 07/31/2022] [Indexed: 11/06/2022]
Abstract
Isoleucyl-tRNA synthetase (IleRS) is an essential enzyme that covalently couples isoleucine to the corresponding tRNA. Bacterial IleRSs group in two clades, ileS1 and ileS2, the latter bringing resistance to the natural antibiotic mupirocin. Generally, bacteria rely on either ileS1 or ileS2 as a standalone housekeeping gene. However, we have found an exception by noticing that Bacillus species with genomic ileS2 consistently also keep ileS1, which appears mandatory in the family Bacillaceae. Taking Priestia (Bacillus) megaterium as a model organism, we showed that PmIleRS1 is constitutively expressed, while PmIleRS2 is stress-induced. Both enzymes share the same level of the aminoacylation accuracy. Yet, PmIleRS1 exhibited a two-fold faster aminoacylation turnover (kcat ) than PmIleRS2 and permitted a notably faster cell-free translation. At the same time, PmIleRS2 displayed a 104 -fold increase in its Ki for mupirocin, arguing that the aminoacylation turnover in IleRS2 could have been traded-off for antibiotic resistance. As expected, a P. megaterium strain deleted for ileS2 was mupirocin-sensitive. Interestingly, an attempt to construct a mupirocin-resistant strain lacking ileS1, a solution not found among species of the family Bacillaceae in nature, led to a viable but compromised strain. Our data suggest that PmIleRS1 is kept to promote fast translation, whereas PmIleRS2 is maintained to provide antibiotic resistance when needed. This is consistent with an emerging picture in which fast-growing organisms predominantly use IleRS1 for competitive survival.
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Affiliation(s)
- Vladimir Zanki
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Bartol Bozic
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marko Mocibob
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
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9
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Zivkovic I, Ivkovic K, Cvetesic N, Marsavelski A, Gruic-Sovulj I. Negative catalysis by the editing domain of class I aminoacyl-tRNA synthetases. Nucleic Acids Res 2022; 50:4029-4041. [PMID: 35357484 PMCID: PMC9023258 DOI: 10.1093/nar/gkac207] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/14/2022] [Accepted: 03/28/2022] [Indexed: 11/19/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARS) translate the genetic code by loading tRNAs with the cognate amino acids. The errors in amino acid recognition are cleared at the AARS editing domain through hydrolysis of misaminoacyl-tRNAs. This ensures faithful protein synthesis and cellular fitness. Using Escherichia coli isoleucyl-tRNA synthetase (IleRS) as a model enzyme, we demonstrated that the class I editing domain clears the non-cognate amino acids well-discriminated at the synthetic site with the same rates as the weakly-discriminated fidelity threats. This unveiled low selectivity suggests that evolutionary pressure to optimize the rates against the amino acids that jeopardize translational fidelity did not shape the editing site. Instead, we propose that editing was shaped to safeguard cognate aminoacyl-tRNAs against hydrolysis. Misediting is prevented by the residues that promote negative catalysis through destabilisation of the transition state comprising cognate amino acid. Such powerful design allows broad substrate acceptance of the editing domain along with its exquisite specificity in the cognate aminoacyl-tRNA rejection. Editing proceeds by direct substrate delivery to the editing domain (in cis pathway). However, we found that class I IleRS also releases misaminoacyl-tRNAIle and edits it in trans. This minor editing pathway was up to now recognized only for class II AARSs.
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Affiliation(s)
- Igor Zivkovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Kate Ivkovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Nevena Cvetesic
- Institute for Clinical Sciences, Faculty of Medicine, Imperial College London and MRC London Institute of Medical Sciences, London, SW7 2AZ, UK
| | - Aleksandra Marsavelski
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
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10
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Abstract
The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key players in an increasing number of other cellular processes, with far-reaching consequences in health and disease. The biochemical versatility of the synthetases has also proven pivotal in efforts to expand the genetic code, further emphasizing the wide-ranging roles of the aminoacyl-tRNA synthetase family in synthetic and natural biology.
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Affiliation(s)
- Miguel Angel Rubio Gomez
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Michael Ibba
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
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11
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Yu Q, Mallory JD, Kolomeisky AB, Ling J, Igoshin OA. Trade-Offs between Speed, Accuracy, and Dissipation in tRNA Ile Aminoacylation. J Phys Chem Lett 2020; 11:4001-4007. [PMID: 32354218 PMCID: PMC7890467 DOI: 10.1021/acs.jpclett.0c01073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Living systems maintain a high fidelity in information processing through kinetic proofreading, a mechanism for preferentially removing incorrect substrates at the cost of energy dissipation and slower speed. Proofreading mechanisms must balance their demand for higher speed, fewer errors, and lower dissipation, but it is unclear how rates of individual reaction steps are evolutionarily tuned to balance these needs, especially when multiple proofreading mechanisms are present. Here, using a discrete-state stochastic model, we analyze the optimization strategies in Escherichia coli isoleucyl-tRNA synthetase. Surprisingly, this enzyme adopts an economic proofreading strategy and improves speed and dissipation as long as the error is tolerable. Through global parameter sampling, we reveal a fundamental dissipation-error relation that bounds the enzyme's optimal performance and explains the importance of the post-transfer editing mechanism. The proximity of native system parameters to this bound demonstrates the importance of energy dissipation as an evolutionary force affecting fitness.
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Affiliation(s)
- Qiwei Yu
- School of Physics, Peking University, Beijing 100871, China; Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Joel D. Mallory
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Anatoly B. Kolomeisky
- Center for Theoretical Biological Physics, Department of Chemistry, Department of Chemical and Biomolecular Engineering, and Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland 20742, United States
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12
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Tawfik DS, Gruic-Sovulj I. How evolution shapes enzyme selectivity - lessons from aminoacyl-tRNA synthetases and other amino acid utilizing enzymes. FEBS J 2020; 287:1284-1305. [PMID: 31891445 DOI: 10.1111/febs.15199] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/08/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) charge tRNA with their cognate amino acids. Many other enzymes use amino acids as substrates, yet discrimination against noncognate amino acids that threaten the accuracy of protein translation is a hallmark of AARSs. Comparing AARSs to these other enzymes allowed us to recognize patterns in molecular recognition and strategies used by evolution for exercising selectivity. Overall, AARSs are 2-3 orders of magnitude more selective than most other amino acid utilizing enzymes. AARSs also reveal the physicochemical limits of molecular discrimination. For example, amino acids smaller by a single methyl moiety present a discrimination ceiling of ~200, while larger ones can be discriminated by up to 105 -fold. In contrast, substrates larger by a hydroxyl group challenge AARS selectivity, due to promiscuous H-bonding with polar active site groups. This 'hydroxyl paradox' is resolved by editing. Indeed, when the physicochemical discrimination limits are reached, post-transfer editing - hydrolysis of tRNAs charged with noncognate amino acids, evolved. The editing site often selectively recognizes the edited noncognate substrate using the very same feature that the synthetic site could not efficiently discriminate against. Finally, the comparison to other enzymes also reveals that the selectivity of AARSs is an explicitly evolved trait, showing some clear examples of how selection acted not only to optimize catalytic efficiency with the target substrate, but also to abolish activity with noncognate threat substrates ('negative selection').
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Affiliation(s)
- Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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13
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Zivkovic I, Moschner J, Koksch B, Gruic‐Sovulj I. Mechanism of discrimination of isoleucyl‐tRNA synthetase against nonproteinogenic α‐aminobutyrate and its fluorinated analogues. FEBS J 2019; 287:800-813. [DOI: 10.1111/febs.15053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/12/2019] [Accepted: 08/30/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Igor Zivkovic
- Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Johann Moschner
- Institute of Chemistry and Biochemistry – Organic Chemistry Freie Universitat Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry – Organic Chemistry Freie Universitat Berlin Germany
| | - Ita Gruic‐Sovulj
- Department of Chemistry Faculty of Science University of Zagreb Croatia
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14
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Bilus M, Semanjski M, Mocibob M, Zivkovic I, Cvetesic N, Tawfik DS, Toth-Petroczy A, Macek B, Gruic-Sovulj I. On the Mechanism and Origin of Isoleucyl-tRNA Synthetase Editing against Norvaline. J Mol Biol 2019; 431:1284-1297. [PMID: 30711543 DOI: 10.1016/j.jmb.2019.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 11/17/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs), the enzymes responsible for coupling tRNAs to their cognate amino acids, minimize translational errors by intrinsic hydrolytic editing. Here, we compared norvaline (Nva), a linear amino acid not coded for protein synthesis, to the proteinogenic, branched valine (Val) in their propensity to mistranslate isoleucine (Ile) in proteins. We show that in the synthetic site of isoleucyl-tRNA synthetase (IleRS), Nva and Val are activated and transferred to tRNA at similar rates. The efficiency of the synthetic site in pre-transfer editing of Nva and Val also appears to be similar. Post-transfer editing was, however, more rapid with Nva and consequently IleRS misaminoacylates Nva-tRNAIle at slower rate than Val-tRNAIle. Accordingly, an Escherichia coli strain lacking IleRS post-transfer editing misincorporated Nva and Val in the proteome to a similar extent and at the same Ile positions. However, Nva mistranslation inflicted higher toxicity than Val, in agreement with IleRS editing being optimized for hydrolysis of Nva-tRNAIle. Furthermore, we found that the evolutionary-related IleRS, leucyl- and valyl-tRNA synthetases (I/L/VRSs), all efficiently hydrolyze Nva-tRNAs even when editing of Nva seems redundant. We thus hypothesize that editing of Nva-tRNAs had already existed in the last common ancestor of I/L/VRSs, and that the editing domain of I/L/VRSs had primarily evolved to prevent infiltration of Nva into modern proteins.
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Affiliation(s)
- Mirna Bilus
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Maja Semanjski
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen 72076, Germany
| | - Marko Mocibob
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Igor Zivkovic
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia
| | - Nevena Cvetesic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, and the MRC London Institute of Medical Sciences, London, W12 0NN, United Kingdom
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Boris Macek
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen 72076, Germany
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb 10000, Croatia.
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15
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Francklyn CS, Mullen P. Progress and challenges in aminoacyl-tRNA synthetase-based therapeutics. J Biol Chem 2019; 294:5365-5385. [PMID: 30670594 DOI: 10.1074/jbc.rev118.002956] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are universal enzymes that catalyze the attachment of amino acids to the 3' ends of their cognate tRNAs. The resulting aminoacylated tRNAs are escorted to the ribosome where they enter protein synthesis. By specifically matching amino acids to defined anticodon sequences in tRNAs, ARSs are essential to the physical interpretation of the genetic code. In addition to their canonical role in protein synthesis, ARSs are also involved in RNA splicing, transcriptional regulation, translation, and other aspects of cellular homeostasis. Likewise, aminoacylated tRNAs serve as amino acid donors for biosynthetic processes distinct from protein synthesis, including lipid modification and antibiotic biosynthesis. Thanks to the wealth of details on ARS structures and functions and the growing appreciation of their additional roles regulating cellular homeostasis, opportunities for the development of clinically useful ARS inhibitors are emerging to manage microbial and parasite infections. Exploitation of these opportunities has been stimulated by the discovery of new inhibitor frameworks, the use of semi-synthetic approaches combining chemistry and genome engineering, and more powerful techniques for identifying leads from the screening of large chemical libraries. Here, we review the inhibition of ARSs by small molecules, including the various families of natural products, as well as inhibitors developed by either rational design or high-throughput screening as antibiotics and anti-parasitic therapeutics.
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Affiliation(s)
- Christopher S Francklyn
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
| | - Patrick Mullen
- From the Department of Biochemistry, College of Medicine, University of Vermont, Burlington, Vermont 05405
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16
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11th IUBMB Focused Meeting on the Aminoacyl-tRNA Synthetases: Sailing a New Sea of Complex Functions in Human Biology and Disease. Biomolecules 2018; 8:biom8020022. [PMID: 29723968 PMCID: PMC6023080 DOI: 10.3390/biom8020022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 12/18/2022] Open
Abstract
The 11th IUBMB Focused Meeting on Aminoacyl-tRNA Synthetases was held in Clearwater Beach, Florida from 29 October–2 November 2017, with the aim of presenting the latest research on these enzymes and promoting interchange among aminoacyl-tRNA synthetase (ARS) researchers. Topics covered in the meeting included many areas of investigation, including ARS evolution, mechanism, editing functions, biology in prokaryotic and eukaryotic cells and their organelles, their roles in human diseases, and their application to problems in emerging areas of synthetic biology. In this report, we provide a summary of the major themes of the meeting, citing contributions from the oral presentations in the meeting.
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17
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Vo MN, Terrey M, Lee JW, Roy B, Moresco JJ, Sun L, Fu H, Liu Q, Weber TG, Yates JR, Fredrick K, Schimmel P, Ackerman SL. ANKRD16 prevents neuron loss caused by an editing-defective tRNA synthetase. Nature 2018; 557:510-515. [PMID: 29769718 PMCID: PMC5973781 DOI: 10.1038/s41586-018-0137-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 04/09/2018] [Indexed: 11/29/2022]
Abstract
Editing domains of aminoacyl tRNA synthetases correct tRNA charging errors to maintain translational fidelity. A mutation in the editing domain of alanyl tRNA synthetase (AlaRS) in Aars sti mutant mice results in an increase in the production of serine-mischarged tRNAAla and the degeneration of cerebellar Purkinje cells. Here, using positional cloning, we identified Ankrd16, a gene that acts epistatically with the Aars sti mutation to attenuate neurodegeneration. ANKRD16, a vertebrate-specific protein that contains ankyrin repeats, binds directly to the catalytic domain of AlaRS. Serine that is misactivated by AlaRS is captured by the lysine side chains of ANKRD16, which prevents the charging of serine adenylates to tRNAAla and precludes serine misincorporation in nascent peptides. The deletion of Ankrd16 in the brains of Aarssti/sti mice causes widespread protein aggregation and neuron loss. These results identify an amino-acid-accepting co-regulator of tRNA synthetase editing as a new layer of the machinery that is essential to the prevention of severe pathologies that arise from defects in editing.
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Affiliation(s)
- My-Nuong Vo
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Markus Terrey
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Section of Neurobiology, University of California San Diego, La Jolla, CA, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Jeong Woong Lee
- The Jackson Laboratory, Bar Harbor, ME, USA
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Bappaditya Roy
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - James J Moresco
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Litao Sun
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Hongjun Fu
- The Jackson Laboratory, Bar Harbor, ME, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Qi Liu
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
- Sharklet Technologies, Aurora, CO, USA
| | | | - John R Yates
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, USA
| | - Kurt Fredrick
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Paul Schimmel
- The Skaggs Institute for Chemical Biology, Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA.
- The Scripps Research Institute, Jupiter, FL, USA.
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Section of Neurobiology, University of California San Diego, La Jolla, CA, USA.
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA.
- The Jackson Laboratory, Bar Harbor, ME, USA.
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18
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Dulic M, Cvetesic N, Zivkovic I, Palencia A, Cusack S, Bertosa B, Gruic-Sovulj I. Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase. J Mol Biol 2018; 430:1-16. [DOI: 10.1016/j.jmb.2017.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/02/2017] [Accepted: 10/08/2017] [Indexed: 10/18/2022]
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19
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Crnković A, Čavužić M, Godinić-Mikulčić V, Anderluh G, Weygand-Đurašević I, Gruić-Sovulj I. An archaeal aminoacyl-tRNA synthetase complex for improved substrate quality control. Biochimie 2017; 147:36-45. [PMID: 29273296 DOI: 10.1016/j.biochi.2017.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 12/17/2017] [Indexed: 10/18/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) decode genetic information by coupling tRNAs with cognate amino acids. In the archaeon Methanothermobacter thermautotrophicus arginyl- and seryl-tRNA synthetase (ArgRS and SerRS, respectively) form a complex which enhances serylation and facilitates tRNASer recycling through its association with the ribosome. Yet, the way by which complex formation participates in Arg-tRNAArg synthesis is still unresolved. Here we utilized pull down and surface plasmon resonance experiments with truncated ArgRS variants to demonstrate that ArgRS uses its N-terminal domain to establish analogous interactions with both SerRS and cognate tRNAArg, providing a rationale for the lack of detectable SerRS•[ArgRS•tRNAArg] complex. In contrast, stable ternary ArgRS•[SerRS•tRNASer] complex was easily detected supporting the model wherein ArgRS operates in serylation by modulating SerRS affinity toward tRNASer. We also found that the interaction with SerRS suppresses arginylation of unmodified tRNAArg by ArgRS, which, by itself, does not discriminate against tRNAArg substrates lacking posttranscriptional modifications. Hence, there is a fundamentally different participation of the protein partners in Arg-tRNA and Ser-tRNA synthesis. Propensity of the ArgRS•SerRS complex to exclude unmodified tRNAs from translation leads to an attractive hypothesis that SerRS•ArgRS complex might act in vivo as a safeguarding switch that improves translation accuracy.
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Affiliation(s)
- Ana Crnković
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, 10000 Zagreb, Croatia.
| | - Mirela Čavužić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, 10000 Zagreb, Croatia
| | - Vlatka Godinić-Mikulčić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, 10000 Zagreb, Croatia
| | - Gregor Anderluh
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia; Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ivana Weygand-Đurašević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, 10000 Zagreb, Croatia
| | - Ita Gruić-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, 10000 Zagreb, Croatia.
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20
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Ji QQ, Fang ZP, Ye Q, Chi CW, Wang ED. Self-protective responses to norvaline-induced stress in a leucyl-tRNA synthetase editing-deficient yeast strain. Nucleic Acids Res 2017; 45:7367-7381. [PMID: 28575390 PMCID: PMC5499588 DOI: 10.1093/nar/gkx487] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/24/2017] [Indexed: 12/23/2022] Open
Abstract
The editing function of aminoacyl-tRNA synthetases (aaRSs) is indispensible for formation of the correct aminoacyl-tRNAs. Editing deficiency may lead to growth inhibition and the pathogenesis of various diseases. Herein, we confirmed that norvaline (Nva) but not isoleucine or valine is the major threat to the editing function of Saccharomyces cerevisiae leucyl-tRNA synthetase (ScLeuRS), both in vitro and in vivo. Nva could be misincorporated into the proteome of the LeuRS editing-deficient yeast strain (D419A/ScΔleuS), potentially resulting in dysfunctional protein folding and growth delay. Furthermore, the exploration of the Nva-induced intracellular stress response mechanism in D419A/ScΔleuS revealed that Hsp70 chaperones were markedly upregulated in response to the potential protein misfolding. Additionally, proline (Pro), glutamate (Glu) and glutamine (Gln), which may accumulate due to the conversion of Nva, collectively contributed to the reduction of reactive oxygen species (ROS) levels in Nva-treated D419A/ScΔleuS cells. In conclusion, our study highlights the significance of the editing function of LeuRS and provides clues for understanding the intracellular stress protective mechanisms that are triggered in aaRS editing-deficient organisms.
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Affiliation(s)
- Quan-Quan Ji
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - Zhi-Peng Fang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - Qing Ye
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - Cheng-Wu Chi
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, P. R. China
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21
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Mechanistic Insights Into Catalytic RNA-Protein Complexes Involved in Translation of the Genetic Code. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017. [PMID: 28683922 DOI: 10.1016/bs.apcsb.2017.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The contemporary world is an "RNA-protein world" rather than a "protein world" and tracing its evolutionary origins is of great interest and importance. The different RNAs that function in close collaboration with proteins are involved in several key physiological processes, including catalysis. Ribosome-the complex megadalton cellular machinery that translates genetic information encoded in nucleotide sequence to amino acid sequence-epitomizes such an association between RNA and protein. RNAs that can catalyze biochemical reactions are known as ribozymes. They usually employ general acid-base catalytic mechanism, often involving the 2'-OH of RNA that activates and/or stabilizes a nucleophile during the reaction pathway. The protein component of such RNA-protein complexes (RNPCs) mostly serves as a scaffold which provides an environment conducive for the RNA to function, or as a mediator for other interacting partners. In this review, we describe those RNPCs that are involved at different stages of protein biosynthesis and in which RNA performs the catalytic function; the focus of the account is on highlighting mechanistic aspects of these complexes. We also provide a perspective on such associations in the context of proofreading during translation of the genetic code. The latter aspect is not much appreciated and recent works suggest that this is an avenue worth exploring, since an understanding of the subject can provide useful insights into how RNAs collaborate with proteins to ensure fidelity during these essential cellular processes. It may also aid in comprehending evolutionary aspects of such associations.
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22
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Kermgard E, Yang Z, Michel AM, Simari R, Wong J, Ibba M, Lazazzera BA. Quality Control by Isoleucyl-tRNA Synthetase of Bacillus subtilis Is Required for Efficient Sporulation. Sci Rep 2017; 7:41763. [PMID: 28139725 PMCID: PMC5282499 DOI: 10.1038/srep41763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/22/2016] [Indexed: 11/11/2022] Open
Abstract
Isoleucyl-tRNA synthetase (IleRS) is an aminoacyl-tRNA synthetase whose essential function is to aminoacylate tRNAIle with isoleucine. Like some other aminoacyl-tRNA synthetases, IleRS can mischarge tRNAIle and correct this misacylation through a separate post-transfer editing function. To explore the biological significance of this editing function, we created a ileS(T233P) mutant of Bacillus subtilis that allows tRNAIle mischarging while retaining wild-type Ile-tRNAIle synthesis activity. As seen in other species defective for aminoacylation quality control, the growth rate of the ileS(T233P) strain was not significantly different from wild-type. When the ileS(T233P) strain was assessed for its ability to promote distinct phenotypes in response to starvation, the ileS(T233P) strain was observed to exhibit a significant defect in formation of environmentally resistant spores. The sporulation defect ranged from 3-fold to 30-fold and was due to a delay in activation of early sporulation genes. The loss of aminoacylation quality control in the ileS(T233P) strain resulted in the inability to compete with a wild-type strain under selective conditions that required sporulation. These data show that the quality control function of IleRS is required in B. subtilis for efficient sporulation and suggests that editing by aminoacyl-tRNA synthetases may be important for survival under starvation/nutrient limitation conditions.
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Affiliation(s)
- Elizabeth Kermgard
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Zhou Yang
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Annika-Marisa Michel
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Technische Universität Braunschweig, Institut of Microbiology, Braunschweig, Germany
| | - Rachel Simari
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA
| | - Jacqueline Wong
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA
| | - Michael Ibba
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, Ohio State University, Columbus, Ohio 43210, USA.,Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
| | - Beth A Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics University of California, Los Angeles, California 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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23
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Mistranslation: from adaptations to applications. Biochim Biophys Acta Gen Subj 2017; 1861:3070-3080. [PMID: 28153753 DOI: 10.1016/j.bbagen.2017.01.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The conservation of the genetic code indicates that there was a single origin, but like all genetic material, the cell's interpretation of the code is subject to evolutionary pressure. Single nucleotide variations in tRNA sequences can modulate codon assignments by altering codon-anticodon pairing or tRNA charging. Either can increase translation errors and even change the code. The frozen accident hypothesis argued that changes to the code would destabilize the proteome and reduce fitness. In studies of model organisms, mistranslation often acts as an adaptive response. These studies reveal evolutionary conserved mechanisms to maintain proteostasis even during high rates of mistranslation. SCOPE OF REVIEW This review discusses the evolutionary basis of altered genetic codes, how mistranslation is identified, and how deviations to the genetic code are exploited. We revisit early discoveries of genetic code deviations and provide examples of adaptive mistranslation events in nature. Lastly, we highlight innovations in synthetic biology to expand the genetic code. MAJOR CONCLUSIONS The genetic code is still evolving. Mistranslation increases proteomic diversity that enables cells to survive stress conditions or suppress a deleterious allele. Genetic code variants have been identified by genome and metagenome sequence analyses, suppressor genetics, and biochemical characterization. GENERAL SIGNIFICANCE Understanding the mechanisms of translation and genetic code deviations enables the design of new codes to produce novel proteins. Engineering the translation machinery and expanding the genetic code to incorporate non-canonical amino acids are valuable tools in synthetic biology that are impacting biomedical research. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.
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24
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Völler JS, Dulic M, Gerling-Driessen UIM, Biava H, Baumann T, Budisa N, Gruic-Sovulj I, Koksch B. Discovery and Investigation of Natural Editing Function against Artificial Amino Acids in Protein Translation. ACS CENTRAL SCIENCE 2017; 3:73-80. [PMID: 28149956 PMCID: PMC5269655 DOI: 10.1021/acscentsci.6b00339] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 05/24/2023]
Abstract
Fluorine being not substantially present in the chemistry of living beings is an attractive element in tailoring novel chemical, biophysical, and pharmacokinetic properties of peptides and proteins. The hallmark of ribosome-mediated artificial amino acid incorporation into peptides and proteins is a broad substrate tolerance, which is assumed to rely on the absence of evolutionary pressure for efficient editing of artificial amino acids. We used the well-characterized editing proficient isoleucyl-tRNA synthetase (IleRS) from Escherichia coli to investigate the crosstalk of aminoacylation and editing activities against fluorinated amino acids. We show that translation of trifluoroethylglycine (TfeGly) into proteins is prevented by hydrolysis of TfeGly-tRNAIle in the IleRS post-transfer editing domain. The remarkable observation is that dissociation of TfeGly-tRNAIle from IleRS is significantly slowed down. This finding is in sharp contrast to natural editing reactions by tRNA synthetases wherein fast editing rates for the noncognate substrates are essential to outcompete fast aa-tRNA dissociation rates. Using a post-transfer editing deficient mutant of IleRS (IleRSAla10), we were able to achieve ribosomal incorporation of TfeGly in vivo. Our work expands the knowledge of ribosome-mediated artificial amino acid translation with detailed analysis of natural editing function against an artificial amino acid providing an impulse for further systematic investigations and engineering of the translation and editing of unusual amino acids.
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Affiliation(s)
- Jan-Stefan Völler
- Institute
of Chemistry and Biochemistry − Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Morana Dulic
- Department
of Chemistry, Faculty of Science, University
of Zagreb, Horvatovac
102a, 10000 Zagreb, Croatia
| | - Ulla I. M. Gerling-Driessen
- Institute
of Chemistry and Biochemistry − Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hernan Biava
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Tobias Baumann
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Nediljko Budisa
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Ita Gruic-Sovulj
- Department
of Chemistry, Faculty of Science, University
of Zagreb, Horvatovac
102a, 10000 Zagreb, Croatia
| | - Beate Koksch
- Institute
of Chemistry and Biochemistry − Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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25
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26
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Cvetesic N, Gruic-Sovulj I. Synthetic and editing reactions of aminoacyl-tRNA synthetases using cognate and non-cognate amino acid substrates. Methods 2016; 113:13-26. [PMID: 27713080 DOI: 10.1016/j.ymeth.2016.09.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/29/2016] [Accepted: 09/29/2016] [Indexed: 11/19/2022] Open
Abstract
The covalent coupling of cognate amino acid-tRNA pairs by corresponding aminoacyl-tRNA synthetases (aaRS) defines the genetic code and provides aminoacylated tRNAs for ribosomal protein synthesis. Besides the cognate substrate, some non-cognate amino acids may also compete for tRNA aminoacylation. However, their participation in protein synthesis is generally prevented by an aaRS proofreading activity located in the synthetic site and in a separate editing domain. These mechanisms, coupled with the ability of certain aaRSs to discriminate well against non-cognate amino acids in the synthetic reaction alone, define the accuracy of the aminoacylation reaction. aaRS quality control may also act as a gatekeeper for the standard genetic code and prevents infiltration by natural amino acids that are not normally coded for protein biosynthesis. This latter finding has reinforced interest in understanding the principles that govern discrimination against a range of potential non-cognate amino acids. This paper presents an overview of the kinetic assays that have been established for monitoring synthetic and editing reactions with cognate and non-cognate amino acid substrates. Taking into account the peculiarities of non-cognate reactions, the specific controls needed and the dedicated experimental designs are discussed in detail. Kinetic partitioning within the synthetic and editing sites controls the balance between editing and aminoacylation. We describe in detail steady-state and single-turnover approaches for the analysis of synthetic and editing reactions, which ultimately enable mechanisms of amino acid discrimination to be determined.
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Affiliation(s)
- Nevena Cvetesic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
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27
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Elongation Factor Tu Prevents Misediting of Gly-tRNA(Gly) Caused by the Design Behind the Chiral Proofreading Site of D-Aminoacyl-tRNA Deacylase. PLoS Biol 2016; 14:e1002465. [PMID: 27224426 PMCID: PMC4880308 DOI: 10.1371/journal.pbio.1002465] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/19/2016] [Indexed: 01/07/2023] Open
Abstract
D-aminoacyl-tRNA deacylase (DTD) removes D-amino acids mischarged on tRNAs and is thus implicated in enforcing homochirality in proteins. Previously, we proposed that selective capture of D-aminoacyl-tRNA by DTD's invariant, cross-subunit Gly-cisPro motif forms the mechanistic basis for its enantioselectivity. We now show, using nuclear magnetic resonance (NMR) spectroscopy-based binding studies followed by biochemical assays with both bacterial and eukaryotic systems, that DTD effectively misedits Gly-tRNAGly. High-resolution crystal structure reveals that the architecture of DTD's chiral proofreading site is completely porous to achiral glycine. Hence, L-chiral rejection is the only design principle on which DTD functions, unlike other chiral-specific enzymes such as D-amino acid oxidases, which are specific for D-enantiomers. Competition assays with elongation factor thermo unstable (EF-Tu) and DTD demonstrate that EF-Tu precludes Gly-tRNAGly misediting at normal cellular concentrations. However, even slightly higher DTD levels overcome this protection conferred by EF-Tu, thus resulting in significant depletion of Gly-tRNAGly. Our in vitro observations are substantiated by cell-based studies in Escherichia coli that show that overexpression of DTD causes cellular toxicity, which is largely rescued upon glycine supplementation. Furthermore, we provide direct evidence that DTD is an RNA-based catalyst, since it uses only the terminal 2'-OH of tRNA for catalysis without the involvement of protein side chains. The study therefore provides a unique paradigm of enzyme action for substrate selection/specificity by DTD, and thus explains the underlying cause of DTD's activity on Gly-tRNAGly. It also gives a molecular and functional basis for the necessity and the observed tight regulation of DTD levels, thereby preventing cellular toxicity due to misediting.
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28
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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29
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Richardson CJ, First EA. Altering the Enantioselectivity of Tyrosyl-tRNA Synthetase by Insertion of a Stereospecific Editing Domain. Biochemistry 2016; 55:1541-53. [DOI: 10.1021/acs.biochem.5b01167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Charles J. Richardson
- Department of Biochemistry
and Molecular Biology, Louisiana State University Health Sciences Center in Shreveport, 1501 Kings Highway, Shreveport, Louisiana 71130, United States
| | - Eric A. First
- Department of Biochemistry
and Molecular Biology, Louisiana State University Health Sciences Center in Shreveport, 1501 Kings Highway, Shreveport, Louisiana 71130, United States
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30
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Cvetesic N, Dulic M, Bilus M, Sostaric N, Lenhard B, Gruic-Sovulj I. Naturally Occurring Isoleucyl-tRNA Synthetase without tRNA-dependent Pre-transfer Editing. J Biol Chem 2016; 291:8618-31. [PMID: 26921320 PMCID: PMC4861432 DOI: 10.1074/jbc.m115.698225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 11/23/2022] Open
Abstract
Isoleucyl-tRNA synthetase (IleRS) is unusual among aminoacyl-tRNA synthetases in having a tRNA-dependent pre-transfer editing activity. Alongside the typical bacterial IleRS (such as Escherichia coli IleRS), some bacteria also have the enzymes (eukaryote-like) that cluster with eukaryotic IleRSs and exhibit low sensitivity to the antibiotic mupirocin. Our phylogenetic analysis suggests that the ileS1 and ileS2 genes of contemporary bacteria are the descendants of genes that might have arisen by an ancient duplication event before the separation of bacteria and archaea. We present the analysis of evolutionary constraints of the synthetic and editing reactions in eukaryotic/eukaryote-like IleRSs, which share a common origin but diverged through adaptation to different cell environments. The enzyme from the yeast cytosol exhibits tRNA-dependent pre-transfer editing analogous to E. coli IleRS. This argues for the presence of this proofreading in the common ancestor of both IleRS types and an ancient origin of the synthetic site-based quality control step. Yet surprisingly, the eukaryote-like enzyme from Streptomyces griseus IleRS lacks this capacity; at the same time, its synthetic site displays the 103-fold drop in sensitivity to antibiotic mupirocin relative to the yeast enzyme. The discovery that pre-transfer editing is optional in IleRSs lends support to the notion that the conserved post-transfer editing domain is the main checkpoint in these enzymes. We substantiated this by showing that under error-prone conditions S. griseus IleRS is able to rescue the growth of an E. coli lacking functional IleRS, providing the first evidence that tRNA-dependent pre-transfer editing in IleRS is not essential for cell viability.
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Affiliation(s)
- Nevena Cvetesic
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
| | - Morana Dulic
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
| | - Mirna Bilus
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
| | - Nikolina Sostaric
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
| | - Boris Lenhard
- the Computational Regulatory Genomics Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Ita Gruic-Sovulj
- From the Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia and
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31
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Boyarshin KS, Priss AE, Rayevskiy AV, Ilchenko MM, Dubey IY, Kriklivyi IA, Yaremchuk AD, Tukalo MA. A new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: catalysis of hydrolytic reaction by bacterial-type prolyl-tRNA synthetase. J Biomol Struct Dyn 2016; 35:669-682. [PMID: 26886480 DOI: 10.1080/07391102.2016.1155171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Aminoacyl tRNA synthetases are enzymes that specifically attach amino acids to cognate tRNAs for use in the ribosomal stage of translation. For many aminoacyl tRNA synthetases, the required level of amino acid specificity is achieved either by specific hydrolysis of misactivated aminoacyl-adenylate intermediate (pre-transfer editing) or by hydrolysis of the mischarged aminoacyl-tRNA (post-transfer editing). To investigate the mechanism of post-transfer editing of alanine by prolyl-tRNA synthetase from the pathogenic bacteria Enterococcus faecalis, we used molecular modeling, molecular dynamic simulations, quantum mechanical (QM) calculations, site-directed mutagenesis of the enzyme, and tRNA modification. The results support a new tRNA-assisted mechanism of hydrolysis of misacylated Ala-tRNAPro. The most important functional element of this catalytic mechanism is the 2'-OH group of the terminal adenosine 76 of Ala-tRNAPro, which forms an intramolecular hydrogen bond with the carbonyl group of the alanine residue, strongly facilitating hydrolysis. Hydrolysis was shown by QM methods to proceed via a general acid-base catalysis mechanism involving two functionally distinct water molecules. The transition state of the reaction was identified. Amino acid residues of the editing active site participate in the coordination of substrate and both attacking and assisting water molecules, performing the proton transfer to the 3'-O atom of A76.
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Affiliation(s)
- Konstantin S Boyarshin
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Anastasia E Priss
- b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Alexsey V Rayevskiy
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Mykola M Ilchenko
- c Department of Synthetic Bioregulators , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Igor Ya Dubey
- c Department of Synthetic Bioregulators , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Ivan A Kriklivyi
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Anna D Yaremchuk
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Michael A Tukalo
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
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32
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Rauch BJ, Porter JJ, Mehl RA, Perona JJ. Improved Incorporation of Noncanonical Amino Acids by an Engineered tRNA(Tyr) Suppressor. Biochemistry 2016; 55:618-28. [PMID: 26694948 DOI: 10.1021/acs.biochem.5b01185] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Methanocaldcoccus jannaschii tyrosyl-tRNA synthetase (TyrRS):tRNA(Tyr) cognate pair has been used to incorporate a large number of noncanonical amino acids (ncAAs) into recombinant proteins in Escherichia coli. However, the structural elements of the suppressor tRNA(Tyr) used in these experiments have not been examined for optimal performance. Here, we evaluate the steady-state kinetic parameters of wild-type M. jannaschii TyrRS and an evolved 3-nitrotyrosyl-tRNA synthetase (nitroTyrRS) toward several engineered tRNA(Tyr) suppressors, and we correlate aminoacylation properties with the efficiency and fidelity of superfolder green fluorescent protein (sfGFP) synthesis in vivo. Optimal ncAA-sfGFP synthesis correlates with improved aminoacylation kinetics for a tRNA(Tyr) amber suppressor with two substitutions in the anticodon loop (G34C/G37A), while four additional mutations in the D and variable loops, present in the tRNA(Tyr) used in all directed evolution experiments to date, are deleterious to function both in vivo and in vitro. These findings extend to three of four other evolved TyrRS enzymes that incorporate distinct ncAAs. Suppressor tRNAs elicit decreases in amino acid Km values for both TyrRS and nitroTyrRS, suggesting that direct anticodon recognition by TyrRS need not be an impediment to superior performance of this orthogonal system and offering insight into novel approaches for directed evolution. The G34C/G37A tRNA(Tyr) may enhance future incorporation of many ncAAs by engineered TyrRS enzymes.
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Affiliation(s)
- Benjamin J Rauch
- Department of Chemistry, Portland State University , P.O. Box 751, Portland, Oregon 97207, United States.,Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Joseph J Porter
- Department of Biochemistry and Biophysics, Oregon State University , 2011 Agriculture and Life Sciences Building, Corvallis, Oregon 97331, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University , 2011 Agriculture and Life Sciences Building, Corvallis, Oregon 97331, United States
| | - John J Perona
- Department of Chemistry, Portland State University , P.O. Box 751, Portland, Oregon 97207, United States.,Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
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33
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Cvetesic N, Bilus M, Gruic-Sovulj I. The tRNA A76 Hydroxyl Groups Control Partitioning of the tRNA-dependent Pre- and Post-transfer Editing Pathways in Class I tRNA Synthetase. J Biol Chem 2015; 290:13981-91. [PMID: 25873392 DOI: 10.1074/jbc.m115.648568] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases catalyze ATP-dependent covalent coupling of cognate amino acids and tRNAs for ribosomal protein synthesis. Escherichia coli isoleucyl-tRNA synthetase (IleRS) exploits both the tRNA-dependent pre- and post-transfer editing pathways to minimize errors in translation. However, the molecular mechanisms by which tRNA(Ile) organizes the synthetic site to enhance pre-transfer editing, an idiosyncratic feature of IleRS, remains elusive. Here we show that tRNA(Ile) affects both the synthetic and editing reactions localized within the IleRS synthetic site. In a complex with cognate tRNA, IleRS exhibits a 10-fold faster aminoacyl-AMP hydrolysis and a 10-fold drop in amino acid affinity relative to the free enzyme. Remarkably, the specificity against non-cognate valine was not improved by the presence of tRNA in either of these processes. Instead, amino acid specificity is determined by the protein component per se, whereas the tRNA promotes catalytic performance of the synthetic site, bringing about less error-prone and kinetically optimized isoleucyl-tRNA(Ile) synthesis under cellular conditions. Finally, the extent to which tRNA(Ile) modulates activation and pre-transfer editing is independent of the intactness of its 3'-end. This finding decouples aminoacylation and pre-transfer editing within the IleRS synthetic site and further demonstrates that the A76 hydroxyl groups participate in post-transfer editing only. The data are consistent with a model whereby the 3'-end of the tRNA remains free to sample different positions within the IleRS·tRNA complex, whereas the fine-tuning of the synthetic site is attained via conformational rearrangement of the enzyme through the interactions with the remaining parts of the tRNA body.
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Affiliation(s)
- Nevena Cvetesic
- From the Department of Chemistry, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Mirna Bilus
- From the Department of Chemistry, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Ita Gruic-Sovulj
- From the Department of Chemistry, University of Zagreb, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia
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34
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Hadd A, Perona JJ. Recoding aminoacyl-tRNA synthetases for synthetic biology by rational protein-RNA engineering. ACS Chem Biol 2014; 9:2761-6. [PMID: 25310879 PMCID: PMC4273986 DOI: 10.1021/cb5006596] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We
have taken a rational approach to redesigning the amino acid
binding and aminoacyl–tRNA pairing specificities of bacterial
glutaminyl–tRNA synthetase. The four-stage engineering incorporates
generalizable design principles and improves the pairing efficiency
of noncognate glutamate with tRNAGln by over 105-fold compared to the wild-type enzyme. Better optimized designs
of the protein–RNA complex include substantial reengineering
of the globular core region of the tRNA, demonstrating a role for
specific tRNA nucleotides in specifying the identity of the genetically
encoded amino acid. Principles emerging from this engineering effort
open new prospects for combining rational and genetic selection approaches
to design novel aminoacyl–tRNA synthetases that ligate noncanonical
amino acids onto tRNAs. This will facilitate reconstruction of the
cellular translation apparatus for applications in synthetic biology.
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Affiliation(s)
- Andrew Hadd
- Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - John J. Perona
- Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
- Department
of Chemistry, Portland State University, PO Box 751, Portland, Oregon 97207, United States
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35
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Bullwinkle T, Lazazzera B, Ibba M. Quality Control and Infiltration of Translation by Amino Acids Outside of the Genetic Code. Annu Rev Genet 2014; 48:149-66. [DOI: 10.1146/annurev-genet-120213-092101] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tammy Bullwinkle
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Beth Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
- Ohio State Biochemistry Program and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210;
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36
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Zhou XL, Ruan ZR, Wang M, Fang ZP, Wang Y, Chen Y, Liu RJ, Eriani G, Wang ED. A minimalist mitochondrial threonyl-tRNA synthetase exhibits tRNA-isoacceptor specificity during proofreading. Nucleic Acids Res 2014; 42:13873-86. [PMID: 25414329 PMCID: PMC4267643 DOI: 10.1093/nar/gku1218] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Yeast mitochondria contain a minimalist threonyl-tRNA synthetase (ThrRS) composed only of the catalytic core and tRNA binding domain but lacking the entire editing domain. Besides the usual tRNAThr2, some budding yeasts, such as Saccharomyces cerevisiae, also contain a non-canonical tRNAThr1 with an enlarged 8-nucleotide anticodon loop, reprograming the usual leucine CUN codons to threonine. This raises interesting questions about the aminoacylation fidelity of such ThrRSs and the possible contribution of the two tRNAThrs during editing. Here, we found that, despite the absence of the editing domain, S. cerevisiae mitochondrial ThrRS (ScmtThrRS) harbors a tRNA-dependent pre-transfer editing activity. Remarkably, only the usual tRNAThr2 stimulated pre-transfer editing, thus, establishing the first example of a synthetase exhibiting tRNA-isoacceptor specificity during pre-transfer editing. We also showed that the failure of tRNAThr1 to stimulate tRNA-dependent pre-transfer editing was due to the lack of an editing domain. Using assays of the complementation of a ScmtThrRS gene knockout strain, we showed that the catalytic core and tRNA binding domain of ScmtThrRS co-evolved to recognize the unusual tRNAThr1. In combination, the results provide insights into the tRNA-dependent editing process and suggest that tRNA-dependent pre-transfer editing takes place in the aminoacylation catalytic core.
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Affiliation(s)
- Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Zhi-Rong Ruan
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Meng Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Zhi-Peng Fang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Yong Wang
- School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, 200031 Shanghai, China
| | - Yun Chen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Ru-Juan Liu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Université de Strasbourg, UPR9002 CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, China School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, 200031 Shanghai, China
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37
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Dulic M, Perona JJ, Gruic-Sovulj I. Determinants for tRNA-dependent pretransfer editing in the synthetic site of isoleucyl-tRNA synthetase. Biochemistry 2014; 53:6189-98. [PMID: 25207837 PMCID: PMC4188249 DOI: 10.1021/bi5007699] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
accurate expression of genetic information relies on the fidelity
of amino acid–tRNA coupling by aminoacyl-tRNA synthetases (aaRS).
When the specificity against structurally similar noncognate amino
acids in the synthetic reaction does not support a threshold fidelity
level for translation, the aaRS employ intrinsic hydrolytic editing
to correct errors in aminoacylation. Escherichia coli isoleucyl-tRNA synthetase (EcIleRS) is a class I aaRS that is notable
for its use of tRNA-dependent pretransfer editing to hydrolyze noncognate
valyl-adenylate prior to aminoacyl-tRNA formation. On the basis of
the finding that IleRS possessing an inactivated post-transfer editing
domain is still capable of robust tRNA-dependent editing, we have
recently proposed that the pretransfer editing activity resides within
the synthetic site. Here we apply an improved methodology that allows
quantitation of the AMP fraction that arises particularly from tRNA-dependent
aa-AMP hydrolysis. By this approach, we demonstrate that tRNA-dependent
pretransfer editing accounts for nearly one-third of the total proofreading
by EcIleRS and that a highly conserved tyrosine within the synthetic
site modulates both editing and aminoacylation. Therefore, synthesis
of aminoacyl-tRNA and hydrolysis of aminoacyl-adenylates employ overlapping
amino acid determinants. We suggest that this overlap hindered the
evolution of synthetic site-based pretransfer editing as the predominant
proofreading pathway, because that activity is difficult to accommodate
in the context of efficient aminoacyl-tRNA synthesis. Instead, the
acquisition of a spatially separate domain dedicated to post-transfer
editing alone allowed for the development of a powerful deacylation
machinery that effectively competes with dissociation of misacylated
tRNAs.
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Affiliation(s)
- Morana Dulic
- Department of Chemistry, Faculty of Science, University of Zagreb , Horvatovac 102a, 10000 Zagreb, Croatia
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38
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Cvetesic N, Palencia A, Halasz I, Cusack S, Gruic-Sovulj I. The physiological target for LeuRS translational quality control is norvaline. EMBO J 2014; 33:1639-53. [PMID: 24935946 DOI: 10.15252/embj.201488199] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The fidelity of protein synthesis depends on the capacity of aminoacyl-tRNA synthetases (AARSs) to couple only cognate amino acid-tRNA pairs. If amino acid selectivity is compromised, fidelity can be ensured by an inherent AARS editing activity that hydrolyses mischarged tRNAs. Here, we show that the editing activity of Escherichia coli leucyl-tRNA synthetase (EcLeuRS) is not required to prevent incorrect isoleucine incorporation. Rather, as shown by kinetic, structural and in vivo approaches, the prime biological function of LeuRS editing is to prevent mis-incorporation of the non-standard amino acid norvaline. This conclusion follows from a reassessment of the discriminatory power of LeuRS against isoleucine and the demonstration that a LeuRS editing-deficient E. coli strain grows normally in high concentrations of isoleucine but not under oxygen deprivation conditions when norvaline accumulates to substantial levels. Thus, AARS-based translational quality control is a key feature for bacterial adaptive response to oxygen deprivation. The non-essential role for editing under normal bacterial growth has important implications for the development of resistance to antimicrobial agents targeting the LeuRS editing site.
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Affiliation(s)
- Nevena Cvetesic
- Department of Chemistry, Faculty of Science University of Zagreb, Zagreb, Croatia
| | - Andrés Palencia
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS UMI 3265, France
| | | | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS UMI 3265, France
| | - Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science University of Zagreb, Zagreb, Croatia
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39
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Pang YLJ, Poruri K, Martinis SA. tRNA synthetase: tRNA aminoacylation and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:461-80. [PMID: 24706556 DOI: 10.1002/wrna.1224] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 01/14/2014] [Accepted: 02/06/2014] [Indexed: 01/20/2023]
Abstract
The aminoacyl-tRNA synthetases are prominently known for their classic function in the first step of protein synthesis, where they bear the responsibility of setting the genetic code. Each enzyme is exquisitely adapted to covalently link a single standard amino acid to its cognate set of tRNA isoacceptors. These ancient enzymes have evolved idiosyncratically to host alternate activities that go far beyond their aminoacylation role and impact a wide range of other metabolic pathways and cell signaling processes. The family of aminoacyl-tRNA synthetases has also been suggested as a remarkable scaffold to incorporate new domains that would drive evolution and the emergence of new organisms with more complex function. Because they are essential, the tRNA synthetases have served as pharmaceutical targets for drug and antibiotic development. The recent unfolding of novel important functions for this family of proteins offers new and promising pathways for therapeutic development to treat diverse human diseases.
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Affiliation(s)
- Yan Ling Joy Pang
- Department of Biochemistry, University of Illinois at Urbana, Urbana, IL, USA
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Lloyd AJ, Potter NJ, Fishwick CWG, Roper DI, Dowson CG. Adenosine tetraphosphoadenosine drives a continuous ATP-release assay for aminoacyl-tRNA synthetases and other adenylate-forming enzymes. ACS Chem Biol 2013; 8:2157-63. [PMID: 23898887 DOI: 10.1021/cb400248f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aminoacyl-tRNA synthetases are essential for the correct linkage of amino acids to cognate tRNAs to maintain the fidelity of protein synthesis. Tractable, continuous assays are valuable for characterizing the functions of synthetases and for their exploitation as drug targets. We have exploited the unexplored ability of these enzymes to consume adenosine tetraphosphoadenosine (diadenosine 5',5‴ P(1) P(4) tetraphosphate; Ap4A) and produce ATP to develop such an assay. We have used this assay to probe the stereoselectivity of isoleucyl-tRNA(Ile) and Valyl-tRNA(Val) synthetases and the impact of tRNA on editing by isoleucyl-tRNA(Ile) synthetase (IleRS) and to identify analogues of intermediates of these enzymes that might allow targeting of multiple synthetases. We further report the utility of Ap4A-based assays for identification of synthetase inhibitors with nanomolar to millimolar affinities. Finally, we demonstrate the broad application of Ap4A utilization with a continuous Ap4A-driven RNA ligase assay.
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Affiliation(s)
- Adrian J. Lloyd
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry,
West Midlands CV4 7AL, U.K
| | | | | | - David I. Roper
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry,
West Midlands CV4 7AL, U.K
| | - Christopher G. Dowson
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry,
West Midlands CV4 7AL, U.K
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Zhou X, Wang E. Transfer RNA: a dancer between charging and mis-charging for protein biosynthesis. SCIENCE CHINA-LIFE SCIENCES 2013; 56:921-32. [PMID: 23982864 DOI: 10.1007/s11427-013-4542-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/13/2013] [Indexed: 01/17/2023]
Abstract
Transfer RNA plays a fundamental role in the protein biosynthesis as an adaptor molecule by functioning as a biological link between the genetic nucleotide sequence in the mRNA and the amino acid sequence in the protein. To perform its role in protein biosynthesis, it has to be accurately recognized by aminoacyl-tRNA synthetases (aaRSs) to generate aminoacyl-tRNAs (aa-tRNAs). The correct pairing between an amino acid with its cognate tRNA is crucial for translational quality control. Production and utilization of mis-charged tRNAs are usually detrimental for all the species, resulting in cellular dysfunctions. Correct aa-tRNAs formation is collectively controlled by aaRSs with distinct mechanisms and/or other trans-factors. However, in very limited instances, mis-charged tRNAs are intermediate for specific pathways or essential components for the translational machinery. Here, from the point of accuracy in tRNA charging, we review our understanding about the mechanism ensuring correct aa-tRNA generation. In addition, some unique mis-charged tRNA species necessary for the organism are also briefly described.
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Affiliation(s)
- Xiaolong Zhou
- Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
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Tan M, Wang M, Zhou XL, Yan W, Eriani G, Wang ED. The Yin and Yang of tRNA: proper binding of acceptor end determines the catalytic balance of editing and aminoacylation. Nucleic Acids Res 2013; 41:5513-23. [PMID: 23585282 PMCID: PMC3664829 DOI: 10.1093/nar/gkt252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Faithful translation of the genetic code depends on accurate coupling of amino acids with cognate transfer RNAs (tRNAs) catalyzed by aminoacyl-tRNA synthetases. The fidelity of leucyl-tRNA synthetase (LeuRS) depends mainly on proofreading at the pre- and post-transfer levels. During the catalytic cycle, the tRNA CCA-tail shuttles between the synthetic and editing domains to accomplish the aminoacylation and editing reactions. Previously, we showed that the Y330D mutation of Escherichia coli LeuRS, which blocks the entry of the tRNA CCA-tail into the connective polypeptide 1domain, abolishes both tRNA-dependent pre- and post-transfer editing. In this study, we identified the counterpart substitutions, which constrain the tRNA acceptor stem binding within the synthetic active site. These mutations negatively impact the tRNA charging activity while retaining the capacity to activate the amino acid. Interestingly, the mutated LeuRSs exhibit increased global editing activity in the presence of a non-cognate amino acid. We used a reaction mimicking post-transfer editing to show that these mutations decrease post-transfer editing owing to reduced tRNA aminoacylation activity. This implied that the increased editing activity originates from tRNA-dependent pre-transfer editing. These results, together with our previous work, provide a comprehensive assessment of how intra-molecular translocation of the tRNA CCA-tail balances the aminoacylation and editing activities of LeuRS.
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Affiliation(s)
- Min Tan
- Center for RNA research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai 200031, PR China
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Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in Mycoplasma pathogens. Proc Natl Acad Sci U S A 2013; 110:3817-22. [PMID: 23431144 DOI: 10.1073/pnas.1218374110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mycoplasma leucyl-tRNA synthetases (LeuRSs) have been identified in which the connective polypeptide 1 (CP1) amino acid editing domain that clears mischarged tRNAs are missing (Mycoplasma mobile) or highly degenerate (Mycoplasma synoviae). Thus, these enzymes rely on a clearance pathway called pretransfer editing, which hydrolyzes misactivated aminoacyl-adenylate intermediate via a nebulous mechanism that has been controversial for decades. Even as the sole fidelity pathway for clearing amino acid selection errors in the pathogenic M. mobile, pretransfer editing is not robust enough to completely block mischarging of tRNA(Leu), resulting in codon ambiguity and statistical proteins. A high-resolution X-ray crystal structure shows that M. mobile LeuRS structurally overlaps with other LeuRS cores. However, when CP1 domains from different aminoacyl-tRNA synthetases and origins were fused to this common LeuRS core, surprisingly, pretransfer editing was enhanced. It is hypothesized that the CP1 domain evolved as a molecular rheostat to balance multiple functions. These include distal control of specificity and enzyme activity in the ancient canonical core, as well as providing a separate hydrolytic active site for clearing mischarged tRNA.
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Abstract
The aminoacyl-tRNA synthetases (aaRSs) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate tRNAs. The aaRSs are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. Although the aaRSs have long been viewed as a highly conserved group of enzymes, findings within the last couple of decades have started to demonstrate how diverse and versatile these enzymes really are. Beyond their central role in translation, aaRSs and their numerous homologs have evolved a wide array of alternative functions both inside and outside translation. Current understanding of the emergence of the aaRSs, and their subsequent evolution into a functionally diverse enzyme family, are discussed in this chapter.
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Rokov-Plavec J, Lesjak S, Gruic-Sovulj I, Mocibob M, Dulic M, Weygand-Durasevic I. Substrate recognition and fidelity of maize seryl-tRNA synthetases. Arch Biochem Biophys 2013; 529:122-30. [DOI: 10.1016/j.abb.2012.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/28/2012] [Accepted: 11/29/2012] [Indexed: 12/27/2022]
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Cvetesic N, Akmacic I, Gruic-Sovulj I. Lack of discrimination against non-proteinogenic amino acid norvaline by elongation factor Tu from Escherichia coli.. CROAT CHEM ACTA 2013; 86:73-82. [PMID: 23750044 DOI: 10.5562/cca2173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The GTP-bound form of elongation factor Tu (EF-Tu) brings aminoacylated tRNAs (aa-tRNA) to the A-site of the ribosome. EF-Tu binds all cognate elongator aa-tRNAs with highly similar affinities, and its weaker or tighter binding of misacylated tRNAs may discourage their participation in translation. Norvaline (Nva) is a non-proteinogenic amino acid that is activated and transferred to tRNALeu by leucyl-tRNA synthetase (LeuRS). No notable accumulation of Nva-tRNALeu has been observed in vitro, because of the efficient post-transfer hydrolytic editing activity of LeuRS. However, incorporation of norvaline into proteins in place of leucine does occur under certain conditions in vivo. Here we show that EF-Tu binds Nva-tRNALeu and Leu-tRNALeu with similar affinities, and that Nva-tRNALeu and Leu-tRNALeu dissociate from EF-Tu at comparable rates. The inability of EF-Tu to discriminate against norvaline may have driven evolution of highly efficient LeuRS editing as the main quality control mechanism against misincorporation of norvaline into proteins.
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Affiliation(s)
- Nevena Cvetesic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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Perona JJ, Gruic-Sovulj I. Synthetic and editing mechanisms of aminoacyl-tRNA synthetases. Top Curr Chem (Cham) 2013; 344:1-41. [PMID: 23852030 DOI: 10.1007/128_2013_456] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRS) ensure the faithful transmission of genetic information in all living cells. The 24 known aaRS families are divided into 2 structurally distinct classes (class I and class II), each featuring a catalytic domain with a common fold that binds ATP, amino acid, and the 3'-terminus of tRNA. In a common two-step reaction, each aaRS first uses the energy stored in ATP to synthesize an activated aminoacyl adenylate intermediate. In the second step, either the 2'- or 3'-hydroxyl oxygen atom of the 3'-A76 tRNA nucleotide functions as a nucleophile in synthesis of aminoacyl-tRNA. Ten of the 24 aaRS families are unable to distinguish cognate from noncognate amino acids in the synthetic reactions alone. These enzymes possess additional editing activities for hydrolysis of misactivated amino acids and misacylated tRNAs, with clearance of the latter species accomplished in spatially separate post-transfer editing domains. A distinct class of trans-acting proteins that are homologous to class II editing domains also perform hydrolytic editing of some misacylated tRNAs. Here we review essential themes in catalysis with a view toward integrating the kinetic, stereochemical, and structural mechanisms of the enzymes. Although the aaRS have now been the subject of investigation for many decades, it will be seen that a significant number of questions regarding fundamental catalytic functioning still remain unresolved.
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Affiliation(s)
- John J Perona
- Department of Chemistry, Portland State University, 751, Portland, OR, 97207, USA,
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48
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Abstract
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Perona JJ, Hadd A. Structural diversity and protein engineering of the aminoacyl-tRNA synthetases. Biochemistry 2012; 51:8705-29. [PMID: 23075299 DOI: 10.1021/bi301180x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRS) are the enzymes that ensure faithful transmission of genetic information in all living cells, and are central to the developing technologies for expanding the capacity of the translation apparatus to incorporate nonstandard amino acids into proteins in vivo. The 24 known aaRS families are divided into two classes that exhibit functional evolutionary convergence. Each class features an active site domain with a common fold that binds ATP, the amino acid, and the 3'-terminus of tRNA, embellished by idiosyncratic further domains that bind distal portions of the tRNA and enhance specificity. Fidelity in the expression of the genetic code requires that the aaRS be selective for both amino acids and tRNAs, a substantial challenge given the presence of structurally very similar noncognate substrates of both types. Here we comprehensively review central themes concerning the architectures of the protein structures and the remarkable dual-substrate selectivities, with a view toward discerning the most important issues that still substantially limit our capacity for rational protein engineering. A suggested general approach to rational design is presented, which should yield insight into the identities of the protein-RNA motifs at the heart of the genetic code, while also offering a basis for improving the catalytic properties of engineered tRNA synthetases emerging from genetic selections.
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Affiliation(s)
- John J Perona
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States.
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50
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Zhou XL, Ruan ZR, Huang Q, Tan M, Wang ED. Translational fidelity maintenance preventing Ser mis-incorporation at Thr codon in protein from eukaryote. Nucleic Acids Res 2012; 41:302-14. [PMID: 23093606 PMCID: PMC3592468 DOI: 10.1093/nar/gks982] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aminoacyl-tRNA synthetase (aaRS) catalyzes the first step of protein synthesis, producing aminoacyl-tRNAs as building blocks. Eukaryotic aaRS differs from its prokaryotic counterpart in terminal extension or insertion. Moreover, the editing function of aaRSs is an indispensable checkpoint excluding non-cognate amino acids at a given codon and ensuring overall translational fidelity. We found higher eukaryotes encode two cytoplasmic threonyl-tRNA synthetases (ThrRSs) with difference in N-terminus. The longer isoform is more closely related to the ThrRSs of higher eukaryotes than to those of lower eukaryotes. A yeast strain was generated to include deletion of the thrS gene encoding ThrRS. Combining in vitro biochemical and in vivo genetic data, ThrRSs from eukaryotic cytoplasm were systematically analyzed, and role of the eukaryotic cytoplasmic ThrRS-specific N-terminal extension was elucidated. Furthermore, the mechanisms of aminoacylation and editing activity mediated by Saccharomyces cerevisiae ThrRS (ScThrRS) were clarified. Interestingly, yeast cells were tolerant of variation at the editing active sites of ScThrRS without significant Thr-to-Ser conversion in the proteome even under significant environmental stress, implying checkpoints downstream of aminoacylation to provide a further quality control mechanism for the yeast translation system. This study has provided the first comprehensive elucidation of the translational fidelity control mechanism of eukaryotic ThrRS.
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Affiliation(s)
- Xiao-Long Zhou
- Center for RNA research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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