1
|
Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
Collapse
Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
| | | |
Collapse
|
2
|
Dutta S, Nandi N. Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri. J Phys Chem B 2015; 119:10832-48. [PMID: 25794108 DOI: 10.1021/jp511585w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Saheb Dutta
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
| | - Nilashis Nandi
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
| |
Collapse
|
3
|
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]
|
4
|
Szenes A, Pál G. Mapping hidden potential identity elements by computing the average discriminating power of individual tRNA positions. DNA Res 2012; 19:245-58. [PMID: 22378766 PMCID: PMC3372374 DOI: 10.1093/dnares/dss008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The recently published discrete mathematical method, extended consensus partition (ECP), identifies nucleotide types at each position that are strictly absent from a given sequence set, while occur in other sets. These are defined as discriminating elements (DEs). In this study using the ECP approach, we mapped potential hidden identity elements that discriminate the 20 different tRNA identities. We filtered the tDNA data set for the obligatory presence of well-established tRNA features, and then separately for each identity set, the presence of already experimentally identified strictly present identity elements. The analysis was performed on the three kingdoms of life. We determined the number of DE, e.g. the number of sets discriminated by the given position, for each tRNA position of each tRNA identity set. Then, from the positional DE numbers obtained from the 380 pairwise comparisons of the 20 identity sets, we calculated the average excluding value (AEV) for each tRNA position. The AEV provides a measure on the overall discriminating power of each position. Using a statistical analysis, we show that positional AEVs correlate with the number of already identified identity elements. Positions having high AEV but lacking published identity elements predict hitherto undiscovered tRNA identity elements.
Collapse
Affiliation(s)
- Aron Szenes
- Department of Biochemistry, Eötvös University, Budapest, Hungary
| | | |
Collapse
|
5
|
Fournier GP, Andam CP, Alm EJ, Gogarten JP. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. ORIGINS LIFE EVOL B 2011; 41:621-32. [PMID: 22200905 DOI: 10.1007/s11084-011-9261-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 12/06/2011] [Indexed: 01/02/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRS) consist of several families of functionally conserved proteins essential for translation and protein synthesis. Like nearly all components of the translation machinery, most aaRS families are universally distributed across cellular life, being inherited from the time of the Last Universal Common Ancestor (LUCA). However, unlike the rest of the translation machinery, aaRS have undergone numerous ancient horizontal gene transfers, with several independent events detected between domains, and some possibly involving lineages diverging before the time of LUCA. These transfers reveal the complexity of molecular evolution at this early time, and the chimeric nature of genomes within cells that gave rise to the major domains. Additionally, given the role of these protein families in defining the amino acids used for protein synthesis, sequence reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl- and valyl- RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor. The implications of this observation for the early evolution of RNA-directed protein biosynthesis are discussed.
Collapse
Affiliation(s)
- Gregory P Fournier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | | | | | | |
Collapse
|
6
|
Dulic M, Pozar J, Bilokapic S, Weygand-Durasevic I, Gruic-Sovulj I. An idiosyncratic serine ordering loop in methanogen seryl-tRNA synthetases guides substrates through seryl-tRNASer formation. Biochimie 2011; 93:1761-9. [DOI: 10.1016/j.biochi.2011.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 06/10/2011] [Indexed: 10/18/2022]
|
7
|
The Seryl-tRNA synthetase/tRNASer acceptor stem interface is mediated via a specific network of water molecules. Biochem Biophys Res Commun 2011; 412:532-6. [PMID: 21787751 DOI: 10.1016/j.bbrc.2011.07.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 11/23/2022]
Abstract
tRNAs are aminoacylated by the aminoacyl-tRNA synthetases. There are at least 20 natural amino acids, but due to the redundancy of the genetic code, 64 codons on the mRNA. Therefore, there exist tRNA isoacceptors that are aminoacylated with the same amino acid, but differ in their sequence and in the anticodon. tRNA identity elements, which are sequence or structure motifs, assure the amino acid specificity. The Seryl-tRNA synthetase is an enzyme that depends on rather few and simple identity elements in tRNA(Ser). The Seryl-tRNA-synthetase interacts with the tRNA(Ser) acceptor stem, which makes this part of the tRNA a valuable structural element for investigating motifs of the protein-RNA complex. We solved the high resolution crystal structures of two tRNA(Ser) acceptor stem microhelices and investigated their interaction with the Seryl-tRNA-synthetase by superposition experiments. The results presented here show that the amino acid side chains Ser151 and Ser156 of the synthetase are interacting in a very similar way with the RNA backbone of the microhelix and that the involved water molecules have almost identical positions within the tRNA/synthetase interface.
Collapse
|
8
|
|
9
|
Guitart T, Leon Bernardo T, Sagalés J, Stratmann T, Bernués J, Ribas de Pouplana L. New aminoacyl-tRNA synthetase-like protein in insecta with an essential mitochondrial function. J Biol Chem 2010; 285:38157-66. [PMID: 20870726 PMCID: PMC2992249 DOI: 10.1074/jbc.m110.167486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 09/22/2010] [Indexed: 12/24/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARS) are modular enzymes that aminoacylate transfer RNAs (tRNA) for their use by the ribosome during protein synthesis. ARS are essential and universal components of the genetic code that were almost completely established before the appearance of the last common ancestor of all living species. This long evolutionary history explains the growing number of functions being discovered for ARS, and for ARS homologues, beyond their canonical role in gene translation. Here we present a previously uncharacterized paralogue of seryl-tRNA synthetase named SLIMP (seryl-tRNA synthetase-like insect mitochondrial protein). SLIMP is the result of a duplication of a mitochondrial seryl-tRNA synthetase (SRS) gene that took place in early metazoans and was fixed in Insecta. Here we show that SLIMP is localized in the mitochondria, where it carries out an essential function that is unrelated to the aminoacylation of tRNA. The knockdown of SLIMP by RNA interference (RNAi) causes a decrease in respiration capacity and an increase in mitochondrial mass in the form of aberrant mitochondria.
Collapse
Affiliation(s)
- Tanit Guitart
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
| | - Teresa Leon Bernardo
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
| | - Jessica Sagalés
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
| | - Thomas Stratmann
- the Department of Physiology, University of Barcelona (Biology), Avinguda Diagonal 645, 08028 Barcelona, Catalonia
| | - Jordi Bernués
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
- the Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Parc Cientific de Barcelona, Carrer Baldiri Reixac 12, 08028 Barcelona, Catalonia, and
| | - Lluís Ribas de Pouplana
- From the Institute for Research in Biomedicine (IRB), C/ Baldiri Reixac 12, 08028 Barcelona, Catalonia
- the Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
| |
Collapse
|
10
|
Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov FA, Gundllapalli S, Frolova L, Söll D, Kisselev L. Translation termination in pyrrolysine-utilizing archaea. FEBS Lett 2009; 583:3455-60. [PMID: 19796638 DOI: 10.1016/j.febslet.2009.09.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 09/24/2009] [Indexed: 10/20/2022]
Abstract
Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed.
Collapse
Affiliation(s)
- Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Jaric J, Bilokapic S, Lesjak S, Crnkovic A, Ban N, Weygand-Durasevic I. Identification of amino acids in the N-terminal domain of atypical methanogenic-type Seryl-tRNA synthetase critical for tRNA recognition. J Biol Chem 2009; 284:30643-51. [PMID: 19734148 DOI: 10.1074/jbc.m109.044099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Seryl-tRNA synthetase (SerRS) from methanogenic archaeon Methanosarcina barkeri, contains an idiosyncratic N-terminal domain, composed of an antiparallel beta-sheet capped by a helical bundle, connected to the catalytic core by a short linker peptide. It is very different from the coiled-coil tRNA binding domain in bacterial-type SerRS. Because the crystal structure of the methanogenic-type SerRSxtRNA complex has not been obtained, a docking model was produced, which indicated that highly conserved helices H2 and H3 of the N-terminal domain may be important for recognition of the extra arm of tRNA(Ser). Based on structural information and the docking model, we have mutated various positions within the N-terminal region and probed their involvement in tRNA binding and serylation. Total loss of activity and inability of the R76A variant to form the complex with cognate tRNA identifies Arg(76) located in helix H2 as a crucial tRNA-interacting residue. Alteration of Lys(79) positioned in helix H2 and Arg(94) in the loop between helix H2 and beta-strand A4 have a pronounced effect on SerRSxtRNA(Ser) complex formation and dissociation constants (K(D)) determined by surface plasmon resonance. The replacement of residues Arg(38) (located in the loop between helix H1 and beta-strand A2), Lys(141) and Asn(142) (from H3), and Arg(143) (between H3 and H4) moderately affect both the serylation activity and the K(D) values. Furthermore, we have obtained a striking correlation between these results and in vivo effects of these mutations by quantifying the efficiency of suppression of bacterial amber mutations, after coexpression of the genes for M. barkeri suppressor tRNA(Ser) and a set of mMbSerRS variants in Escherichia coli.
Collapse
Affiliation(s)
- Jelena Jaric
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | | | | | | | | | | |
Collapse
|
12
|
The 1.2A crystal structure of an E. coli tRNASer)acceptor stem microhelix reveals two magnesium binding sites. Biochem Biophys Res Commun 2009; 386:368-73. [PMID: 19527687 DOI: 10.1016/j.bbrc.2009.06.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 06/09/2009] [Indexed: 11/22/2022]
Abstract
tRNA identity elements assure the correct aminoacylation of tRNAs by the cognate aminoacyl-tRNA synthetases. tRNA(Ser) belongs to the so-called class II system, in which the identity elements are rather simple and are mostly located in the acceptor stem region, in contrast to 'class I', where tRNA determinants are more complex and are located within different regions of the tRNA. The structure of an Escherichia coli tRNA(Ser) acceptor stem microhelix was solved by high resolution X-ray structure analysis. The RNA crystallizes in the space group C2, with one molecule per asymmetric unit and with the cell constants a=35.79, b=39.13, c=31.37A, and beta=111.1 degrees . A defined hydration pattern of 97 water molecules surrounds the tRNA(Ser) acceptor stem microhelix. Additionally, two magnesium binding sites were detected in the tRNA(Ser) aminoacyl stem.
Collapse
|
13
|
Bilokapic S, Ivic N, Godinic-Mikulcic V, Piantanida I, Ban N, Weygand-Durasevic I. Idiosyncratic helix-turn-helix motif in Methanosarcina barkeri seryl-tRNA synthetase has a critical architectural role. J Biol Chem 2009; 284:10706-13. [PMID: 19228694 DOI: 10.1074/jbc.m808501200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All seryl-tRNA synthetases (SerRSs) are functional homodimers with a C-terminal active site domain typical for class II aminoacyl-tRNA synthetases and an N-terminal domain involved in tRNA binding. The recently solved three-dimensional structure of Methanosarcina barkeri SerRS revealed the idiosyncratic features of methanogenic-type SerRSs; that is, an active site zinc ion, a unique tRNA binding domain, and an insertion of approximately 30 residues in the catalytic domain, which adopt a helix-turn-helix (HTH) fold. Here, we present biochemical evidence for multiple roles of the HTH motif; it is important for dimerization of the enzyme, contributes to the overall stability, and is critical for the proper positioning of the tRNA binding domain relative to the catalytic domain. The changes in intrinsic fluorescence during denaturation of the wild-type M. barkeri SerRS and of the mutated variant lacking the HTH motif combined with cross-linking and gel analysis of protein subunits during various stages of the unfolding process revealed significantly reduced stability of the mutant dimers. In vitro kinetic analysis of enzymes, mutated in one of the N-terminal helices and the HTH motif, shows impaired tRNA binding and aminoacylation and emphasizes the importance of this domain for the overall architecture of the enzyme. The role of the idiosyncratic HTH motif in dimer stabilization and association between the catalytic and tRNA binding domain has been additionally confirmed by a yeast two-hybrid approach. Furthermore, we provide experimental evidence that tRNA binds across the dimer.
Collapse
Affiliation(s)
- Silvija Bilokapic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, and Divisions of Physical Chemistry and Organic Chemistry and Biochemistry, Rudjer Boskovic Institute, Bijenicka c. 54, HR-10000 Zagreb, Croatia, Switzerland
| | | | | | | | | | | |
Collapse
|
14
|
Gundllapalli S, Ambrogelly A, Umehara T, Li D, Polycarpo C, Söll D. Misacylation of pyrrolysine tRNA in vitro and in vivo. FEBS Lett 2008; 582:3353-8. [PMID: 18775710 DOI: 10.1016/j.febslet.2008.08.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 08/22/2008] [Accepted: 08/22/2008] [Indexed: 11/28/2022]
Abstract
Methanosarcina barkeri inserts pyrrolysine (Pyl) at an in-frame UAG codon in its monomethylamine methyltransferase gene. Pyrrolysyl-tRNA synthetase acylates Pyl onto tRNAPyl, the amber suppressor pyrrolysine Pyl tRNA. Here we show that M. barkeri Fusaro tRNAPyl can be misacylated with serine by the M. barkeri bacterial-type seryl-tRNA synthetase in vitro and in vivo in Escherichia coli. Compared to the M. barkeri Fusaro tRNA, the M. barkeri MS tRNAPyl contains two base changes; a G3:U70 pair, the known identity element for E. coli alanyl-tRNA synthetase (AlaRS). While M. barkeri MS tRNAPyl cannot be alanylated by E. coli AlaRS, mutation of the MS tRNAPyl A4:U69 pair into C4:G69 allows aminoacylation by E. coli AlaRS both in vitro and in vivo.
Collapse
Affiliation(s)
- Sarath Gundllapalli
- Departments of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, 266 Whitney Avenue, New Haven, CT 06520-8114, USA
| | | | | | | | | | | |
Collapse
|
15
|
Bilokapic S, Rokov Plavec J, Ban N, Weygand-Durasevic I. Structural flexibility of the methanogenic-type seryl-tRNA synthetase active site and its implication for specific substrate recognition. FEBS J 2008; 275:2831-44. [DOI: 10.1111/j.1742-4658.2008.06423.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
16
|
Sherrer RL, Ho JML, Söll D. Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase. Nucleic Acids Res 2008; 36:1871-80. [PMID: 18267971 PMCID: PMC2330242 DOI: 10.1093/nar/gkn036] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Selenocysteine (Sec) biosynthesis in archaea and eukaryotes requires three steps: serylation of tRNASec by seryl-tRNA synthetase (SerRS), phosphorylation of Ser-tRNASec by O-phosphoseryl-tRNASec kinase (PSTK), and conversion of O-phosphoseryl-tRNASec (Sep-tRNASec) by Sep-tRNA:Sec-tRNA synthase (SepSecS) to Sec-tRNASec. Although SerRS recognizes both tRNASec and tRNASer species, PSTK must discriminate Ser-tRNASec from Ser-tRNASer. Based on a comparison of the sequences and secondary structures of archaeal tRNASec and tRNASer, we introduced mutations into Methanococcus maripaludis tRNASec to investigate how Methanocaldococcus jannaschii PSTK distinguishes tRNASec from tRNASer. Unlike eukaryotic PSTK, the archaeal enzyme was found to recognize the acceptor stem rather than the length and secondary structure of the D-stem. While the D-arm and T-loop provide minor identity elements, the acceptor stem base pairs G2-C71 and C3-G70 in tRNASec were crucial for discrimination from tRNASer. Furthermore, the A5-U68 base pair in tRNASer has some antideterminant properties for PSTK. Transplantation of these identity elements into the tRNASerUGA scaffold resulted in phosphorylation of the chimeric Ser-tRNA. The chimera was able to stimulate the ATPase activity of PSTK albeit at a lower level than tRNASec, whereas tRNASer did not. Additionally, the seryl moiety of Ser-tRNASec is not required for enzyme recognition, as PSTK efficiently phosphorylated Thr-tRNASec.
Collapse
Affiliation(s)
- R Lynn Sherrer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | | | | |
Collapse
|
17
|
Förster C, Brauer ABE, Fürste JP, Betzel C, Weber M, Cordes F, Erdmann VA. Superposition of a tRNASer acceptor stem microhelix into the seryl-tRNA synthetase complex. Biochem Biophys Res Commun 2007; 362:415-8. [PMID: 17719008 DOI: 10.1016/j.bbrc.2007.07.178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 07/31/2007] [Indexed: 11/18/2022]
Abstract
Aminoacyl-tRNA synthetases catalyze the formation of aminoacyl-tRNAs. Seryl-tRNA synthetase is a class II synthetase, which depends on rather few and simple identity elements in tRNA(Ser) to determine the amino acid specificity. tRNA(Ser) acceptor stem microhelices can be aminoacylated with serine, which makes this part of the tRNA a valuable tool for investigating the structural motifs in a tRNA(Ser)-seryl-tRNA synthetase complex. A 1.8A-resolution tRNA(Ser) acceptor stem crystal structure was superimposed to a 2.9A-resolution crystal structure of a tRNA(Ser)-seryl-tRNA synthetase complex for a visualization of the binding environment of the tRNA(Ser) microhelix.
Collapse
MESH Headings
- Anticodon/chemistry
- Anticodon/metabolism
- Crystallization
- Crystallography, X-Ray
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/metabolism
- Serine-tRNA Ligase/chemistry
- Serine-tRNA Ligase/metabolism
Collapse
Affiliation(s)
- C Förster
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | | | | | | | | | | | | |
Collapse
|
18
|
Vasil'eva IA, Moor NA. Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition. BIOCHEMISTRY (MOSCOW) 2007; 72:247-63. [PMID: 17447878 DOI: 10.1134/s0006297907030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review summarizes results of numerous (mainly functional) studies that have been accumulated over recent years on the problem of tRNA recognition by aminoacyl-tRNA synthetases. Development and employment of approaches that use synthetic mutant and chimeric tRNAs have demonstrated general principles underlying highly specific interaction in different systems. The specificity of interaction is determined by a certain number of nucleotides and structural elements of tRNA (constituting the set of recognition elements or specificity determinants), which are characteristic of each pair. Crystallographic structures available for many systems provide the details of the molecular basis of selective interaction. Diversity and identity of biochemical functions of the recognition elements make substantial contribution to the specificity of such interactions.
Collapse
Affiliation(s)
- I A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | | |
Collapse
|
19
|
Abstract
At the time of its discovery four decades ago, the genetic code was viewed as the result of a "frozen accident." Our current knowledge of the translation process and of the detailed structure of its components highlights the roles of RNA structure (in mRNA and tRNA), RNA modification (in tRNA), and aminoacyl-tRNA synthetase diversity in the evolution of the genetic code. The diverse assortment of codon reassignments present in subcellular organelles and organisms of distinct lineages has 'thawed' the concept of a universal immutable code; it may not be accidental that out of more than 140 amino acids found in natural proteins, only two (selenocysteine and pyrrolysine) are known to have been added to the standard 20-member amino acid alphabet. The existence of phosphoseryl-tRNA (in the form of tRNACys and tRNASec) may presage the discovery of other cotranslationally inserted modified amino acids.
Collapse
Affiliation(s)
- Alexandre Ambrogelly
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
| | | | | |
Collapse
|
20
|
Hohn MJ, Park HS, O'Donoghue P, Schnitzbauer M, Söll D. Emergence of the universal genetic code imprinted in an RNA record. Proc Natl Acad Sci U S A 2006; 103:18095-100. [PMID: 17110438 PMCID: PMC1838712 DOI: 10.1073/pnas.0608762103] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The molecular basis of the genetic code manifests itself in the interaction of the aminoacyl-tRNA synthetases and their cognate tRNAs. The fundamental biological question regarding these enzymes' role in the evolution of the genetic code remains open. Here we probe this question in a system in which the same tRNA species is aminoacylated by two unrelated synthetases. Should this tRNA possess major identity elements common to both enzymes, this would favor a scenario where the aminoacyl-tRNA synthetases evolved in the context of preestablished tRNA identity, i.e., after the universal genetic code emerged. An experimental system is provided by the recently discovered O-phosphoseryl-tRNA synthetase (SepRS), which acylates tRNA(Cys) with phosphoserine (Sep), and the well known cysteinyl-tRNA synthetase, which charges the same tRNA with cysteine. We determined the identity elements of Methanocaldococcus jannaschii tRNA(Cys) in the aminoacylation reaction for the two Methanococcus maripaludis synthetases SepRS (forming Sep-tRNA(Cys)) and cysteinyl-tRNA synthetase (forming Cys-tRNA(Cys)). The major elements, the discriminator base and the three anticodon bases, are shared by both tRNA synthetases. An evolutionary analysis of archaeal, bacterial, and eukaryotic tRNA(Cys) sequences predicted additional SepRS-specific minor identity elements (G37, A47, and A59) and suggested the dominance of vertical inheritance for tRNA(Cys) from a single common ancestor. Transplantation of the identified identity elements into the Escherichia coli tRNA(Gly) scaffold endowed facile phosphoserylation activity on the resulting chimera. Thus, tRNA(Cys) identity is an ancient RNA record that depicts the emergence of the universal genetic code before the evolution of the modern aminoacylation systems.
Collapse
Affiliation(s)
| | - Hee-Sung Park
- Departments of *Molecular Biophysics and Biochemistry and
| | | | | | - Dieter Söll
- Departments of *Molecular Biophysics and Biochemistry and
- Chemistry, Yale University, New Haven, CT 06520-8114
- To whom correspondence should be addressed at:
Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, 266 Whitney Avenue, New Haven, CT 06520-8114. E-mail:
| |
Collapse
|
21
|
Geslain R, Aeby E, Guitart T, Jones TE, Castro de Moura M, Charrière F, Schneider A, Ribas de Pouplana L. Trypanosoma seryl-tRNA synthetase is a metazoan-like enzyme with high affinity for tRNASec. J Biol Chem 2006; 281:38217-25. [PMID: 17040903 DOI: 10.1074/jbc.m607862200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosomatids are important human pathogens that form a basal branch of eukaryotes. Their evolutionary history is still unclear as are many aspects of their molecular biology. Here we characterize essential components required for the incorporation of serine and selenocysteine into the proteome of Trypanosoma. First, the biological function of a putative Trypanosoma seryl-tRNA synthetase was characterized in vivo. Secondly, the molecular recognition by Trypanosoma seryl-tRNA synthetase of its cognate tRNAs was dissected in vitro. The cellular distribution of tRNA(Sec) was studied, and the catalytic constants of its aminoacylation were determined. These were found to be markedly different from those reported in other organisms, indicating that this reaction is particularly efficient in trypanosomatids. Our functional data were analyzed in the context of a new phylogenetic analysis of eukaryotic seryl-tRNA synthetases that includes Trypanosoma and Leishmania sequences. Our results show that trypanosomatid seryl-tRNA synthetases are functionally and evolutionarily more closely related to their metazoan homologous enzymes than to other eukaryotic enzymes. This conclusion is supported by sequence synapomorphies that clearly connect metazoan and trypanosomatid seryl-tRNA synthetases.
Collapse
Affiliation(s)
- Renaud Geslain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Institute for Research in Biomedicine, Barcelona, Barcelona Science Park, C/Samitier 1-5, Barcelona 08015, Catalonia, Spain
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Gruic-Sovulj I, Jaric J, Dulic M, Cindric M, Weygand-Durasevic I. Shuffling of discrete tRNASer regions reveals differently utilized identity elements in yeast and methanogenic archaea. J Mol Biol 2006; 361:128-39. [PMID: 16822522 DOI: 10.1016/j.jmb.2006.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 06/05/2006] [Accepted: 06/06/2006] [Indexed: 10/24/2022]
Abstract
Seryl-tRNA synthetases (SerRSs) from methanogenic archaea possess distinct evolutionary origin and show minimal sequence similarity with counterparts from bacteria, eukaryotes and other archaea. Here we show that SerRS from yeast Saccharomyces cerevisiae and archaeon Methanococcus maripaludis (ScSerRS and MmSerRS, respectively) display significantly different ability to serylate heterologous tRNA(Ser). Recognition in yeast was shown to be more stringent than in archaeon. While cross-aminoacylation of M. maripaludis tRNA(Ser) (MmtRNA(Ser)) by yeast SerRS barely occurs, yeast tRNA(Ser) (SctRNA(Ser)) was shown to be a good substrate for heterologous MmSerRS. To investigate the contribution of different tRNA regions for the recognition by yeast and archaeal SerRS, chimeric tRNAs bearing separated domains of SctRNA(Ser) in MmtRNA(Ser) framework were produced by in vitro transcription and subjected to kinetic and gel mobility shift analysis with both enzymes. Generally, the recognition in M. maripaludis seems to be relatively relaxed toward tertiary elements of tRNA(Ser) structure and relies on the direct recognition of identity nucleotides. On the other hand, expression of tRNA(Ser) identity elements in yeast seems to be more sensitive toward surrounding sequence context. In both systems variable arm of tRNA was recognized as a major identity region with a strong influence on SerRS:tRNA binding. Acceptor domain of SctRNA(Ser) was also shown to be important for serylation in yeast. We propose that cognate interactions between N-terminal domain of yeast SerRS and variable region of SctRNA(Ser) place the acceptor stem into the enzyme's active site and lead to increased affinity toward serine and efficient serylation of tRNA. The same effect was not observed in M. maripaludis. Unlike its yeast counterpart, MmSerRS forms only one type of covalent complex with MmtRNA(Ser), regardless of the tRNA/SerRS molar ratio. Stoichiometry of the complex, one tRNA per dimeric SerRS, was revealed by mass spectrometry. Our studies indicate that different SerRS:tRNA recognition mode is utilized by these two systems.
Collapse
Affiliation(s)
- Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
| | | | | | | | | |
Collapse
|
23
|
Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Söll D, Weygand-Durasevic I, Ban N. Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition. EMBO J 2006; 25:2498-509. [PMID: 16675947 PMCID: PMC1478180 DOI: 10.1038/sj.emboj.7601129] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Accepted: 04/11/2006] [Indexed: 11/09/2022] Open
Abstract
Methanogenic archaea possess unusual seryl-tRNA synthetase (SerRS), evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. The two types of SerRSs show only minimal sequence similarity, primarily within class II conserved motifs 1, 2 and 3. Here, we report a 2.5 A resolution crystal structure of the atypical methanogenic Methanosarcina barkeri SerRS and its complexes with ATP, serine and the nonhydrolysable seryl-adenylate analogue 5'-O-(N-serylsulfamoyl)adenosine. The structures reveal two idiosyncratic features of methanogenic SerRSs: a novel N-terminal tRNA-binding domain and an active site zinc ion. The tetra-coordinated Zn2+ ion is bound to three conserved protein ligands (Cys306, Glu355 and Cys461) and binds the amino group of the serine substrate. The absolute requirement of the metal ion for enzymatic activity was confirmed by mutational analysis of the direct zinc ion ligands. This zinc-dependent serine recognition mechanism differs fundamentally from the one employed by the bacterial-type SerRSs. Consequently, SerRS represents the only known aminoacyl-tRNA synthetase system that evolved two distinct mechanisms for the recognition of the same amino-acid substrate.
Collapse
Affiliation(s)
| | - Timm Maier
- Institute of Molecular Biology and Biophyscis, Swiss Federal Institute of Technology, ETH Zürich, ETH Hoenggerberg, Zürich, Switzerland
| | - Dragana Ahel
- Department of Chemistry, University of Zagreb, Zagreb, Croatia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Ivana Weygand-Durasevic
- Department of Chemistry, University of Zagreb, Zagreb, Croatia
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb 10 000, Croatia. Tel.: +385 1 460 6230; Fax: +385 1 460 6401; E-mail:
| | - Nenad Ban
- Institute of Molecular Biology and Biophyscis, Swiss Federal Institute of Technology, ETH Zürich, ETH Hoenggerberg, Zürich, Switzerland
- Institute of Molecular Biology and Biophyscis, Swiss Federal Institute of Technology, ETH Zurich, ETH Hoenggerberg, HPK Bld., Zurich 8093, Switzerland. Tel.: +41 1 633 27 85; Fax: +41 1 633 12 46; E-mail:
| |
Collapse
|
24
|
Sabina J, Söll D. The RNA-binding PUA domain of archaeal tRNA-guanine transglycosylase is not required for archaeosine formation. J Biol Chem 2006; 281:6993-7001. [PMID: 16407303 DOI: 10.1074/jbc.m512841200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial tRNA-guanine transglycosylase (TGT) replaces the G in position 34 of tRNA with preQ(1), the precursor to the modified nucleoside queuosine. Archaeal TGT, in contrast, substitutes preQ(0) for the G in position 15 of tRNA as the first step in archaeosine formation. The archaeal enzyme is about 60% larger than the bacterial protein; a carboxyl-terminal extension of 230 amino acids contains the PUA domain known to contact the four 3'-terminal nucleotides of tRNA. Here we show that the C-terminal extension of the enzyme is not required for the selection of G15 as the site of base exchange; truncated forms of Pyrococcus furiosus TGT retain their specificity for guanine exchange at position 15. Deletion of the PUA domain causes a 4-fold drop in the observed k(cat) (2.8 x 10(-3) s(-1)) and results in a 75-fold increased K(m) for tRNA(Asp)(1.2 x 10(-5) m) compared with full-length TGT. Mutations in tRNA(Asp) altering or abolishing interactions with the PUA domain can compete with wild-type tRNA(Asp) for binding to full-length and truncated TGT enzymes. Whereas the C-terminal domains do not appear to play a role in selection of the modification site, their relevance for enzyme function and their role in vivo remains to be discovered.
Collapse
Affiliation(s)
- Jeffrey Sabina
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | | |
Collapse
|
25
|
Chimnaronk S, Gravers Jeppesen M, Suzuki T, Nyborg J, Watanabe K. Dual-mode recognition of noncanonical tRNAs(Ser) by seryl-tRNA synthetase in mammalian mitochondria. EMBO J 2005; 24:3369-79. [PMID: 16163389 PMCID: PMC1276171 DOI: 10.1038/sj.emboj.7600811] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Accepted: 08/22/2005] [Indexed: 11/09/2022] Open
Abstract
The secondary structures of metazoan mitochondrial (mt) tRNAs(Ser) deviate markedly from the paradigm of the canonical cloverleaf structure; particularly, tRNA(Ser)(GCU) corresponding to the AGY codon (Y=U and C) is highly truncated and intrinsically missing the entire dihydrouridine arm. None of the mt serine isoacceptors possesses the elongated variable arm, which is the universal landmark for recognition by seryl-tRNA synthetase (SerRS). Here, we report the crystal structure of mammalian mt SerRS from Bos taurus in complex with seryl adenylate at an atomic resolution of 1.65 A. Coupling structural information with a tRNA-docking model and the mutagenesis studies, we have unraveled the key elements that establish tRNA binding specificity, differ from all other known bacterial and eukaryotic systems, are the characteristic extensions in both extremities, as well as a few basic residues residing in the amino-terminal helical arm of mt SerRS. Our data further uncover an unprecedented mechanism of a dual-mode recognition employed to discriminate two distinct 'bizarre' mt tRNAs(Ser) by alternative combination of interaction sites.
Collapse
Affiliation(s)
- Sarin Chimnaronk
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | | | - Tsutomu Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | - Jens Nyborg
- Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Kimitsuna Watanabe
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
- Present address: Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Biological Information Research Center, National Institute of Advanced Industrial Science & Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan. Tel.:+81 3 3599 8106; Fax: +81 3 5530 2064; E-mail:
| |
Collapse
|
26
|
Ahel D, Slade D, Mocibob M, Söll D, Weygand-Durasevic I. Selective inhibition of divergent seryl-tRNA synthetases by serine analogues. FEBS Lett 2005; 579:4344-8. [PMID: 16054140 DOI: 10.1016/j.febslet.2005.06.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Revised: 06/23/2005] [Accepted: 06/29/2005] [Indexed: 10/25/2022]
Abstract
Seryl-tRNA synthetases (SerRSs) fall into two distinct evolutionary groups of enzymes, bacterial and methanogenic. These two types of SerRSs display only minimal sequence similarity, primarily within the class II conserved motifs, and possess distinct modes of tRNA(Ser) recognition. In order to determine whether the two types of SerRSs also differ in their recognition of the serine substrate, we compared the sensitivity of the representative methanogenic and bacterial-type SerRSs to serine hydroxamate and two previously unidentified inhibitors, serinamide and serine methyl ester. Our kinetic data showed selective inhibition of the methanogenic SerRS by serinamide, suggesting a lack of mechanistic uniformity in serine recognition between the evolutionarily distinct SerRSs.
Collapse
Affiliation(s)
- Dragana Ahel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | | | | | | | | |
Collapse
|
27
|
Randau L, Pearson M, Söll D. The complete set of tRNA species in Nanoarchaeum equitans. FEBS Lett 2005; 579:2945-7. [PMID: 15893316 DOI: 10.1016/j.febslet.2005.04.051] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Accepted: 04/25/2005] [Indexed: 11/25/2022]
Abstract
The archaeal parasite Nanoarchaeum equitans was found to generate five tRNA species via a unique process requiring the assembly of seperate 5' and 3' tRNA halves [Randau, L., Munch, R., Hohn, M.J., Jahn, D. and Soll, D. (2005) Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Nature 433, 537-541]. Biochemical evidence was missing for one of the computationally-predicted, joined tRNAs designated as tRNA(Trp). Our RT-PCR and sequencing results identify this tRNA as tRNA(Lys) (CUU) joined at the alternative position between bases 30 and 31. We show that the intron-containing tRNA(Trp) was misidentified in the initial Nanoarchaeum equitans genome annotation [E. Waters et al. (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. USA 100, 12984-12988]. Along with a previously unidentified joined tRNA(Gln) (UUG), Nanoarchaeum equitans exhibits 44 tRNAs and is enabled to read all 61 sense codons. Features unique to this set of tRNA molecules are discussed.
Collapse
Affiliation(s)
- Lennart Randau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | | | | |
Collapse
|