1
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Brytan W, Shortall K, Duarte F, Soulimane T, Padrela L. Contribution of a C-Terminal Extension to the Substrate Affinity and Oligomeric Stability of Aldehyde Dehydrogenase from Thermus thermophilus HB27. Biochemistry 2024; 63:1075-1088. [PMID: 38602394 PMCID: PMC11080044 DOI: 10.1021/acs.biochem.3c00698] [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: 12/14/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
Aldehyde dehydrogenase enzymes (ALDHs) are widely studied for their roles in disease propagation and cell metabolism. Their use in biocatalysis applications, for the conversion of aldehydes to carboxylic acids, has also been recognized. Understanding the structural features and functions of both prokaryotic and eukaryotic ALDHs is key to uncovering novel applications of the enzyme and probing its role in disease propagation. The thermostable enzyme ALDHTt originating fromThermus thermophilus, strain HB27, possesses a unique extension of its C-terminus, which has been evolutionarily excluded from mesophilic counterparts and other thermophilic enzymes in the same genus. In this work, the thermophilic adaptation is studied by the expression and optimized purification of mutant ALDHTt-508, with a 22-amino acid truncation of the C-terminus. The mutant shows increased activity throughout production compared to native ALDHTt, indicating an opening of the active site upon C-terminus truncation and giving rationale into the evolutionary exclusion of the C-terminal extension from similar thermophilic and mesophilic ALDH proteins. Additionally, the C-terminus is shown to play a role in controlling substrate specificity of native ALDH, particularly in excluding catalysis of certain large and certain aromatic ortho-substituted aldehydes, as well as modulating the protein's pH tolerance by increasing surface charge. Dynamic light scattering and size-exclusion HPLC methods are used to show the role of the C-terminus in ALDHTt oligomeric stability at the cost of catalytic efficiency. Studying the aggregation rate of ALDHTt with and without a C-terminal extension leads to the conclusion that ALDHTt follows a monomolecular reaction aggregation mechanism.
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Affiliation(s)
- Wiktoria Brytan
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
| | - Kim Shortall
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
| | - Francisco Duarte
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
| | - Tewfik Soulimane
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
− The Science Foundation Ireland Research Centre for Pharmaceuticals, Limerick V94 T9PX,Ireland
| | - Luis Padrela
- Department
of Chemical Sciences, Bernal Institute,
University of Limerick, Limerick V94 T9PX, Ireland
- SSPC
− The Science Foundation Ireland Research Centre for Pharmaceuticals, Limerick V94 T9PX,Ireland
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2
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Hu QH, Huang Q, Wang ED. Crucial role of the C-terminal domain of Mycobacterium tuberculosis leucyl-tRNA synthetase in aminoacylation and editing. Nucleic Acids Res 2012; 41:1859-72. [PMID: 23268443 PMCID: PMC3561953 DOI: 10.1093/nar/gks1307] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The C-terminal extension of prokaryotic leucyl-tRNA synthetase (LeuRS) has been shown to make contacts with the tertiary structure base pairs of tRNA(Leu) as well as its long variable arm. However, the precise role of the flexibly linked LeuRS C-terminal domain (CTD) in aminoacylation and editing processes has not been clarified. In this study, we carried out aspartic acid scanning within the CTD of Mycobacterium tuberculosis LeuRS (MtbLeuRS) and studied the effects on tRNA(Leu)-binding capacity and enzymatic activity. Several critical residues were identified to impact upon the interactions between LeuRS and tRNA(Leu) due to their contributions in the maintenance of structural stability or a neutral interaction interface between the CTD platform and tRNA(Leu) elbow region. Moreover, we propose Arg921 as a crucial recognition site for the tRNA(Leu) long variable arm in aminoacylation and tRNA-dependent pre-transfer editing. We also show here the CTD flexibility conferred by Val910 in regulation of LeuRS-tRNA(Leu) interaction. Taken together, our results suggest the structural importance of the CTD in modulating precise interactions between LeuRS and tRNA(Leu) during the quality control of leucyl-tRNA(Leu) synthesis. This system for the investigation of the interactions between MtbLeuRS and tRNA(Leu) provides a platform for the development of novel antitubercular drugs.
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Affiliation(s)
- Qing-Hua Hu
- State Key Laboratory of Molecular Biology, Center for RNA research, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
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3
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Artero JB, Teixeira SCM, Mitchell EP, Kron MA, Forsyth VT, Haertlein M. Crystallization and preliminary X-ray diffraction analysis of human cytosolic seryl-tRNA synthetase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1521-4. [PMID: 21045311 PMCID: PMC3001664 DOI: 10.1107/s1744309110037346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 09/17/2010] [Indexed: 11/10/2022]
Abstract
Human cytosolic seryl-tRNA synthetase (hsSerRS) is responsible for the covalent attachment of serine to its cognate tRNA(Ser). Significant differences between the amino-acid sequences of eukaryotic, prokaryotic and archaebacterial SerRSs indicate that the domain composition of hsSerRS differs from that of its eubacterial and archaebacterial analogues. As a consequence of an N-terminal insertion and a C-terminal extra-sequence, the binding mode of tRNA(Ser) to hsSerRS is expected to differ from that in prokaryotes. Recombinant hsSerRS protein was purified to homogeneity and crystallized. Diffraction data were collected to 3.13 Å resolution. The structure of hsSerRS has been solved by the molecular-replacement method.
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Affiliation(s)
- Jean-Baptiste Artero
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Susana C. M. Teixeira
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Edward P. Mitchell
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
- ESRF, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Michael A. Kron
- Department of Medicine, Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - V. Trevor Forsyth
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Michael Haertlein
- Institut Laue–Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
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4
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Mocibob M, Weygand-Durasevic I. The proximal region of a noncatalytic eukaryotic seryl-tRNA synthetase extension is required for protein stability in vitro and in vivo. Arch Biochem Biophys 2008; 470:129-38. [DOI: 10.1016/j.abb.2007.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 11/17/2007] [Accepted: 11/19/2007] [Indexed: 11/25/2022]
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5
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Godinic V, Mocibob M, Rocak S, Ibba M, Weygand-Durasevic I. Peroxin Pex21p interacts with the C-terminal noncatalytic domain of yeast seryl-tRNA synthetase and forms a specific ternary complex with tRNA(Ser). FEBS J 2007; 274:2788-99. [PMID: 17451428 DOI: 10.1111/j.1742-4658.2007.05812.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The seryl-tRNA synthetase from Saccharomyces cerevisiae interacts with the peroxisome biogenesis-related factor Pex21p. Several deletion mutants of seryl-tRNA synthetase were constructed and inspected for their ability to interact with Pex21p in a yeast two-hybrid assay, allowing mapping of the synthetase domain required for complex assembly. Deletion of the 13 C-terminal amino acids abolished Pex21p binding to seryl-tRNA synthetase. The catalytic parameters of purified truncated seryl-tRNA synthetase, determined in the serylation reaction, were found to be almost identical to those of the native enzyme. In vivo loss of interaction with Pex21p was confirmed in vitro by coaffinity purification. These data indicate that the C-terminally appended domain of yeast seryl-tRNA synthetase does not participate in substrate binding, but instead is required for association with Pex21p. We further determined that Pex21p does not directly bind tRNA, and nor does it possess a tRNA-binding motif, but it instead participates in the formation of a specific ternary complex with seryl-tRNA synthetase and tRNA(Ser), strengthening the interaction of seryl-tRNA synthetase with its cognate tRNA(Ser).
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Affiliation(s)
- Vlatka Godinic
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
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6
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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.
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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
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7
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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.
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Affiliation(s)
- Dragana Ahel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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8
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Gruic-Sovulj I, Landeka I, Söll D, Weygand-Durasevic I. tRNA-dependent amino acid discrimination by yeast seryl-tRNA synthetase. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:5271-9. [PMID: 12392560 DOI: 10.1046/j.1432-1033.2002.03241.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ability of aminoacyl-tRNA synthetases to distinguish between similar amino acids is crucial for accurate translation of the genetic code. Saccharomyces cerevisiae seryl-tRNA synthetase (SerRS) employs tRNA-dependent recognition of its cognate amino acid serine [Lenhard, B., Filipic, S., Landeka, I., Skrtic, I., Söll, D. & Weygand-Durasevic, I. (1997) J. Biol. Chem.272, 1136-1141]. Here we show that dimeric SerRS enzyme complexed with one molecule of tRNASer is more specific and more efficient in catalyzing seryl-adenylate formation than the apoenzyme alone. Sequence-specific tRNA-protein interactions enhance discrimination of the amino acid substrate by yeast SerRS and diminish the misactivation of the structurally similar noncognate threonine. This may proceed via a tRNA-induced conformational change in the enzyme's active site. The 3'-terminal adenosine of tRNASer is not important in effecting the rearrangement of the serine binding site. Our results do not provide an indication for a readjustment of ATP binding in a tRNA-assisted manner. The stoichiometric analyses of the complexes between the enzyme and tRNASer revealed that two cognate tRNA molecules can be bound to dimeric SerRS, however, with very different affinities.
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Affiliation(s)
- Ita Gruic-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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9
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Rocak S, Landeka I, Weygand-Durasevic I. Identifying Pex21p as a protein that specifically interacts with yeast seryl-tRNA synthetase. FEMS Microbiol Lett 2002; 214:101-6. [PMID: 12204379 DOI: 10.1111/j.1574-6968.2002.tb11331.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The interaction of Saccharomyces cerevisiae seryl-tRNA synthetase (SerRS) with peroxin Pex21p was identified in a two-hybrid screen with SerRS as bait. This was confirmed by an in vitro binding assay with truncated Pex21p fused to glutathione S-transferase. Furthermore, purified Pex21p acts as an activator of yeast seryl-tRNA synthetase in aminoacylation in vitro, revealing the functional significance of the Pex21p-SerRS interaction. Pex21p is a protein involved in the peroxisome biogenesis [Purdue, P.E., Yang, X. and Lazarow, P.B., J. Cell Biol. 143 (1998) 1859-1869]. Since eukaryotic aminoacyl-tRNA synthetases are known to participate in assembles with other synthetases and non-synthetase proteins, we propose that this unusual interaction reflects another function of the peroxin.
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Affiliation(s)
- Sanda Rocak
- Department of Chemistry, Faculty of Science, University of Zagreb, Strossmayerov trg 14, Croatia
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10
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Rokov-Plavec J, Lesjak S, Landeka I, Mijakovic I, Weygand-Durasevic I. Maize seryl-tRNA synthetase: specificity of substrate recognition by the organellar enzyme. Arch Biochem Biophys 2002; 397:40-50. [PMID: 11747308 DOI: 10.1006/abbi.2001.2600] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In our study of seryl-tRNA formation in maize, we investigated the enzymes involved in serylation. Only two dissimilar seryl-tRNA synthetase (SerRS) cDNA clones were identified in the Zea mays EST (expressed sequence tag) databases. One encodes a seryl-tRNA synthetase, which presumably functions in the organelles (SerZMm), while the other synthetase product is more similar to eukaryotic cytosolic counterparts (SerZMc). The expression of SerZMm in Saccharomyces cerevisiae resulted in complementation of mutant respiratory phenotype, caused by a disruption of the nuclear gene, presumably encoding yeast mitochondrial seryl-tRNA synthetase (SerSCm). Purified mature SerZMm displays tRNA-assisted serine activation and aminoacylates maize mitochondrial and chloroplast tRNA(Ser) transcripts with similar efficiencies, raising the possibility that only two isoforms of seryl-tRNA synthetase may be sufficient to catalyze seryl-tRNA(Ser) formation in three cellular compartments of Zea mays. Phylogenetic analysis suggests that SerZMm is of mitochondrial origin.
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Affiliation(s)
- Jasmina Rokov-Plavec
- Department of Chemistry, Faculty of Science, University of Zagreb, Strossmayerov trg 14, 10000 Zagreb, Croatia
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11
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Galani K, Großhans H, Deinert K, Hurt EC, Simos G. The intracellular location of two aminoacyl-tRNA synthetases depends on complex formation with Arc1p. EMBO J 2001; 20:6889-98. [PMID: 11726524 PMCID: PMC125769 DOI: 10.1093/emboj/20.23.6889] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In yeast, two aminoacyl-tRNA synthetases, MetRS and GluRS, are associated with Arc1p. We have studied the mechanism of this complex formation and found that the non-catalytic N-terminally appended domains of MetRS and GluRS are necessary and sufficient for binding to Arc1p. Similarly, it is the N-terminal domain of Arc1p that contains distinct but overlapping binding sites for MetRS and GluRS. Localization of Arc1p, MetRS and GluRS in living cells using green fluorescent protein showed that these three proteins are cytoplasmic and largely excluded from the nucleus. However, when their assembly into a complex is inhibited, significant amounts of MetRS, GluRS and Arc1p can enter the nucleus. We suggest that the organization of aminoacyl-tRNA synthetases into a multimeric complex not only affects catalysis, but is also a means of segregating the tRNA- aminoacylation machinery mainly to the cytoplasmic compartment.
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Affiliation(s)
| | - Helge Großhans
- Biochemie-Zentrum Heidelberg (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
Present address: MCDB Department, KBT 940 Yale University, PO Box 208103, 266 Whitney Avenue, New Haven, CT 06520, USA Present address: Laboratory of Biochemistry, School of Medicine, University of Thessaly, 22 Papakiriazi str., 41222 Larissa, Greece Corresponding author e-mail:
| | | | | | - George Simos
- Biochemie-Zentrum Heidelberg (BZH), Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
Present address: MCDB Department, KBT 940 Yale University, PO Box 208103, 266 Whitney Avenue, New Haven, CT 06520, USA Present address: Laboratory of Biochemistry, School of Medicine, University of Thessaly, 22 Papakiriazi str., 41222 Larissa, Greece Corresponding author e-mail:
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12
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O'Sullivan JM, Mihr MJ, Santos MA, Tuite MF. Seryl-tRNA synthetase is not responsible for the evolution of CUG codon reassignment in Candida albicans. Yeast 2001; 18:313-22. [PMID: 11223940 DOI: 10.1002/1097-0061(20010315)18:4<313::aid-yea673>3.0.co;2-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A number of Candida species translate the standard leucine-CUG codon as serine using a novel ser-tRNA(CAG). This tRNA, which has an unusual anticodon stem-loop structure, has been implicated in the evolution of this codon reassignment. However, such a sense codon reassignment might also require a change in the specificity of the cognate aminoacyl tRNA-synthetase, in this case the ser-tRNA synthetase. Here we describe the cloning and sequence analysis of the C. albicans seryl aminoacyl-tRNA synthetase (CaSerRS) gene (CaSES1). The predicted CaSerRS sequence shows a significant level of amino acid identity to SerRs from other organisms and fully complements a S. cerevisiae SerRS null strain without any apparent defect in growth rate. This suggests that the SerRS recognizes and charges S. cerevisiae ser-tRNAs with similar efficiency to that of the S. cerevisiae SerRS. Using an antibody raised against CaSerRS, we also demonstrate the presence of SerRS in a range of Candida spp. showing CUG codon reassignment. We conclude that the key element in CUG reassigment in Candida spp. is the tRNA that decodes the CUG codon rather than a SerRS structural change. The nucleotide sequence of the CaSES1 gene has been deposited at GenBank under Accession No. AF290915.
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Affiliation(s)
- J M O'Sullivan
- Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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13
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Deinert K, Fasiolo F, Hurt EC, Simos G. Arc1p organizes the yeast aminoacyl-tRNA synthetase complex and stabilizes its interaction with the cognate tRNAs. J Biol Chem 2001; 276:6000-8. [PMID: 11069915 DOI: 10.1074/jbc.m008682200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic aminoacyl-tRNA synthetases, in contrast to their prokaryotic counterparts, are often part of high molecular weight complexes. In yeast, two enzymes, the methionyl- and glutamyl-tRNA synthetases associate in vivo with the tRNA-binding protein Arc1p. To study the assembly and function of this complex, we have reconstituted it in vitro from individually purified recombinant proteins. Our results show that Arc1p can readily bind to either or both of the two enzymes, mediating the formation of the respective binary or ternary complexes. Under competition conditions, Arc1p alone exhibits broad specificity and interacts with a defined set of tRNA species. Nevertheless, the in vitro reconstituted Arc1p-containing enzyme complexes can bind only to their cognate tRNAs and tighter than the corresponding monomeric enzymes. These results demonstrate that the organization of aminoacyl-tRNA synthetases with general tRNA-binding proteins into multimeric complexes can stimulate their catalytic efficiency and, therefore, offer a significant advantage to the eukaryotic cell.
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Affiliation(s)
- K Deinert
- Biochemie-Zentrum Heidelberg (BZH), University of Heidelberg, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
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14
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Landeka I, Filipic-Rocak S, Zinic B, Weygand-Durasevic I. Characterization of yeast seryl-tRNA synthetase active site mutants with improved discrimination against substrate analogues. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1480:160-70. [PMID: 11004561 DOI: 10.1016/s0167-4838(00)00066-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The involvement of amino acids within the motif 2 loop of Saccharomyces cerevisiae seryl-tRNA synthetase (SerRS) in serine and ATP binding was demonstrated previously [B. Lenhard et al., J. Biol. Chem. 272 (1997) 1136-1141]. In our attempt to analyze the structural basis for the substrate specificity and to explore further the catalytic mechanism employed by S. cerevisiae SerRS, two new active site mutants, SerRS11 and SerRS12, were constructed. The catalytic effects of amino acid replacement at positions Lys287, Asp288 and Ala289 with purified wild-type and mutant seryl-tRNA synthetases were tested. The alteration of these semi-conserved amino acids interferes with tRNA-dependent optimization of serine recognition. Additionally, mutated enzymes SerRS11 (Lys287Thr, Asp288Tyr, Ala289Val) and SerRS12 (Lys287Arg) are less sensitive to inhibition by two competitive inhibitors: serine hydroxamate, an analogue of serine, and 5'-O-[N-(L-seryl)-sulfamoyl]adenosine, a stable analogue of aminoacyl adenylate, than the wild-type enzyme. SerRS mutants also display different activation kinetics for serine and serine hydroxamate, indicating that specificity toward the substrates is modulated by amino acid replacement in the motif 2 loop.
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Affiliation(s)
- I Landeka
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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15
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Kim T, Park SG, Kim JE, Seol W, Ko YG, Kim S. Catalytic peptide of human glutaminyl-tRNA synthetase is essential for its assembly to the aminoacyl-tRNA synthetase complex. J Biol Chem 2000; 275:21768-72. [PMID: 10801842 DOI: 10.1074/jbc.m002404200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human glutaminyl-tRNA synthetase (QRS) is one of several mammalian aminoacyl-tRNA synthetases (ARSs) that form a macromolecular protein complex. To understand the mechanism of QRS targeting to the multi-ARS complex, we analyzed both exogenous and endogenous QRSs by immunoprecipitation after overexpression of various Myc-tagged QRS mutants in human embryonic kidney 293 cells. Whereas a deletion mutant containing only the catalytic domain (QRS-C) was targeted to the multi-ARS complex, a mutant QRS containing only the N-terminal appended domain (QRS-N) was not. Deletion mapping showed that the ATP-binding Rossman fold was necessary for targeting of QRS to the multi-ARS complex. Furthermore, exogenous Myc-tagged QRS-C was co-immunoprecipitated with endogenous QRS. Since glutaminylation of tRNA was dramatically increased in cells transfected with the full-length QRS, but not with either QRS-C or QRS-N, both the QRS catalytic domain and the N-terminal appended domain were required for full aminoacylation activity. When QRS-C was overexpressed, arginyl-tRNA synthetase and p43 were released from the multi-ARS complex along with endogenous QRS, suggesting that the N-terminal appendix of QRS is required to keep arginyl-tRNA synthetase and p43 within the complex. Thus, the eukaryote-specific N-terminal appendix of QRS appears to stabilize the association of other components in the multi-ARS complex, whereas the C-terminal catalytic domain is necessary for QRS association with the multi-ARS complex.
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Affiliation(s)
- T Kim
- National Creative Research Initiatives Center for ARS Network, Sung Kyun Kwan University, Suwon, Kyunggido 440-746, Korea
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16
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Yokogawa T, Shimada N, Takeuchi N, Benkowski L, Suzuki T, Omori A, Ueda T, Nishikawa K, Spremulli LL, Watanabe K. Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase. J Biol Chem 2000; 275:19913-20. [PMID: 10764807 DOI: 10.1074/jbc.m908473199] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Animal mitochondrial protein synthesis systems contain two serine tRNAs (tRNAs(Ser)) corresponding to the codons AGY and UCN, each possessing an unusual secondary structure; the former lacks the entire D arm, and the latter has a slightly different cloverleaf structure. To elucidate whether these two tRNAs(Ser) can be recognized by the single animal mitochondrial seryl-tRNA synthetase (mt SerRS), we purified mt SerRS from bovine liver 2400-fold and showed that it can aminoacylate both of them. Specific interaction between mt SerRS and either of the tRNAs(Ser) was also observed in a gel retardation assay. cDNA cloning of bovine mt SerRS revealed that the deduced amino acid sequence of the enzyme contains 518 amino acid residues. The cDNAs of human and mouse mt SerRS were obtained by reverse transcription-polymerase chain reaction and expressed sequence tag data base searches. Elaborate inspection of primary sequences of mammalian mt SerRSs revealed diversity in the N-terminal domain responsible for tRNA recognition, indicating that the recognition mechanism of mammalian mt SerRS differs considerably from that of its prokaryotic counterpart. In addition, the human mt SerRS gene was found to be located on chromosome 19q13.1, to which the autosomal deafness locus DFNA4 is mapped.
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Affiliation(s)
- T Yokogawa
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagito, Gifu 501-1193, Japan
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17
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Krzyzaniak A, Siatecka M, Szyk A, Mucha P, Rekowski P, Kupryszewski G, Barciszewski J. Specific induction of Z-DNA conformation by a nuclear localization signal peptide of lupin glutaminyl tRNA synthetase. Mol Biol Rep 2000; 27:51-4. [PMID: 10939526 DOI: 10.1023/a:1007146516710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recently we have sequenced cDNA of plant glutaminyl-tRNA synthetase (GlnRS) from Lupinus luteus. At the N terminal part the protein contains a lysine rich polypeptide (KPKKKKEK), which is identical to a nuclear localization signal (NLS). In this paper we showed that two synthetic peptides (20 and 8 amino acids long), which were derived from lupin GlnRS containing the NLS sequence interact with DNA, but one of them (8aa long) changing its conformation from the B to the Z form. This observation clearly suggests that the presence of the NLS polypeptide in a leader sequence of GlnRS is required not only for protein transport into nucleus but also for regulation of a gene expression. This is the first report suggesting a role of the NLS signal peptide in structural changes of DNA.
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Affiliation(s)
- A Krzyzaniak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznañ
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18
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Bullard JM, Cai YC, Spremulli LL. Expression and characterization of the human mitochondrial leucyl-tRNA synthetase. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1490:245-58. [PMID: 10684970 DOI: 10.1016/s0167-4781(99)00240-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A cDNA clone encoding the human mitochondrial leucyl-tRNA synthetase (mtLeuRS) has been identified from the EST databases. Analysis of the protein encoded by this cDNA indicates that the protein is 903 amino acids in length and contains a mitochondrial signal sequence that is predicted to encompass the first 21 amino acids. Sequence analysis shows that this protein contains the characteristic motifs of class I aminoacyl-tRNA synthetases and regions of high homology to other mitochondrial and bacterial LeuRS proteins. The mature form of this protein has been cloned and expressed in Escherichia coli. Gel filtration indicates that human mtLeuRS is active in a monomeric state, with an apparent molecular mass of 101 kDa. The human mtLeuRS is capable of aminoacylating E. coli tRNA(Leu). Its activity is inhibited at high levels of either monovalent or divalent cations. K(M) and k(cat) values for ATP:PP(i) exchange and for the aminoacylation reaction have been determined.
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Affiliation(s)
- J M Bullard
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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Lenhard B, Orellana O, Ibba M, Weygand-Durasević I. tRNA recognition and evolution of determinants in seryl-tRNA synthesis. Nucleic Acids Res 1999; 27:721-9. [PMID: 9889265 PMCID: PMC148239 DOI: 10.1093/nar/27.3.721] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have analyzed the evolution of recognition of tRNAsSerby seryl-tRNA synthetases, and compared it to other type 2 tRNAs, which contain a long extra arm. In Eubacteria and chloroplasts this type of tRNA is restricted to three families: tRNALeu, tRNASer and tRNATyr. tRNALeuand tRNASer also carry a long extra arm in Archaea, Eukarya and all organelles with the exception of animal mitochondria. In contrast, the long extra arm of tRNATyr is far less conserved: it was drastically shortened after the separation of Archaea and Eukarya from Eubacteria, and it is also truncated in animal mitochondria. The high degree of phylo-genetic divergence in the length of tRNA variable arms, which are recognized by both class I and class II aminoacyl-tRNA synthetases, makes type 2 tRNA recognition an ideal system with which to study how tRNA discrimination may have evolved in tandem with the evolution of other components of the translation machinery.
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Affiliation(s)
- B Lenhard
- Department of Chemistry, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
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20
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Lenhard B, Praetorius-Ibba M, Filipic S, Söll D, Weygand-Durasevic I. C-terminal truncation of yeast SerRS is toxic for Saccharomyces cerevisiae due to altered mechanism of substrate recognition. FEBS Lett 1998; 439:235-40. [PMID: 9845329 DOI: 10.1016/s0014-5793(98)01376-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Like all other eukaryal cytosolic seryl-tRNA synthetase (SerRS) enzymes, Saccharomyces cerevisiae SerRS contains a C-terminal extension not found in the enzymes of eubacterial and archaeal origin. Overexpression of C-terminally truncated SerRS lacking the 20-amino acid appended domain (SerRSC20) is toxic to S. cerevisiae possibly because of altered substrate recognition. Compared to wild-type SerRS the truncated enzyme displays impaired tRNA-dependent serine recognition and is less stable. This suggests that the C-terminal peptide is important for the formation or maintenance of the enzyme structure optimal for substrate binding and catalysis.
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Affiliation(s)
- B Lenhard
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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21
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Simos G, Sauer A, Fasiolo F, Hurt EC. A conserved domain within Arc1p delivers tRNA to aminoacyl-tRNA synthetases. Mol Cell 1998; 1:235-42. [PMID: 9659920 DOI: 10.1016/s1097-2765(00)80024-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Two yeast enzymes that catalyze aminoacylation of tRNAs, MetRS and GluRS, form a complex with the protein Arc1p. We show here that association of Arc1p with MetRS and GluRS is required in vivo for effective recruitment of the corresponding cognate tRNAs within this complex. Arc1p is linked to MetRS and GluRS through its amino-terminal domain, while its middle and carboxy-terminal parts comprise a novel tRNA-binding domain. This results in high affinity binding of cognate tRNAs and increased aminoacylation efficiency. These findings suggest that Arc1p operates as a mobile, trans-acting tRNA-binding synthetase domain and provide new insight into the role of eukaryotic multimeric synthetase complexes.
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Affiliation(s)
- G Simos
- Biochemie-Zentrum Heidelberg, University of Heidelberg, Germany
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22
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Gruić-Sovulj I, Lüdemann HC, Hillenkamp F, Peter-Katalinić J. Detection of noncovalent tRNA.aminoacyl-tRNA synthetase complexes by matrix-assisted laser desorption/ionization mass spectrometry. J Biol Chem 1997; 272:32084-91. [PMID: 9405405 DOI: 10.1074/jbc.272.51.32084] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS) was used for the study of complexes formed by yeast seryl-tRNA synthetase (SerRS) and tyrosyl-tRNA synthetase (TyrRS) with tRNASer and tRNATyr. Cognate and noncognate complexes were easily distinguished due to a large mass difference between the two tRNAs. Both homodimeric synthetases gave MS spectra indicating intact desorption of dimers. The spectra of synthetase-cognate tRNA mixtures showed peaks of free components and peaks assigned to complexes. Noncognate complexes were also detected. In competition experiments, where both tRNA species were mixed with each enzyme only cognate alpha2.tRNA complexes were observed. Only cognate alpha2.tRNA2 complexes were detected with each enzyme. These results demonstrate that MALDI-MS can be used successfully for accurate mass and, thus, stoichiometry determination of specific high molecular weight noncovalent protein-nucleic acid complexes.
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Affiliation(s)
- I Gruić-Sovulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Strossmayerov trg 14, 10000 Zagreb, Croatia
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23
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Vincent C, Tarbouriech N, Härtlein M. Genomic organization, cDNA sequence, bacterial expression, and purification of human seryl-tRNA synthase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 250:77-84. [PMID: 9431993 DOI: 10.1111/j.1432-1033.1997.00077.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this paper, we report the cDNA sequence and deduced primary sequence for human cytosolic seryl-tRNA synthetase, and its expression in Escherichia coli. Two human brain cDNA clones of different origin, containing overlapping fragments coding for human seryl-tRNA synthetase were sequenced: HFBDN14 (fetal brain clone); and IB48 (infant brain clone). For both clones the 5' region of the cDNA was missing. This 5' region was obtained via PCR methods using a human brain 5' RACE-Ready cDNA library. The complete cDNA sequence allowed us to define primers to isolate and characterize the intron/exon structure of the serS gene, consisting of 10 introns and 11 exons. The introns' sizes range from 283 bp to more than 3000 bp and the size of the exons from 71 bp to 222 bp. The availability of the gene structure of the human enzyme could help to clarify some aspects of the molecular evolution of class-II aminoacyl-tRNA synthetases. The human seryl-tRNA synthetase has been expressed in E. coli, purified (95% pure as determined by SDS/PAGE) and kinetic parameters have been measured for its substrate tRNA. The human seryl-tRNA synthetase sequence (514 amino acid residues) shows significant sequence identity with seryl-tRNA synthetases from E. coli (25%), Saccharomyces cerevisiae (40%), Arabidopsis thaliana (41%) and Caenorhabditis elegans (60%). The partial sequences from published mammalian seryl-tRNA synthetases are very similar to the human enzyme (94% and 92% identity for mouse and Chinese hamster seryl-tRNA synthetase, respectively). Human seryl-tRNA synthetase, similar to several other class-I and class-II human aminoacyl-tRNA synthetases, is clearly related to its bacterial counterparts, independent of an additional C-terminal domain and a N-terminal insertion identified in the human enzyme. In functional studies, the enzyme aminoacylates calf liver tRNA and prokaryotic E. coli tRNA.
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Lenhard B, Filipić S, Landeka I, Skrtić I, Söll D, Weygand-Durasević I. Defining the active site of yeast seryl-tRNA synthetase. Mutations in motif 2 loop residues affect tRNA-dependent amino acid recognition. J Biol Chem 1997; 272:1136-41. [PMID: 8995413 DOI: 10.1074/jbc.272.2.1136] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The active site of class II aminoacyl-tRNA synthetases contains the motif 2 loop, which is involved in binding of ATP, amino acid, and the acceptor end of tRNA. In order to characterize the active site of Saccharomyces cerevisiae seryl-tRNA synthetase (SerRS), we performed in vitro mutagenesis of the portion of the SES1 gene encoding the motif 2 loop. Substitutions of amino acids conserved in the motif 2 loop of seryl-tRNA synthetases from other sources led to loss of complementation of a yeast SES1 null allele strain by the mutant yeast SES1 genes. Steady-state kinetic analyses of the purified mutant SerRS proteins revealed elevated Km values for serine and ATP, accompanied by decreases in kcat (as expected for replacement of residues involved in aminoacyl-adenylate formation). The differences in the affinities for serine and ATP, in the absence and presence of tRNA are consistent with the proposed conformational changes induced by positioning the 3'-end of tRNA into the active site, as observed recently in structural studies of Thermus thermophilus SerRS (Cusack, S., Yaremchuk, A., and Tukalo, M. (1996) EMBO J. 15, 2834-2842). The crystal structure of this moderately homologous prokaryotic counterpart of the yeast enzyme allowed us to produce a model of the yeast SerRS structure and to place the mutations in a structural context. In conjunction with structural data for T. thermophilus SerRS, the kinetic data presented here suggest that yeast seryl-tRNA synthetase displays tRNA-dependent amino acid recognition.
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Affiliation(s)
- B Lenhard
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
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