1
|
Lewis AM, Fallon T, Dittemore GA, Sheppard K. Evolution and variation in amide aminoacyl-tRNA synthesis. IUBMB Life 2024. [PMID: 38391119 DOI: 10.1002/iub.2811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
The amide proteogenic amino acids, asparagine and glutamine, are two of the twenty amino acids used in translation by all known life. The aminoacyl-tRNA synthetases for asparagine and glutamine, asparaginyl-tRNA synthetase and glutaminyl tRNA synthetase, evolved after the split in the last universal common ancestor of modern organisms. Before that split, life used two-step indirect pathways to synthesize asparagine and glutamine on their cognate tRNAs to form the aminoacyl-tRNA used in translation. These two-step pathways were retained throughout much of the bacterial and archaeal domains of life and eukaryotic organelles. The indirect routes use non-discriminating aminoacyl-tRNA synthetases (non-discriminating aspartyl-tRNA synthetase and non-discriminating glutamyl-tRNA synthetase) to misaminoacylate the tRNA. The misaminoacylated tRNA formed is then transamidated into the amide aminoacyl-tRNA used in protein synthesis by tRNA-dependent amidotransferases (GatCAB and GatDE). The enzymes and tRNAs involved assemble into complexes known as transamidosomes to help maintain translational fidelity. These pathways have evolved to meet the varied cellular needs across a diverse set of organisms, leading to significant variation. In certain bacteria, the indirect pathways may provide a means to adapt to cellular stress by reducing the fidelity of protein synthesis. The retention of these indirect pathways versus acquisition of asparaginyl-tRNA synthetase and glutaminyl tRNA synthetase in lineages likely involves a complex interplay of the competing uses of glutamine and asparagine beyond translation, energetic costs, co-evolution between enzymes and tRNA, and involvement in stress response that await further investigation.
Collapse
Affiliation(s)
- Alexander M Lewis
- Chemistry Department, Skidmore College, Saratoga Springs, New York, USA
| | - Trevor Fallon
- Chemistry Department, Skidmore College, Saratoga Springs, New York, USA
| | | | - Kelly Sheppard
- Chemistry Department, Skidmore College, Saratoga Springs, New York, USA
| |
Collapse
|
2
|
Behra PRK, Pettersson BMF, Ramesh M, Das S, Dasgupta S, Kirsebom LA. Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA. BMC Genomics 2022; 23:704. [PMID: 36243697 PMCID: PMC9569102 DOI: 10.1186/s12864-022-08927-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines. RESULTS We provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria. CONCLUSIONS Phages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.
Collapse
Affiliation(s)
- Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - B M Fredrik Pettersson
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Malavika Ramesh
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Sarbashis Das
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden.
| |
Collapse
|
3
|
Meng K, Chung CZ, Söll D, Krahn N. Unconventional genetic code systems in archaea. Front Microbiol 2022; 13:1007832. [PMID: 36160229 PMCID: PMC9499178 DOI: 10.3389/fmicb.2022.1007832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.
Collapse
Affiliation(s)
- Kexin Meng
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Christina Z. Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- *Correspondence: Natalie Krahn,
| |
Collapse
|
4
|
Mukai T, Amikura K, Fu X, Söll D, Crnković A. Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems. Front Genet 2022; 12:794509. [PMID: 35047015 PMCID: PMC8762117 DOI: 10.3389/fgene.2021.794509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/18/2021] [Indexed: 01/23/2023] Open
Abstract
Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.
Collapse
Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| |
Collapse
|
5
|
Abstract
Most bacteria employ a two-step indirect tRNA aminoacylation pathway for the synthesis of aminoacylated tRNAGln and tRNAAsn. The heterotrimeric enzyme GatCAB performs a critical amidotransferase reaction in the second step of this pathway. We have previously demonstrated in mycobacteria that this two-step pathway is error prone and translational errors contribute to adaptive phenotypes such as antibiotic tolerance. Furthermore, we identified clinical isolates of the globally important pathogen Mycobacterium tuberculosis with partial loss-of-function mutations in gatA, and demonstrated that these mutations result in high, specific rates of translational error and increased rifampin tolerance. However, the mechanisms by which these clinically derived mutations in gatA impact GatCAB function were unknown. Here, we describe biochemical and biophysical characterization of M. tuberculosis GatCAB, containing either wild-type gatA or one of two gatA mutants from clinical strains. We show that these mutations have minimal impact on enzymatic activity of GatCAB; however, they result in destabilization of the GatCAB complex as well as that of the ternary asparaginyl-transamidosome. Stabilizing complex formation with the solute trehalose increases specific translational fidelity of not only the mutant strains but also of wild-type mycobacteria. Therefore, our data suggest that alteration of GatCAB stability may be a mechanism for modulation of translational fidelity. IMPORTANCE Most bacteria use a two-step indirect pathway to aminoacylate tRNAGln and tRNAAsn, despite the fact that the indirect pathway consumes more energy and is error prone. We have previously shown that the higher protein synthesis errors from this indirect pathway in mycobacteria allow adaptation to hostile environments such as antibiotic treatment through generation of novel alternate proteins not coded by the genome. However, the precise mechanisms of how translational fidelity is tuned were not known. Here, we biochemically and biophysically characterize the critical enzyme of the Mycobacterium tuberculosis indirect pathway, GatCAB, as well as two mutant enzymes previously identified from clinical isolates that were associated with increased mistranslation. We show that the mutants dysregulate the pathway via destabilizing the enzyme complex. Importantly, increasing stability improves translational fidelity in both wild-type and mutant bacteria, demonstrating a mechanism by which mycobacteria may tune mistranslation rates.
Collapse
|
6
|
Ehrlich R, Davyt M, López I, Chalar C, Marín M. On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions? Front Mol Biosci 2021; 8:643701. [PMID: 33796548 PMCID: PMC8007984 DOI: 10.3389/fmolb.2021.643701] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Cellular tRNAs appear today as a diverse population of informative macromolecules with conserved general elements ensuring essential common functions and different and distinctive features securing specific interactions and activities. Their differential expression and the variety of post-transcriptional modifications they are subject to, lead to the existence of complex repertoires of tRNA populations adjusted to defined cellular states. Despite the tRNA-coding genes redundancy in prokaryote and eukaryote genomes, it is surprising to note the absence of genes coding specific translational-active isoacceptors throughout the phylogeny. Through the analysis of different releases of tRNA databases, this review aims to provide a general summary about those “missing tRNA genes.” This absence refers to both tRNAs that are not encoded in the genome, as well as others that show critical sequence variations that would prevent their activity as canonical translation adaptor molecules. Notably, while a group of genes are universally missing, others are absent in particular kingdoms. Functional information available allows to hypothesize that the exclusion of isodecoding molecules would be linked to: 1) reduce ambiguities of signals that define the specificity of the interactions in which the tRNAs are involved; 2) ensure the adaptation of the translational apparatus to the cellular state; 3) divert particular tRNA variants from ribosomal protein synthesis to other cellular functions. This leads to consider the “missing tRNA genes” as a source of putative non-canonical tRNA functions and to broaden the concept of adapter molecules in ribosomal-dependent protein synthesis.
Collapse
Affiliation(s)
- Ricardo Ehrlich
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay.,Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcos Davyt
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Ignacio López
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Cora Chalar
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Mónica Marín
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| |
Collapse
|
7
|
Did Amino Acid Side Chain Reactivity Dictate the Composition and Timing of Aminoacyl-tRNA Synthetase Evolution? Genes (Basel) 2021; 12:genes12030409. [PMID: 33809136 PMCID: PMC8001834 DOI: 10.3390/genes12030409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA synthetases (aaRSs). In this conceptual paper, we propose that the chemical reactivity of some amino acid side chains (e.g., lysine, cysteine, homocysteine, ornithine, homoserine, and selenocysteine) delayed or prohibited the emergence of the corresponding aaRSs and helped define the amino acids in the standard genetic code. We also consider the possibility that amino acid chemistry delayed the emergence of the glutaminyl- and asparaginyl-tRNA synthetases, neither of which are ubiquitous in extant organisms. We argue that fundamental chemical principles played critical roles in fixation of some aspects of the genetic code pre- and post-LUCA.
Collapse
|
8
|
Bouz G, Zitko J. Inhibitors of aminoacyl-tRNA synthetases as antimycobacterial compounds: An up-to-date review. Bioorg Chem 2021; 110:104806. [PMID: 33799176 DOI: 10.1016/j.bioorg.2021.104806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 11/26/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are crucial for the correct assembly of amino acids to cognate tRNA to maintain the fidelity of proteosynthesis. AaRSs have become a hot target in antimicrobial research. Three aaRS inhibitors are already in clinical practice; antibacterial mupirocin inhibits the synthetic site of isoleucyl-tRNA synthetase, antifungal tavaborole inhibits the editing site of leucyl-tRNA synthetase, and antiprotozoal halofuginone inhibits proline-tRNA synthetase. According to the World Health Organization, tuberculosis globally remains the leading cause of death from a single infectious agent. The rising incidence of multidrug-resistant tuberculosis is alarming and urges the search for new antimycobacterial compounds, preferably with yet unexploited mechanism of action. In this literature review, we have covered the up-to-date state in the field of inhibitors of mycobacterial aaRSs. The most studied aaRS in mycobacteria is LeuRS with at least four structural types of inhibitors, followed by TyrRS and AspRS. Inhibitors of MetRS, LysRS, and PheRS were addressed in a single significant study each. In many cases, the enzyme inhibition activity translated into micromolar or submicromolar inhibition of growth of mycobacteria. The most promising aaRS inhibitor as an antimycobacterial compound is GSK656 (compound 8), the only aaRS inhibitor in clinical trials (Phase IIa) for systemic use against tuberculosis. GSK656 is orally available and shares the oxaborole tRNA-trapping mechanism of action with antifungal tavaborole.
Collapse
Affiliation(s)
- Ghada Bouz
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy, Charles University
| | - Jan Zitko
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy, Charles University.
| |
Collapse
|
9
|
Cai RJ, Su HW, Li YY, Javid B. Forward Genetics Reveals a gatC-gatA Fusion Polypeptide Causes Mistranslation and Rifampicin Tolerance in Mycobacterium smegmatis. Front Microbiol 2020; 11:577756. [PMID: 33072044 PMCID: PMC7541841 DOI: 10.3389/fmicb.2020.577756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 12/26/2022] Open
Abstract
Most bacteria, including mycobacteria, utilize a two-step indirect tRNA aminoacylation pathway to generate correctly aminoacylated glutaminyl and asparaginyl tRNAs. This involves an initial step in which a non-discriminatory aminoacyl tRNA synthetase misacylates the tRNA, followed by a second step in which the essential amidotransferase, GatCAB, amidates the misacylated tRNA to its correct, cognate form. It had been previously demonstrated that mutations in gatA can mediate increased error rates specifically of glutamine to glutamate or asparagine to aspartate in protein synthesis. However, the role of mutations in gatB or gatC in mediating mistranslation are unknown. Here, we applied a forward genetic screen to enrich for mistranslating mutants of Mycobacterium smegmatis. The majority (57/67) of mutants had mutations in one of the gatCAB genes. Intriguingly, the most common mutation identified was an insertion in the 3' of gatC, abolishing its stop codon, and resulting in a fused GatC-GatA polypeptide. Modeling the effect of the fusion on GatCAB structure suggested a disruption of the interaction of GatB with the CCA-tail of the misacylated tRNA, suggesting a potential mechanism by which this mutation may mediate increased translational errors. Furthermore, we confirm that the majority of mutations in gatCAB that result in increased mistranslation also cause increased tolerance to rifampicin, although there was not a perfect correlation between mistranslation rates and degree of tolerance. Overall, our study identifies that mutations in all three gatCAB genes can mediate adaptive mistranslation and that mycobacteria are extremely tolerant to perturbation in the indirect tRNA aminoacylation pathway.
Collapse
Affiliation(s)
- Rong-Jun Cai
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Hong-Wei Su
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Yang-Yang Li
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Babak Javid
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China.,Beijing Advanced Innovation Center in Structural Biology, Beijing, China.,Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| |
Collapse
|
10
|
The phylogenetic distribution of the glutaminyl-tRNA synthetase and Glu-tRNA Gln amidotransferase in the fundamental lineages would imply that the ancestor of archaea, that of eukaryotes and LUCA were progenotes. Biosystems 2020; 196:104174. [PMID: 32535177 DOI: 10.1016/j.biosystems.2020.104174] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 12/21/2022]
Abstract
The function of the glutaminyl-tRNA synthetase and Glu-tRNAGln amidotransferase might be related to the origin of the genetic code because, for example, glutaminyl-tRNA synthetase catalyses the fundamental reaction that makes the genetic code. If the evolutionary stage of the origin of these two enzymes could be unambiguously identified, then the genetic code should still have been originating at that particular evolutionary stage because the fundamental reaction that makes the code itself was still evidently evolving. This would result in that particular evolutionary moment being attributed to the evolutionary stage of the progenote because it would have a relationship between the genotype and the phenotype not yet fully realized because the genetic code was precisely still originating. I then analyzed the distribution of the glutaminyl-tRNA synthetase and Glu-tRNAGln aminodotrasferase in the main phyletic lineages. Since in some cases the origin of these two enzymes can be related to the evolutionary stages of ancestors of archaea and eukaryotes, this would indicate these ancestors as progenotes because at that evolutionary moment the genetic code was evidently still evolving, thus realizing the definition of progenote. The conclusion that the ancestor of archaea and that of eukaryotes were progenotes would imply that even the last universal common ancestor (LUCA) was a progenote because it appeared, on the tree of life, temporally before these ancestors.
Collapse
|
11
|
Behra PRK, Pettersson BMF, Das S, Dasgupta S, Kirsebom LA. Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA. BMC Evol Biol 2019; 19:124. [PMID: 31215393 PMCID: PMC6582537 DOI: 10.1186/s12862-019-1447-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 05/27/2019] [Indexed: 02/07/2023] Open
Abstract
Background Mycobacteria occupy various ecological niches and can be isolated from soil, tap water and ground water. Several cause diseases in humans and animals. To get deeper insight into our understanding of mycobacterial evolution focusing on tRNA and non-coding (nc)RNA, we conducted a comparative genome analysis of Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clade members. Results Genome sizes for Mmuc- and Mneo-clade members vary between 5.4 and 6.5 Mbps with the complete MmucT (type strain) genome encompassing 6.1 Mbp. The number of tRNA genes range between 46 and 79 (including one pseudo tRNA gene) with 39 tRNA genes common among the members of these clades, while additional tRNA genes were probably acquired through horizontal gene transfer. Selected tRNAs and ncRNAs (RNase P RNA, tmRNA, 4.5S RNA, Ms1 RNA and 6C RNA) are expressed, and the levels for several of these are higher in stationary phase compared to exponentially growing cells. The rare tRNAIleTAT isoacceptor and two for mycobacteria novel ncRNAs: the Lactobacillales-derived GOLLD RNA and a homolog to the antisense Salmonella typhimurium phage Sar RNA, were shown to be present and expressed in certain Mmuc-clade members. Conclusions Phages, IS elements, horizontally transferred tRNA gene clusters, and phage-derived ncRNAs appears to have influenced the evolution of the Mmuc- and Mneo-clades. While the number of predicted coding sequences correlates with genome size, the number of tRNA coding genes does not. The majority of the tRNA genes in mycobacteria are transcribed mainly from single genes and the levels of certain ncRNAs, including RNase P RNA (essential for the processing of tRNAs), are higher at stationary phase compared to exponentially growing cells. We provide supporting evidence that Ms1 RNA represents a mycobacterial 6S RNA variant. The evolutionary routes for the ncRNAs RNase P RNA, tmRNA and Ms1 RNA are different from that of the core genes. Electronic supplementary material The online version of this article (10.1186/s12862-019-1447-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - B M Fredrik Pettersson
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Sarbashis Das
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden.
| |
Collapse
|
12
|
Chaudhuri S, Li L, Zimmerman M, Chen Y, Chen YX, Toosky MN, Gardner M, Pan M, Li YY, Kawaji Q, Zhu JH, Su HW, Martinot AJ, Rubin EJ, Dartois VA, Javid B. Kasugamycin potentiates rifampicin and limits emergence of resistance in Mycobacterium tuberculosis by specifically decreasing mycobacterial mistranslation. eLife 2018; 7:36782. [PMID: 30152756 PMCID: PMC6160228 DOI: 10.7554/elife.36782] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/27/2018] [Indexed: 12/23/2022] Open
Abstract
Most bacteria use an indirect pathway to generate aminoacylated glutamine and/or asparagine tRNAs. Clinical isolates of Mycobacterium tuberculosis with increased rates of error in gene translation (mistranslation) involving the indirect tRNA-aminoacylation pathway have increased tolerance to the first-line antibiotic rifampicin. Here, we identify that the aminoglycoside kasugamycin can specifically decrease mistranslation due to the indirect tRNA pathway. Kasugamycin but not the aminoglycoside streptomycin, can limit emergence of rifampicin resistance in vitro and increases mycobacterial susceptibility to rifampicin both in vitro and in a murine model of infection. Moreover, despite parenteral administration of kasugamycin being unable to achieve the in vitro minimum inhibitory concentration, kasugamycin alone was able to significantly restrict growth of Mycobacterium tuberculosis in mice. These data suggest that pharmacologically reducing mistranslation may be a novel mechanism for targeting bacterial adaptation. A bacterium called Mycobacterium tuberculosis is responsible for nearly 98% of cases of tuberculosis, which kills more people worldwide than any other infectious disease. This is due, in part, to the time it takes to cure individuals of the disease: patients have to take antibiotics continuously for at least six months to eradicate M. tuberculosis in the body. Bacteria, like all cells, make proteins using instructions contained within their genetic code. Cell components called ribosomes are responsible for translating these instructions and assembling the new proteins. Sometimes the ribosomes produce proteins that are slightly different to what the cell’s genetic code specified. These ‘incorrect proteins’ may not work properly so it is generally thought that cells try to prevent the mistakes from happening. However, scientists have recently found that the ribosomes in M. tuberculosis often assemble incorrect proteins. The more mistakes the ribosomes let happen, the more likely the bacteria are to survive when they are exposed to rifampicin, an antibiotic which is often used to treat tuberculosis infections. This suggests that it may be possible to make antibiotics more effective against M. tuberculosis by using them alongside a second drug that decreases the number of ribosome mistakes. Chaudhuri, Li et al. investigated the effect of a drug called kasugamycin on M. tuberculosis when the bacterium is cultured in the lab, and when it infects mice. The experiments found that Kasugamycin decreased the number of incorrect proteins assembled by the M. tuberculosis bacterium. When the drug was present, rifampicin also killed M. tuberculosis cells more efficiently. Furthermore, in the mice but not the cell cultures, kasugamycin alone was able to restrict the growth of the bacteria. This implies that M. tuberculosis cells may use ribosome mistakes as a strategy to survive in humans and other hosts. When it was given with rifampicin, kasugamycin caused several unwanted side effects in the mice, including weight loss; this may mean that the drug is currently not suitable to use in humans. Further studies may be able to find safer ways to decrease ribosome mistakes in M. tuberculosis, which could speed up the treatment of tuberculosis.
Collapse
Affiliation(s)
- Swarnava Chaudhuri
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Liping Li
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, United States
| | - Matthew Zimmerman
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, United States
| | - Yuemeng Chen
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Yu-Xiang Chen
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Melody N Toosky
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China.,Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Michelle Gardner
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Miaomiao Pan
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Yang-Yang Li
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Qingwen Kawaji
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Jun-Hao Zhu
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Hong-Wei Su
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Amanda J Martinot
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, United States
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| | - Veronique Anne Dartois
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, United States
| | - Babak Javid
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China.,Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, United States
| |
Collapse
|
13
|
Srivastava A, Asahara H, Zhang M, Zhang W, Liu H, Cui S, Jin Q, Chong S. Reconstitution of Protein Translation of Mycobacterium Reveals Functional Conservation and Divergence with the Gram-Negative Bacterium Escherichia coli. PLoS One 2016; 11:e0162020. [PMID: 27564552 PMCID: PMC5001721 DOI: 10.1371/journal.pone.0162020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022] Open
Abstract
Protein translation is essential for all bacteria pathogens. It has also been a major focus of structural and functional studies and an important target of antibiotics. Here we report our attempts to biochemically reconstitute mycobacterial protein translation in vitro from purified components. This mycobacterial translation system consists of individually purified recombinant translation factors from Mycobacterium tuberculosis (M. tuberculosis), purified tRNAs and ribosomes from Mycobacterium smegmatis (M. smegmatis), and an aminoacyl-tRNA synthetase (AARS) mixture from the cell-extract of M. smegmatis. We demonstrate that such mycobacterial translation system was efficient in in vitro protein synthesis, and enabled functional comparisons of translational components between the gram-positive Mycobacterium and the gram-negative E. coli. Although mycobacterial translation factors and ribosomes were highly compatible with their E. coli counterparts, M. smegmatis tRNAs were not properly charged by the E. coli AARSs to allow efficient translation of a reporter. In contrast, both E. coli and M. smegmatis tRNAs exhibited similar activity with the semi-purified M. smegmatis AARSs mixture for in vitro translation. We further demonstrated the use of both mycobacterial and E. coli translation systems as comparative in vitro assays for small-molecule antibiotics that target protein translation. While mycobacterial and E. coli translation were both inhibited at the same IC50 by the antibiotic spectinomycin, mycobacterial translation was preferentially inhibited by the antibiotic tetracycline, suggesting that there may be structural differences at the antibiotic binding sites between the ribosomes of Mycobacterium and E. coli. Our results illustrate an alternative approach for antibiotic discovery and functional studies of protein translation in mycobacteria and possibly other bacterial pathogens.
Collapse
Affiliation(s)
- Aashish Srivastava
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, United States of America
| | - Haruichi Asahara
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, United States of America
| | - Meng Zhang
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Weijia Zhang
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Haiying Liu
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Sheng Cui
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Qi Jin
- Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Shaorong Chong
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, United States of America
- * E-mail:
| |
Collapse
|
14
|
Pham VH, Maaroufi H, Levesque RC, Lapointe J. Cyclic peptides identified by phage display are competitive inhibitors of the tRNA-dependent amidotransferase of Helicobacter pylori. Peptides 2016; 79:8-15. [PMID: 26976271 DOI: 10.1016/j.peptides.2016.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 02/07/2023]
Abstract
In Helicobacter pylori, the heterotrimeric tRNA-dependent amidotransferase (GatCAB) is essential for protein biosynthesis because it catalyzes the conversion of misacylated Glu-tRNA(Gln) and Asp-tRNA(Asn) into Gln-tRNA(Gln) and Asn-tRNA(Asn), respectively. In this study, we used a phage library to identify peptide inhibitors of GatCAB. A library displaying loop-constrained heptapeptides was used to screen for phages binding to the purified GatCAB. To optimize the probability of obtaining competitive inhibitors of GatCAB with respect to its substrate Glu-tRNA(Gln), we used that purified substrate in the biopanning process of the phage-display technique to elute phages bound to GatCAB at the third round of the biopanning process. Among the eluted phages, we identified several that encode cyclic peptides rich in Trp and Pro that inhibit H. pylori GatCAB in vitro. Peptides P10 and P9 were shown to be competitive inhibitors of GatCAB with respect to its substrate Glu-tRNA(Gln), with Ki values of 126 and 392μM, respectively. The docking models revealed that the Trp residues of these peptides form π-π stacking interactions with Tyr81 of the synthetase active site, as does the 3'-terminal A76 of tRNA, supporting their competitive behavior with respect to Glu-tRNA(Gln) in the transamidation reaction. These peptides can be used as scaffolds in the search for novel antibiotics against the pathogenic bacteria that require GatCAB for Gln-tRNA(Gln) and/or Asn-tRNA(Asn) formation.
Collapse
Affiliation(s)
- Van Hau Pham
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada; The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec G1V 0A6, Canada.
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada; Département de Biologie Médicale, Faculté de Médicine, Université Laval, Québec G1V 0A6, Canada
| | - Jacques Lapointe
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada; The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec G1V 0A6, Canada.
| |
Collapse
|
15
|
Nair N, Raff H, Islam MT, Feen M, Garofalo DM, Sheppard K. The Bacillus subtilis and Bacillus halodurans Aspartyl-tRNA Synthetases Retain Recognition of tRNA(Asn). J Mol Biol 2016; 428:618-630. [PMID: 26804570 DOI: 10.1016/j.jmb.2016.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 12/19/2022]
Abstract
Synthesis of asparaginyl-tRNA (Asn-tRNA(Asn)) in bacteria can be formed either by directly ligating Asn to tRNA(Asn) using an asparaginyl-tRNA synthetase (AsnRS) or by synthesizing Asn on the tRNA. In the latter two-step indirect pathway, a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) attaches Asp to tRNA(Asn) and the amidotransferase GatCAB transamidates the Asp to Asn on the tRNA. GatCAB can be similarly used for Gln-tRNA(Gln) formation. Most bacteria are predicted to use only one route for Asn-tRNA(Asn) formation. Given that Bacillus halodurans and Bacillus subtilis encode AsnRS for Asn-tRNA(Asn) formation and Asn synthetases to synthesize Asn and GatCAB for Gln-tRNA(Gln) synthesis, their AspRS enzymes were thought to be specific for tRNA(Asp). However, we demonstrate that the AspRSs are non-discriminating and can be used with GatCAB to synthesize Asn. The results explain why B. subtilis with its Asn synthetase genes knocked out is still an Asn prototroph. Our phylogenetic analysis suggests that this may be common among Firmicutes and 30% of all bacteria. In addition, the phylogeny revealed that discrimination toward tRNA(Asp) by AspRS has evolved independently multiple times. The retention of the indirect pathway in B. subtilis and B. halodurans likely reflects the ancient link between Asn biosynthesis and its use in translation that enabled Asn to be added to the genetic code.
Collapse
Affiliation(s)
- Nilendra Nair
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA
| | - Hannah Raff
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA
| | | | - Melanie Feen
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA
| | - Denise M Garofalo
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA
| | - Kelly Sheppard
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA.
| |
Collapse
|
16
|
Pett W, Lavrov DV. Cytonuclear Interactions in the Evolution of Animal Mitochondrial tRNA Metabolism. Genome Biol Evol 2015; 7:2089-101. [PMID: 26116918 PMCID: PMC4558845 DOI: 10.1093/gbe/evv124] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The evolution of mitochondrial information processing pathways, including replication, transcription and translation, is characterized by the gradual replacement of mitochondrial-encoded proteins with nuclear-encoded counterparts of diverse evolutionary origins. Although the ancestral enzymes involved in mitochondrial transcription and replication have been replaced early in eukaryotic evolution, mitochondrial translation is still carried out by an apparatus largely inherited from the α-proteobacterial ancestor. However, variation in the complement of mitochondrial-encoded molecules involved in translation, including transfer RNAs (tRNAs), provides evidence for the ongoing evolution of mitochondrial protein synthesis. Here, we investigate the evolution of the mitochondrial translational machinery using recent genomic and transcriptomic data from animals that have experienced the loss of mt-tRNAs, including phyla Cnidaria and Ctenophora, as well as some representatives of all four classes of Porifera. We focus on four sets of mitochondrial enzymes that directly interact with tRNAs: Aminoacyl-tRNA synthetases, glutamyl-tRNA amidotransferase, tRNAIle lysidine synthetase, and RNase P. Our results support the observation that the fate of nuclear-encoded mitochondrial proteins is influenced by the evolution of molecules encoded in mitochondrial DNA, but in a more complex manner than appreciated previously. The data also suggest that relaxed selection on mitochondrial translation rather than coevolution between mitochondrial and nuclear subunits is responsible for elevated rates of evolution in mitochondrial translational proteins.
Collapse
Affiliation(s)
- Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University Present address: Laboratoire de Biométrie et Biologie Évolutive CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
| | - Dennis V Lavrov
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| |
Collapse
|
17
|
Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis. Proc Natl Acad Sci U S A 2014; 112:382-7. [PMID: 25548166 DOI: 10.1073/pnas.1423314112] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many prokaryotes lack a tRNA synthetase to attach asparagine to its cognate tRNA(Asn), and instead synthesize asparagine from tRNA(Asn)-bound aspartate. This conversion involves two enzymes: a nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) that forms Asp-tRNA(Asn), and a heterotrimeric amidotransferase GatCAB that amidates Asp-tRNA(Asn) to form Asn-tRNA(Asn) for use in protein synthesis. ND-AspRS, GatCAB, and tRNA(Asn) may assemble in an ∼400-kDa complex, known as the Asn-transamidosome, which couples the two steps of asparagine biosynthesis in space and time to yield Asn-tRNA(Asn). We report the 3.7-Å resolution crystal structure of the Pseudomonas aeruginosa Asn-transamidosome, which represents the most common machinery for asparagine biosynthesis in bacteria. We show that, in contrast to a previously described archaeal-type transamidosome, a bacteria-specific GAD domain of ND-AspRS provokes a principally new architecture of the complex. Both tRNA(Asn) molecules in the transamidosome simultaneously serve as substrates and scaffolds for the complex assembly. This architecture rationalizes an elevated dynamic and a greater turnover of ND-AspRS within bacterial-type transamidosomes, and possibly may explain a different evolutionary pathway of GatCAB in organisms with bacterial-type vs. archaeal-type Asn-transamidosomes. Importantly, because the two-step pathway for Asn-tRNA(Asn) formation evolutionarily preceded the direct attachment of Asn to tRNA(Asn), our structure also may reflect the mechanism by which asparagine was initially added to the genetic code.
Collapse
|
18
|
Alperstein A, Ulrich B, Garofalo DM, Dreisbach R, Raff H, Sheppard K. The predatory bacterium Bdellovibrio bacteriovorus aspartyl-tRNA synthetase recognizes tRNAAsn as a substrate. PLoS One 2014; 9:e110842. [PMID: 25338061 PMCID: PMC4206432 DOI: 10.1371/journal.pone.0110842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/20/2014] [Indexed: 11/29/2022] Open
Abstract
The predatory bacterium Bdellovibrio bacteriovorus preys on other Gram-negative bacteria and was predicted to be an asparagine auxotroph. However, despite encoding asparaginyl-tRNA synthetase and glutaminyl-tRNA synthetase, B. bacteriovorus also contains the amidotransferase GatCAB. Deinococcus radiodurans, and Thermus thermophilus also encode both of these aminoacyl-tRNA synthetases with GatCAB. Both also code for a second aspartyl-tRNA synthetase and use the additional aspartyl-tRNA synthetase with GatCAB to synthesize asparagine on tRNAAsn. Unlike those two bacteria, B. bacteriovorus encodes only one aspartyl-tRNA synthetase. Here we demonstrate the lone B. bacteriovorus aspartyl-tRNA synthetase catalyzes aspartyl-tRNAAsn formation that GatCAB can then amidate to asparaginyl-tRNAAsn. This non-discriminating aspartyl-tRNA synthetase with GatCAB thus provides B. bacteriovorus a second route for Asn-tRNAAsn formation with the asparagine synthesized in a tRNA-dependent manner. Thus, in contrast to a previous prediction, B. bacteriovorus codes for a biosynthetic route for asparagine. Analysis of bacterial genomes suggests a significant number of other bacteria may also code for both routes for Asn-tRNAAsn synthesis with only a limited number encoding a second aspartyl-tRNA synthetase.
Collapse
Affiliation(s)
- Ariel Alperstein
- Chemistry Department, Skidmore College, Saratoga Springs, New York, United States of America
| | - Brittany Ulrich
- Chemistry Department, Skidmore College, Saratoga Springs, New York, United States of America
| | - Denise M. Garofalo
- Chemistry Department, Skidmore College, Saratoga Springs, New York, United States of America
| | - Ruth Dreisbach
- Chemistry Department, Skidmore College, Saratoga Springs, New York, United States of America
| | - Hannah Raff
- Chemistry Department, Skidmore College, Saratoga Springs, New York, United States of America
| | - Kelly Sheppard
- Chemistry Department, Skidmore College, Saratoga Springs, New York, United States of America
- * E-mail:
| |
Collapse
|
19
|
Hadd A, Perona JJ. Coevolution of specificity determinants in eukaryotic glutamyl- and glutaminyl-tRNA synthetases. J Mol Biol 2014; 426:3619-33. [PMID: 25149203 DOI: 10.1016/j.jmb.2014.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/10/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022]
Abstract
The glutaminyl-tRNA synthetase (GlnRS) enzyme, which pairs glutamine with tRNA(Gln) for protein synthesis, evolved by gene duplication in early eukaryotes from a nondiscriminating glutamyl-tRNA synthetase (GluRS) that aminoacylates both tRNA(Gln) and tRNA(Glu) with glutamate. This ancient GluRS also separately differentiated to exclude tRNA(Gln) as a substrate, and the resulting discriminating GluRS and GlnRS further acquired additional protein domains assisting function in cis (the GlnRS N-terminal Yqey domain) or in trans (the Arc1p protein associating with GluRS). These added domains are absent in contemporary bacterial GlnRS and GluRS. Here, using Saccharomyces cerevisiae enzymes as models, we find that the eukaryote-specific protein domains substantially influence amino acid binding, tRNA binding and aminoacylation efficiency, but they play no role in either specific nucleotide readout or discrimination against noncognate tRNA. Eukaryotic tRNA(Gln) and tRNA(Glu) recognition determinants are found in equivalent positions and are mutually exclusive to a significant degree, with key nucleotides located adjacent to portions of the protein structure that differentiated during the evolution of archaeal nondiscriminating GluRS to GlnRS. These findings provide important corroboration for the evolutionary model and suggest that the added eukaryotic domains arose in response to distinctive selective pressures associated with the greater complexity of the eukaryotic translational apparatus. We also find that the affinity of GluRS for glutamate is significantly increased when Arc1p is not associated with the enzyme. This is consistent with the lower concentration of intracellular glutamate and the dissociation of the Arc1p:GluRS complex upon the diauxic shift to respiratory conditions.
Collapse
Affiliation(s)
- Andrew Hadd
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA
| | - John J Perona
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA; Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA.
| |
Collapse
|
20
|
On How Many Fundamental Kinds of Cells are Present on Earth: Looking for Phylogenetic Traits that Would Allow the Identification of the Primary Lines of Descent. J Mol Evol 2014; 78:313-20. [DOI: 10.1007/s00239-014-9626-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/21/2014] [Indexed: 11/26/2022]
|
21
|
Glutamyl-tRNAGln amidotransferase is essential for mammalian mitochondrial translation in vivo. Biochem J 2014; 460:91-101. [DOI: 10.1042/bj20131107] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have demonstrated that in mitochondria of mammalian cells the aminoacylation of tRNAGln is produced by an indirect pathway involving the enzyme glutamyl-tRNAGln amidotransferase. Misaminoacylated Glu-tRNAGln is rejected from the ribosomes maintaining the fidelity of the mitochondrial protein synthesis.
Collapse
|
22
|
Mladenova SR, Stein KR, Bartlett L, Sheppard K. Relaxed tRNA specificity of theStaphylococcus aureusaspartyl-tRNA synthetase enables RNA-dependent asparagine biosynthesis. FEBS Lett 2014; 588:1808-12. [DOI: 10.1016/j.febslet.2014.03.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 10/25/2022]
|
23
|
Zhou X, Wang E. Transfer RNA: a dancer between charging and mis-charging for protein biosynthesis. SCIENCE CHINA-LIFE SCIENCES 2013; 56:921-32. [PMID: 23982864 DOI: 10.1007/s11427-013-4542-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/13/2013] [Indexed: 01/17/2023]
Abstract
Transfer RNA plays a fundamental role in the protein biosynthesis as an adaptor molecule by functioning as a biological link between the genetic nucleotide sequence in the mRNA and the amino acid sequence in the protein. To perform its role in protein biosynthesis, it has to be accurately recognized by aminoacyl-tRNA synthetases (aaRSs) to generate aminoacyl-tRNAs (aa-tRNAs). The correct pairing between an amino acid with its cognate tRNA is crucial for translational quality control. Production and utilization of mis-charged tRNAs are usually detrimental for all the species, resulting in cellular dysfunctions. Correct aa-tRNAs formation is collectively controlled by aaRSs with distinct mechanisms and/or other trans-factors. However, in very limited instances, mis-charged tRNAs are intermediate for specific pathways or essential components for the translational machinery. Here, from the point of accuracy in tRNA charging, we review our understanding about the mechanism ensuring correct aa-tRNA generation. In addition, some unique mis-charged tRNA species necessary for the organism are also briefly described.
Collapse
Affiliation(s)
- Xiaolong Zhou
- Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | | |
Collapse
|
24
|
Lin Y, St. Maurice M. The structure of allophanate hydrolase from Granulibacter bethesdensis provides insights into substrate specificity in the amidase signature family. Biochemistry 2013; 52:690-700. [PMID: 23282241 PMCID: PMC3568674 DOI: 10.1021/bi301242m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Allophanate hydrolase (AH) catalyzes the hydrolysis of allophanate, an intermediate in atrazine degradation and urea catabolism pathways, to NH(3) and CO(2). AH belongs to the amidase signature family, which is characterized by a conserved block of 130 amino acids rich in Gly and Ser and a Ser-cis-Ser-Lys catalytic triad. In this study, the first structures of AH from Granulibacter bethesdensis were determined, with and without the substrate analogue malonate, to 2.2 and 2.8 Å, respectively. The structures confirm the identity of the catalytic triad residues and reveal an altered dimerization interface that is not conserved in the amidase signature family. The structures also provide insights into previously unrecognized substrate specificity determinants in AH. Two residues, Tyr(299) and Arg(307), are within hydrogen bonding distance of a carboxylate moiety of malonate. Both Tyr(299) and Arg(307) were mutated, and the resulting modified enzymes revealed >3 order of magnitude reductions in both catalytic efficiency and substrate stringency. It is proposed that Tyr(299) and Arg(307) serve to anchor and orient the substrate for attack by the catalytic nucleophile, Ser(172). The structure further suggests the presence of a unique C-terminal domain in AH. While this domain is conserved, it does not contribute to catalysis or to the structural integrity of the core domain, suggesting that it may play a role in mediating transient and specific interactions with the urea carboxylase component of urea amidolyase. Analysis of the AH active site architecture offers new insights into common determinants of catalysis and specificity among divergent members of the amidase signature family.
Collapse
Affiliation(s)
- Yi Lin
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Martin St. Maurice
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA,To whom correspondence should be addressed: Marquette University, Department of Biological Sciences, PO Box 1881, Milwaukee, WI 53201 Ph: 414 288 2087, Fax: 414 288 7357,
| |
Collapse
|
25
|
Perona JJ, Hadd A. Structural diversity and protein engineering of the aminoacyl-tRNA synthetases. Biochemistry 2012; 51:8705-29. [PMID: 23075299 DOI: 10.1021/bi301180x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRS) are the enzymes that ensure faithful transmission of genetic information in all living cells, and are central to the developing technologies for expanding the capacity of the translation apparatus to incorporate nonstandard amino acids into proteins in vivo. The 24 known aaRS families are divided into two classes that exhibit functional evolutionary convergence. Each class features an active site domain with a common fold that binds ATP, the amino acid, and the 3'-terminus of tRNA, embellished by idiosyncratic further domains that bind distal portions of the tRNA and enhance specificity. Fidelity in the expression of the genetic code requires that the aaRS be selective for both amino acids and tRNAs, a substantial challenge given the presence of structurally very similar noncognate substrates of both types. Here we comprehensively review central themes concerning the architectures of the protein structures and the remarkable dual-substrate selectivities, with a view toward discerning the most important issues that still substantially limit our capacity for rational protein engineering. A suggested general approach to rational design is presented, which should yield insight into the identities of the protein-RNA motifs at the heart of the genetic code, while also offering a basis for improving the catalytic properties of engineered tRNA synthetases emerging from genetic selections.
Collapse
Affiliation(s)
- John J Perona
- Department of Chemistry, Portland State University, Portland, Oregon 97207, United States.
| | | |
Collapse
|
26
|
Patten CL, Blakney AJC, Coulson TJD. Activity, distribution and function of indole-3-acetic acid biosynthetic pathways in bacteria. Crit Rev Microbiol 2012; 39:395-415. [PMID: 22978761 DOI: 10.3109/1040841x.2012.716819] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The capacity to produce the phytohormone indole-3-acetic acid (IAA) is widespread among bacteria that inhabit diverse environments such as soils, fresh and marine waters, and plant and animal hosts. Three major pathways for bacterial IAA synthesis have been characterized that remove the amino and carboxyl groups from the α-carbon of tryptophan via the intermediates indolepyruvate, indoleacetamide, or indoleacetonitrile; the oxidized end product IAA is typically secreted. The enzymes in these pathways often catabolize a broad range of substrates including aromatic amino acids and in some cases the branched chain amino acids. Moreover, expression of some of the genes encoding key IAA biosynthetic enzymes is induced by all three aromatic amino acids. The broad distribution and substrate specificity of the enzymes suggests a role for these pathways beyond plant-microbe interactions in which bacterial IAA has been best studied.
Collapse
Affiliation(s)
- Cheryl L Patten
- Department of Biology, University of New Brunswick , Fredericton, New Brunswick , Canada
| | | | | |
Collapse
|
27
|
Saad NY, Schiel B, Brayé M, Heap JT, Minton NP, Dürre P, Becker HD. Riboswitch (T-box)-mediated control of tRNA-dependent amidation in Clostridium acetobutylicum rationalizes gene and pathway redundancy for asparagine and asparaginyl-trnaasn synthesis. J Biol Chem 2012; 287:20382-94. [PMID: 22505715 DOI: 10.1074/jbc.m111.332304] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Analysis of the Gram-positive Clostridium acetobutylicum genome reveals an inexplicable level of redundancy for the genes putatively involved in asparagine (Asn) and Asn-tRNA(Asn) synthesis. Besides a duplicated set of gatCAB tRNA-dependent amidotransferase genes, there is a triplication of aspartyl-tRNA synthetase genes and a duplication of asparagine synthetase B genes. This genomic landscape leads to the suspicion of the incoherent simultaneous use of the direct and indirect pathways of Asn and Asn-tRNA(Asn) formation. Through a combination of biochemical and genetic approaches, we show that C. acetobutylicum forms Asn and Asn-tRNA(Asn) by tRNA-dependent amidation. We demonstrate that an entire transamidation pathway composed of aspartyl-tRNA synthetase and one set of GatCAB genes is organized as an operon under the control of a tRNA(Asn)-dependent T-box riboswitch. Finally, our results suggest that this exceptional gene redundancy might be interconnected to control tRNA-dependent Asn synthesis, which in turn might be involved in controlling the metabolic switch from acidogenesis to solventogenesis in C. acetobutylicum.
Collapse
Affiliation(s)
- Nizar Y Saad
- Unité Mixte de Recherche "Génétique Moléculaire, Génomique, Microbiologie," CNRS, Université de Strasbourg, 21 rue René Descartes, 67084 Strasbourg, France
| | | | | | | | | | | | | |
Collapse
|
28
|
Grant TD, Snell EH, Luft JR, Quartley E, Corretore S, Wolfley JR, Snell ME, Hadd A, Perona JJ, Phizicky EM, Grayhack EJ. Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase. Nucleic Acids Res 2011; 40:3723-31. [PMID: 22180531 PMCID: PMC3333875 DOI: 10.1093/nar/gkr1223] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In all organisms, aminoacyl tRNA synthetases covalently attach amino acids to their cognate tRNAs. Many eukaryotic tRNA synthetases have acquired appended domains, whose origin, structure and function are poorly understood. The N-terminal appended domain (NTD) of glutaminyl-tRNA synthetase (GlnRS) is intriguing since GlnRS is primarily a eukaryotic enzyme, whereas in other kingdoms Gln-tRNAGln is primarily synthesized by first forming Glu-tRNAGln, followed by conversion to Gln-tRNAGln by a tRNA-dependent amidotransferase. We report a functional and structural analysis of the NTD of Saccharomyces cerevisiae GlnRS, Gln4. Yeast mutants lacking the NTD exhibit growth defects, and Gln4 lacking the NTD has reduced complementarity for tRNAGln and glutamine. The 187-amino acid Gln4 NTD, crystallized and solved at 2.3 Å resolution, consists of two subdomains, each exhibiting an extraordinary structural resemblance to adjacent tRNA specificity-determining domains in the GatB subunit of the GatCAB amidotransferase, which forms Gln-tRNAGln. These subdomains are connected by an apparent hinge comprised of conserved residues. Mutation of these amino acids produces Gln4 variants with reduced affinity for tRNAGln, consistent with a hinge-closing mechanism proposed for GatB recognition of tRNA. Our results suggest a possible origin and function of the NTD that would link the phylogenetically diverse mechanisms of Gln-tRNAGln synthesis.
Collapse
Affiliation(s)
- Thomas D Grant
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase. Proc Natl Acad Sci U S A 2011; 108:20485-90. [PMID: 22158897 DOI: 10.1073/pnas.1117294108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The specificity of most aminoacyl-tRNA synthetases for an amino acid and cognate tRNA pair evolved before the divergence of the three domains of life. Glutaminyl-tRNA synthetase (GlnRS) evolved later and is derived from the archaeal-type nondiscriminating glutamyl-tRNA synthetase (GluRS), an enzyme with relaxed tRNA specificity capable of forming both Glu-tRNA(Glu) and Glu-tRNA(Gln). The archaea lack GlnRS and use a specialized amidotransferase to convert Glu-tRNA(Gln) to Gln-tRNA(Gln) needed for protein synthesis. We show that the Methanothermobacter thermautotrophicus GluRS is active toward tRNA(Glu) and the two tRNA(Gln) isoacceptors the organism encodes, but with a significant catalytic preference for tRNA(Gln2)(CUG). The less active tRNA(Gln1)(UUG) responds to the less common CAA codon for Gln. From a biochemical characterization of M. thermautotrophicus GluRS variants, we found that the evolution of tRNA specificity in GlnRS could be recapitulated by converting the M. thermautotrophicus GluRS to a tRNA(Gln) specific enzyme, solely through the addition of an acceptor stem loop present in bacterial GlnRS. One designed GluRS variant is also highly specific for the tRNA(Gln2)(CUG) isoacceptor, which responds to the CAG codon, and shows no activity toward tRNA(Gln1)(UUG). Because it is now possible to eliminate particular codons from the genome of Escherichia coli, additional codons will become available for genetic code engineering. Isoacceptor-specific aminoacyl-tRNA synthetases will enable the reassignment of more open codons while preserving accurate encoding of the 20 canonical amino acids.
Collapse
|
30
|
Globisch D, Pearson D, Hienzsch A, Brückl T, Wagner M, Thoma I, Thumbs P, Reiter V, Kneuttinger AC, Müller M, Sieber SA, Carell T. Systems-based analysis of modified tRNA bases. Angew Chem Int Ed Engl 2011; 50:9739-42. [PMID: 21882308 DOI: 10.1002/anie.201103229] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Indexed: 01/08/2023]
Affiliation(s)
- Daniel Globisch
- Center for Integrated Protein Science, Department of Chemistry, Ludwig Maximilian University Munich, Butenandtstrasse 5-13, 81377 Munich, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Globisch D, Pearson D, Hienzsch A, Brückl T, Wagner M, Thoma I, Thumbs P, Reiter V, Kneuttinger AC, Müller M, Sieber SA, Carell T. Systembasierte Analyse von modifizierten tRNA-Basen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103229] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
32
|
Huot JL, Fischer F, Corbeil J, Madore E, Lorber B, Diss G, Hendrickson TL, Kern D, Lapointe J. Gln-tRNAGln synthesis in a dynamic transamidosome from Helicobacter pylori, where GluRS2 hydrolyzes excess Glu-tRNAGln. Nucleic Acids Res 2011; 39:9306-15. [PMID: 21813455 PMCID: PMC3241645 DOI: 10.1093/nar/gkr619] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In many bacteria and archaea, an ancestral pathway is used where asparagine and glutamine are formed from their acidic precursors while covalently linked to tRNAAsn and tRNAGln, respectively. Stable complexes formed by the enzymes of these indirect tRNA aminoacylation pathways are found in several thermophilic organisms, and are called transamidosomes. We describe here a transamidosome forming Gln-tRNAGln in Helicobacter pylori, an ε-proteobacterium pathogenic for humans; this transamidosome displays novel properties that may be characteristic of mesophilic organisms. This ternary complex containing the non-canonical GluRS2 specific for Glu-tRNAGln formation, the tRNA-dependent amidotransferase GatCAB and tRNAGln was characterized by dynamic light scattering. Moreover, we observed by interferometry a weak interaction between GluRS2 and GatCAB (KD = 40 ± 5 µM). The kinetics of Glu-tRNAGln and Gln-tRNAGln formation indicate that conformational shifts inside the transamidosome allow the tRNAGln acceptor stem to interact alternately with GluRS2 and GatCAB despite their common identity elements. The integrity of this dynamic transamidosome depends on a critical concentration of tRNAGln, above which it dissociates into separate GatCAB/tRNAGln and GluRS2/tRNAGln complexes. Ester bond protection assays show that both enzymes display a good affinity for tRNAGln regardless of its aminoacylation state, and support a mechanism where GluRS2 can hydrolyze excess Glu-tRNAGln, ensuring faithful decoding of Gln codons.
Collapse
Affiliation(s)
- Jonathan L Huot
- Département de Biochimie, de Microbiologie et de Bio-informatique, PROTEO et IBIS, Université Laval, 1045 av de la Médecine, Québec, Québec, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Hurto RL. Unexpected functions of tRNA and tRNA processing enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 722:137-55. [PMID: 21915787 DOI: 10.1007/978-1-4614-0332-6_9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
tRNA and tRNA processing enzymes impact more than protein production. Studies have uncovered roles for tRNA in the regulation of transcription, translation and protein turnover. Induced by stress or as a programmed part of development, nonrandom tRNA fragments can guide mRNA cleavage, inhibit translation and promote morphological changes. Similarly, tRNA processing enzymes, such as RNaseP and tRNA aminoacyl-synthetases participate in tasks affecting more than tRNA function (i.e., mRNA function and cellular signaling). Unraveling the complexities of their functions will increase our understanding of how mutations associated with disease impact these functions and the downstream consequences. This chapter focuses on how tRNA and tRNA processing enzymes influence cellular function and RNA-infrastructure via pathways beyond the decoding activities that tRNA are known for.
Collapse
Affiliation(s)
- Rebecca L Hurto
- Department of Molecular Genetics, The Ohio State University, Columbus, USA.
| |
Collapse
|
34
|
Capes MD, Coker JA, Gessler R, Grinblat-Huse V, DasSarma SL, Jacob CG, Kim JM, DasSarma P, DasSarma S. The information transfer system of halophilic archaea. Plasmid 2010; 65:77-101. [PMID: 21094181 DOI: 10.1016/j.plasmid.2010.11.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/08/2010] [Accepted: 11/15/2010] [Indexed: 10/18/2022]
Abstract
Information transfer is fundamental to all life forms. In the third domain of life, the archaea, many of the genes functioning in these processes are similar to their eukaryotic counterparts, including DNA replication and repair, basal transcription, and translation genes, while many transcriptional regulators and the overall genome structure are more bacterial-like. Among halophilic (salt-loving) archaea, the genomes commonly include extrachromosomal elements, many of which are large megaplasmids or minichromosomes. With the sequencing of genomes representing ten different genera of halophilic archaea and the availability of genetic systems in two diverse models, Halobacterium sp. NRC-1 and Haloferax volcanii, a large number of genes have now been annotated, classified, and studied. Here, we review the comparative genomic, genetic, and biochemical work primarily aimed at the information transfer system of halophilic archaea, highlighting gene conservation and differences in the chromosomes and the large extrachromosomal elements among these organisms.
Collapse
Affiliation(s)
- Melinda D Capes
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Rodríguez-Hernández A, Bhaskaran H, Hadd A, Perona JJ. Synthesis of Glu-tRNA(Gln) by engineered and natural aminoacyl-tRNA synthetases. Biochemistry 2010; 49:6727-36. [PMID: 20617848 DOI: 10.1021/bi100886z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A protein engineering approach to delineating which distinct elements of homologous tRNA synthetase architectures are responsible for divergent RNA-amino acid pairing specificities is described. Previously, we constructed a hybrid enzyme in which 23 amino acids from the catalytic domain of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) were replaced with the corresponding residues of human glutamyl-tRNA synthetase (GluRS). The engineered hybrid (GlnRS S1/L1/L2) synthesizes Glu-tRNA(Gln) more than 10(4)-fold more efficiently than GlnRS. Detailed comparison of kinetic parameters between GlnRS S1/L1/L2 and the naturally occurring Methanothermobacter thermautotrophicus GluRS(ND), which is also capable of Glu-tRNA(Gln) synthesis, now shows that both k(cat) and K(m) for glutamate are recapitulated in the engineered enzyme, but that K(m) for tRNA is 200-fold higher. Thus, the simultaneous optimization of paired amino acid and tRNA binding sites found in a naturally occurring enzyme is not recapitulated in a hybrid that is successfully engineered for amino acid complementarity. We infer that the GlnRS architecture has differentiated to match only cognate amino acid-RNA pairs, and that the substrate selection functions do not operate independently of each other. Design and characterization of four additional hybrids identify further residues involved in improving complementarity for glutamate and in communicating between amino acid and tRNA binding sites. The robust catalytic function demonstrated in this engineered system offers a novel platform for exploring the stereochemical origins of coding as a property of the ancient Rossmann fold.
Collapse
Affiliation(s)
- Annia Rodríguez-Hernández
- Department of Chemistry and Biochemistry and Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
| | | | | | | |
Collapse
|
36
|
Nureki O, O'Donoghue P, Watanabe N, Ohmori A, Oshikane H, Araiso Y, Sheppard K, Söll D, Ishitani R. Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation. Nucleic Acids Res 2010; 38:7286-97. [PMID: 20601684 PMCID: PMC2978374 DOI: 10.1093/nar/gkq605] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The molecular basis of the genetic code relies on the specific ligation of amino acids to their cognate tRNA molecules. However, two pathways exist for the formation of Gln-tRNAGln. The evolutionarily older indirect route utilizes a non-discriminating glutamyl-tRNA synthetase (ND-GluRS) that can form both Glu-tRNAGlu and Glu-tRNAGln. The Glu-tRNAGln is then converted to Gln-tRNAGln by an amidotransferase. Since the well-characterized bacterial ND-GluRS enzymes recognize tRNAGlu and tRNAGln with an unrelated α-helical cage domain in contrast to the β-barrel anticodon-binding domain in archaeal and eukaryotic GluRSs, the mode of tRNAGlu/tRNAGln discrimination in archaea and eukaryotes was unknown. Here, we present the crystal structure of the Methanothermobacter thermautotrophicus ND-GluRS, which is the evolutionary predecessor of both the glutaminyl-tRNA synthetase (GlnRS) and the eukaryotic discriminating GluRS. Comparison with the previously solved structure of the Escherichia coli GlnRS-tRNAGln complex reveals the structural determinants responsible for specific tRNAGln recognition by GlnRS compared to promiscuous recognition of both tRNAs by the ND-GluRS. The structure also shows the amino acid recognition pocket of GluRS is more variable than that found in GlnRS. Phylogenetic analysis is used to reconstruct the key events in the evolution from indirect to direct genetic encoding of glutamine.
Collapse
Affiliation(s)
- Osamu Nureki
- Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Rampias T, Sheppard K, Söll D. The archaeal transamidosome for RNA-dependent glutamine biosynthesis. Nucleic Acids Res 2010; 38:5774-83. [PMID: 20457752 PMCID: PMC2943598 DOI: 10.1093/nar/gkq336] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Archaea make glutaminyl-tRNA (Gln-tRNAGln) in a two-step process; a non-discriminating glutamyl-tRNA synthetase (ND-GluRS) forms Glu-tRNAGln, while the heterodimeric amidotransferase GatDE converts this mischarged tRNA to Gln-tRNAGln. Many prokaryotes synthesize asparaginyl-tRNA (Asn-tRNAAsn) in a similar manner using a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) and the heterotrimeric amidotransferase GatCAB. The transamidosome, a complex of tRNA synthetase, amidotransferase and tRNA, was first described for the latter system in Thermus thermophilus [Bailly, M., Blaise, M., Lorber, B., Becker, H.D. and Kern, D. (2007) The transamidosome: a dynamic ribonucleoprotein particle dedicated to prokaryotic tRNA-dependent asparagine biosynthesis. Mol. Cell, 28, 228–239.]. Here, we show a similar complex for Gln-tRNAGln formation in Methanothermobacter thermautotrophicus that allows the mischarged Glu-tRNAGln made by the tRNA synthetase to be channeled to the amidotransferase. The association of archaeal ND-GluRS with GatDE (KD = 100 ± 22 nM) sequesters the tRNA synthetase for Gln-tRNAGln formation, with GatDE reducing the affinity of ND-GluRS for tRNAGlu by at least 13-fold. Unlike the T. thermophilus transamidosome, the archaeal complex does not require tRNA for its formation, is not stable through product (Gln-tRNAGln) formation, and has no major effect on the kinetics of tRNAGln glutamylation nor transamidation. The differences between the two transamidosomes may be a consequence of the fact that ND-GluRS is a class I aminoacyl-tRNA synthetase, while ND-AspRS belongs to the class II family.
Collapse
Affiliation(s)
- Theodoros Rampias
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | | | | |
Collapse
|
38
|
Nakamura A, Sheppard K, Yamane J, Yao M, Söll D, Tanaka I. Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition. Nucleic Acids Res 2010; 38:672-82. [PMID: 19906721 PMCID: PMC2811023 DOI: 10.1093/nar/gkp955] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In many prokaryotes the biosynthesis of the amide aminoacyl-tRNAs, Gln-tRNA(Gln) and Asn-tRNA(Asn), proceeds by an indirect route in which mischarged Glu-tRNA(Gln) or Asp-tRNA(Asn) is amidated to the correct aminoacyl-tRNA catalyzed by a tRNA-dependent amidotransferase (AdT). Two types of AdTs exist: bacteria, archaea and organelles possess heterotrimeric GatCAB, while heterodimeric GatDE occurs exclusively in archaea. Bacterial GatCAB and GatDE recognize the first base pair of the acceptor stem and the D-loop of their tRNA substrates, while archaeal GatCAB recognizes the tertiary core of the tRNA, but not the first base pair. Here, we present the crystal structure of the full-length Staphylococcus aureus GatCAB. Its GatB tail domain possesses a conserved Lys rich motif that is situated close to the variable loop in a GatCAB:tRNA(Gln) docking model. This motif is also conserved in the tail domain of archaeal GatCAB, suggesting this basic region may recognize the tRNA variable loop to discriminate Asp-tRNA(Asn) from Asp-tRNA(Asp) in archaea. Furthermore, we identified a 3(10) turn in GatB that permits the bacterial GatCAB to distinguish a U1-A72 base pair from a G1-C72 pair; the absence of this element in archaeal GatCAB enables the latter enzyme to recognize aminoacyl-tRNAs with G1-C72 base pairs.
Collapse
Affiliation(s)
- Akiyoshi Nakamura
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Faculty of Advanced Life Science, Hokkaido University, kita-10, nishi-8, Sapporo, Hokkaido, 060-0810, Japan and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Kelly Sheppard
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Faculty of Advanced Life Science, Hokkaido University, kita-10, nishi-8, Sapporo, Hokkaido, 060-0810, Japan and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Junji Yamane
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Faculty of Advanced Life Science, Hokkaido University, kita-10, nishi-8, Sapporo, Hokkaido, 060-0810, Japan and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Min Yao
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Faculty of Advanced Life Science, Hokkaido University, kita-10, nishi-8, Sapporo, Hokkaido, 060-0810, Japan and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Faculty of Advanced Life Science, Hokkaido University, kita-10, nishi-8, Sapporo, Hokkaido, 060-0810, Japan and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Isao Tanaka
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, Faculty of Advanced Life Science, Hokkaido University, kita-10, nishi-8, Sapporo, Hokkaido, 060-0810, Japan and Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA,*To whom correspondence should be addressed. Tel/Fax: +81 11 706 3221;
| |
Collapse
|
39
|
Bhatt TK, Kapil C, Khan S, Jairajpuri MA, Sharma V, Santoni D, Silvestrini F, Pizzi E, Sharma A. A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum. BMC Genomics 2009; 10:644. [PMID: 20042123 PMCID: PMC2813244 DOI: 10.1186/1471-2164-10-644] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 12/31/2009] [Indexed: 12/14/2022] Open
Abstract
Background Plasmodium parasites are causative agents of malaria which affects >500 million people and claims ~2 million lives annually. The completion of Plasmodium genome sequencing and availability of PlasmoDB database has provided a platform for systematic study of parasite genome. Aminoacyl-tRNA synthetases (aaRSs) are pivotal enzymes for protein translation and other vital cellular processes. We report an extensive analysis of the Plasmodium falciparum genome to identify and classify aaRSs in this organism. Results Using various computational and bioinformatics tools, we have identified 37 aaRSs in P. falciparum. Our key observations are: (i) fraction of proteome dedicated to aaRSs in P. falciparum is very high compared to many other organisms; (ii) 23 out of 37 Pf-aaRS sequences contain signal peptides possibly directing them to different cellular organelles; (iii) expression profiles of Pf-aaRSs vary considerably at various life cycle stages of the parasite; (iv) several PfaaRSs posses very unusual domain architectures; (v) phylogenetic analyses reveal evolutionary relatedness of several parasite aaRSs to bacterial and plants aaRSs; (vi) three dimensional structural modelling has provided insights which could be exploited in inhibitor discovery against parasite aaRSs. Conclusion We have identified 37 Pf-aaRSs based on our bioinformatics analysis. Our data reveal several unique attributes in this protein family. We have annotated all 37 Pf-aaRSs based on predicted localization, phylogenetics, domain architectures and their overall protein expression profiles. The sets of distinct features elaborated in this work will provide a platform for experimental dissection of this family of enzymes, possibly for the discovery of novel drugs against malaria.
Collapse
Affiliation(s)
- Tarun Kumar Bhatt
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Charrière F, O'Donoghue P, Helgadóttir S, Maréchal-Drouard L, Cristodero M, Horn EK, Söll D, Schneider A. Dual targeting of a tRNAAsp requires two different aspartyl-tRNA synthetases in Trypanosoma brucei. J Biol Chem 2009; 284:16210-16217. [PMID: 19386587 PMCID: PMC2713517 DOI: 10.1074/jbc.m109.005348] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 04/07/2009] [Indexed: 11/06/2022] Open
Abstract
The mitochondrion of the parasitic protozoon Trypanosoma brucei does not encode any tRNAs. This deficiency is compensated for by partial import of nearly all of its cytosolic tRNAs. Most trypanosomal aminoacyl-tRNA synthetases are encoded by single copy genes, suggesting the use of the same enzyme in the cytosol and in the mitochondrion. However, the T. brucei genome encodes two distinct genes for eukaryotic aspartyl-tRNA synthetase (AspRS), although the cell has a single tRNAAsp isoacceptor only. Phylogenetic analysis showed that the two T. brucei AspRSs evolved from a duplication early in kinetoplastid evolution and also revealed that eight other major duplications of AspRS occurred in the eukaryotic domain. RNA interference analysis established that both Tb-AspRS1 and Tb-AspRS2 are essential for growth and required for cytosolic and mitochondrial Asp-tRNAAsp formation, respectively. In vitro charging assays demonstrated that the mitochondrial Tb-AspRS2 aminoacylates both cytosolic and mitochondrial tRNAAsp, whereas the cytosolic Tb-AspRS1 selectively recognizes cytosolic but not mitochondrial tRNAAsp. This indicates that cytosolic and mitochondrial tRNAAsp, although derived from the same nuclear gene, are physically different, most likely due to a mitochondria-specific nucleotide modification. Mitochondrial Tb-AspRS2 defines a novel group of eukaryotic AspRSs with an expanded substrate specificity that are restricted to trypanosomatids and therefore may be exploited as a novel drug target.
Collapse
Affiliation(s)
- Fabien Charrière
- From the Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Patrick O'Donoghue
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8114
| | - Sunna Helgadóttir
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8114
| | - Laurence Maréchal-Drouard
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357 du CNRS, University of Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg Cedex, France
| | - Marina Cristodero
- From the Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Elke K Horn
- From the Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, New Haven, Connecticut 06520-8114
| | - André Schneider
- From the Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| |
Collapse
|
41
|
Wu J, Bu W, Sheppard K, Kitabatake M, Kwon ST, Söll D, Smith JL. Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme. J Mol Biol 2009; 391:703-16. [PMID: 19520089 DOI: 10.1016/j.jmb.2009.06.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 04/16/2009] [Accepted: 06/04/2009] [Indexed: 11/18/2022]
Abstract
Many bacteria form Gln-tRNA(Gln) and Asn-tRNA(Asn) by conversion of the misacylated Glu-tRNA(Gln) and Asp-tRNA(Asn) species catalyzed by the GatCAB amidotransferase in the presence of ATP and an amide donor (glutamine or asparagine). Here, we report the crystal structures of GatCAB from the hyperthermophilic bacterium Aquifex aeolicus, complexed with glutamine, asparagine, aspartate, ADP, or ATP. In contrast to the Staphylococcus aureus GatCAB, the A. aeolicus enzyme formed acyl-enzyme intermediates with either glutamine or asparagine, in line with the equally facile use by the amidotransferase of these amino acids as amide donors in the transamidation reaction. A water-filled ammonia channel is open throughout the length of the A. aeolicus GatCAB from the GatA active site to the synthetase catalytic pocket in the B-subunit. A non-catalytic Zn(2+) site in the A. aeolicus GatB stabilizes subunit contacts and the ammonia channel. Judged from sequence conservation in the known GatCAB sequences, the Zn(2+) binding motif was likely present in the primordial GatB/E, but became lost in certain lineages (e.g., S. aureus GatB). Two divalent metal binding sites, one permanent and the other transient, are present in the catalytic pocket of the A. aeolicus GatB. The two sites enable GatCAB to first phosphorylate the misacylated tRNA substrate and then amidate the activated intermediate to form the cognate products, Gln-tRNA(Gln) or Asn-tRNA(Asn).
Collapse
Affiliation(s)
- Jing Wu
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, 48109, USA
| | | | | | | | | | | | | |
Collapse
|
42
|
Park S, Ely RL. Whole-genome transcriptional and physiological responses ofNitrosomonas europaeato cyanide: Identification of cyanide stress response genes. Biotechnol Bioeng 2009; 102:1645-53. [DOI: 10.1002/bit.22194] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
43
|
Di Giulio M. An extension of the coevolution theory of the origin of the genetic code. Biol Direct 2008; 3:37. [PMID: 18775066 PMCID: PMC2538516 DOI: 10.1186/1745-6150-3-37] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 09/05/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids. However, this theory does not seem to attribute a role to the biosynthetic relationships between the earliest amino acids that evolved along the pathways of energetic metabolism. As a result, the coevolution theory is unable to clearly define the very earliest phases of genetic code origin. In order to remove this difficulty, I here suggest an extension of the coevolution theory that attributes a crucial role to the first amino acids that evolved along these biosynthetic pathways and to their biosynthetic relationships, even when defined by the non-amino acid molecules that are their precursors. RESULTS It is re-observed that the first amino acids to evolve along these biosynthetic pathways are predominantly those codified by codons of the type GNN, and this observation is found to be statistically significant. Furthermore, the close biosynthetic relationships between the sibling amino acids Ala-Ser, Ser-Gly, Asp-Glu, and Ala-Val are not random in the genetic code table and reinforce the hypothesis that the biosynthetic relationships between these six amino acids played a crucial role in defining the very earliest phases of genetic code origin. CONCLUSION All this leads to the hypothesis that there existed a code, GNS, reflecting the biosynthetic relationships between these six amino acids which, as it defines the very earliest phases of genetic code origin, removes the main difficulty of the coevolution theory. Furthermore, it is here discussed how this code might have naturally led to the code codifying only for the domains of the codons of precursor amino acids, as predicted by the coevolution theory. Finally, the hypothesis here suggested also removes other problems of the coevolution theory, such as the existence for certain pairs of amino acids with an unclear biosynthetic relationship between the precursor and product amino acids and the collocation of Ala between the amino acids Val and Leu belonging to the pyruvate biosynthetic family, which the coevolution theory considered as belonging to different biosyntheses. REVIEWERS This article was reviewed by Rob Knight, Paul Higgs (nominated by Laura Landweber), and Eugene Koonin.
Collapse
Affiliation(s)
- Massimo Di Giulio
- Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P. Castellino, 111, 80131 Naples, Napoli, Italy.
| |
Collapse
|
44
|
Sun FJ, Caetano-Anollés G. Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code. PLoS One 2008; 3:e2799. [PMID: 18665254 PMCID: PMC2474678 DOI: 10.1371/journal.pone.0002799] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Accepted: 07/02/2008] [Indexed: 01/06/2023] Open
Abstract
Transfer RNA (tRNA) molecules play vital roles during protein synthesis. Their acceptor arms are aminoacylated with specific amino acid residues while their anticodons delimit codon specificity. The history of these two functions has been generally linked in evolutionary studies of the genetic code. However, these functions could have been differentially recruited as evolutionary signatures were left embedded in tRNA molecules. Here we built phylogenies derived from the sequence and structure of tRNA, we forced taxa into monophyletic groups using constraint analyses, tested competing evolutionary hypotheses, and generated timelines of amino acid charging and codon discovery. Charging of Sec, Tyr, Ser and Leu appeared ancient, while specificities related to Asn, Met, and Arg were derived. The timelines also uncovered an early role of the second and then first codon bases, identified codons for Ala and Pro as the most ancient, and revealed important evolutionary take-overs related to the loss of the long variable arm in tRNA. The lack of correlation between ancestries of amino acid charging and encoding indicated that the separate discoveries of these functions reflected independent histories of recruitment. These histories were probably curbed by co-options and important take-overs during early diversification of the living world.
Collapse
Affiliation(s)
- Feng-Jie Sun
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| |
Collapse
|
45
|
Abstract
The accurate formation of cognate aminoacyl-transfer RNAs (aa-tRNAs) is essential for the fidelity of translation. Most amino acids are esterified onto their cognate tRNA isoacceptors directly by aa-tRNA synthetases. However, in the case of four amino acids (Gln, Asn, Cys and Sec), aminoacyl-tRNAs are made through indirect pathways in many organisms across all three domains of life. The process begins with the charging of noncognate amino acids to tRNAs by a specialized synthetase in the case of Cys-tRNA(Cys) formation or by synthetases with relaxed specificity, such as the non-discriminating glutamyl-tRNA, non-discriminating aspartyl-tRNA and seryl-tRNA synthetases. The resulting misacylated tRNAs are then converted to cognate pairs through transformation of the amino acids on the tRNA, which is catalyzed by a group of tRNA-dependent modifying enzymes, such as tRNA-dependent amidotransferases, Sep-tRNA:Cys-tRNA synthase, O-phosphoseryl-tRNA kinase and Sep-tRNA:Sec-tRNA synthase. The majority of these indirect pathways are widely spread in all domains of life and thought to be part of the evolutionary process.
Collapse
Affiliation(s)
- Jing Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | | | | |
Collapse
|
46
|
Sheppard K, Yuan J, Hohn MJ, Jester B, Devine KM, Söll D. From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucleic Acids Res 2008; 36:1813-25. [PMID: 18252769 PMCID: PMC2330236 DOI: 10.1093/nar/gkn015] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Aminoacyl-tRNAs (aa-tRNAs) are the essential substrates for translation. Most aa-tRNAs are formed by direct aminoacylation of tRNA catalyzed by aminoacyl-tRNA synthetases. However, a smaller number of aa-tRNAs (Asn-tRNA, Gln-tRNA, Cys-tRNA and Sec-tRNA) are made by synthesizing the amino acid on the tRNA by first attaching a non-cognate amino acid to the tRNA, which is then converted to the cognate one catalyzed by tRNA-dependent modifying enzymes. Asn-tRNA or Gln-tRNA formation in most prokaryotes requires amidation of Asp-tRNA or Glu-tRNA by amidotransferases that couple an amidase or an asparaginase to liberate ammonia with a tRNA-dependent kinase. Both archaeal and eukaryotic Sec-tRNA biosynthesis and Cys-tRNA synthesis in methanogens require O-phosophoseryl-tRNA formation. For tRNA-dependent Cys biosynthesis, O-phosphoseryl-tRNA synthetase directly attaches the amino acid to the tRNA which is then converted to Cys by Sep-tRNA: Cys-tRNA synthase. In Sec-tRNA synthesis, O-phosphoseryl-tRNA kinase phosphorylates Ser-tRNA to form the intermediate which is then modified to Sec-tRNA by Sep-tRNA:Sec-tRNA synthase. Complex formation between enzymes in the same pathway may protect the fidelity of protein synthesis. How these tRNA-dependent amino acid biosynthetic routes are integrated into overall metabolism may explain why they are still retained in so many organisms.
Collapse
Affiliation(s)
- Kelly Sheppard
- Department of Molecular Biophysics, Yale University, New Haven, CT 06520-8114, USA
| | | | | | | | | | | |
Collapse
|