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
|
Figuccia S, Degiorgi A, Ceccatelli Berti C, Baruffini E, Dallabona C, Goffrini P. Mitochondrial Aminoacyl-tRNA Synthetase and Disease: The Yeast Contribution for Functional Analysis of Novel Variants. Int J Mol Sci 2021; 22:ijms22094524. [PMID: 33926074 PMCID: PMC8123711 DOI: 10.3390/ijms22094524] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022] Open
Abstract
In most eukaryotes, mitochondrial protein synthesis is essential for oxidative phosphorylation (OXPHOS) as some subunits of the respiratory chain complexes are encoded by the mitochondrial DNA (mtDNA). Mutations affecting the mitochondrial translation apparatus have been identified as a major cause of mitochondrial diseases. These mutations include either heteroplasmic mtDNA mutations in genes encoding for the mitochondrial rRNA (mtrRNA) and tRNAs (mttRNAs) or mutations in nuclear genes encoding ribosomal proteins, initiation, elongation and termination factors, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases (mtARSs). Aminoacyl-tRNA synthetases (ARSs) catalyze the attachment of specific amino acids to their cognate tRNAs. Differently from most mttRNAs, which are encoded by mitochondrial genome, mtARSs are encoded by nuclear genes and then imported into the mitochondria after translation in the cytosol. Due to the extensive use of next-generation sequencing (NGS), an increasing number of mtARSs variants associated with large clinical heterogeneity have been identified in recent years. Being most of these variants private or sporadic, it is crucial to assess their causative role in the disease by functional analysis in model systems. This review will focus on the contributions of the yeast Saccharomyces cerevisiae in the functional validation of mutations found in mtARSs genes associated with human disorders.
Collapse
Affiliation(s)
| | | | | | | | - Cristina Dallabona
- Correspondence: (C.D.); (P.G.); Tel.: +39-0521-905600 (C.D.); +39-0521-905107 (P.G.)
| | - Paola Goffrini
- Correspondence: (C.D.); (P.G.); Tel.: +39-0521-905600 (C.D.); +39-0521-905107 (P.G.)
| |
Collapse
|
3
|
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
|
4
|
Abstract
Diverse models have been advanced for the evolution of the genetic code. Here, models for tRNA, aminoacyl-tRNA synthetase (aaRS) and genetic code evolution were combined with an understanding of EF-Tu suppression of tRNA 3rd anticodon position wobbling. The result is a highly detailed scheme that describes the placements of all amino acids in the standard genetic code. The model describes evolution of 6-, 4-, 3-, 2- and 1-codon sectors. Innovation in column 3 of the code is explained. Wobbling and code degeneracy are explained. Separate distribution of serine sectors between columns 2 and 4 of the code is described. We conclude that very little chaos contributed to evolution of the genetic code and that the pattern of evolution of aaRS enzymes describes a history of the evolution of the code. A model is proposed to describe the biological selection for the earliest evolution of the code and for protocell evolution.
Collapse
Affiliation(s)
- Lei Lei
- Department of Biology, University of New England, Biddeford, ME, USA
| | - Zachary Frome Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, E. Lansing, MI, USA
| |
Collapse
|
5
|
Vudhya Gowrisankar Y, Manne Mudhu S, Pasupuleti SK, Suthi S, Chaudhury A, Sarma PVGK. Staphylococcus aureus grown in anaerobic conditions exhibits elevated glutamine biosynthesis and biofilm units. Can J Microbiol 2020; 67:323-331. [PMID: 33136443 DOI: 10.1139/cjm-2020-0434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The enormous spread of Staphylococcus aureus infections through biofilms is a major concern in hospital-acquired infections. Biofilm formation by S. aureus on any surface is facilitated by adjusting its redox status. This organism is a facultative anaerobe shift more towards reductive conditions by enhancing nitrogen metabolism where glutamine synthesis plays a key role. Glutamine is synthesized by glutamine synthetase (GS) encoded by the glnA gene. The gene was amplified by PCR from the chromosomal DNA of S. aureus, sequenced (HQ329146.1), and cloned. The pure recombinant GS exhibited Km of 11.06 ± 0.05 mmol·L-1 for glutamate and 2.4 ± 0.03 mmol·L-1 for ATP. The glnA gene sequence showed a high degree of variability with its human counterpart, while it was highly conserved in bacteria. Structural analysis revealed that the GS structure of S. aureus showed close homology with other Gram-positive bacteria and exhibited a high degree of variation with Escherichia coli GS. In the present study, we observed the increased presence of GS activity in multidrug-resistant strains of S. aureus with elevated biofilm units, grown in brain heart infusion broth; among them methicillin-resistant strains S. aureus LMV 3, 4, and 5 showed higher biofilm units. All these results explain the important role of glutamine biosynthesis with elevated biofilm units in the pathogenesis of S. aureus.
Collapse
Affiliation(s)
- Yugandhar Vudhya Gowrisankar
- Microbial Genetics Laboratory, Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India.,Department of Cosmeceutics, College of Pharmacy, China Medical University, Taichung 40402, Taiwan (Republic of China)
| | - Sunitha Manne Mudhu
- Microbial Genetics Laboratory, Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India
| | - Santhosh Kumar Pasupuleti
- Microbial Genetics Laboratory, Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India.,Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 West Walnut Street, Indianapolis, IN 46202, USA
| | - Subbarayudu Suthi
- Microbial Genetics Laboratory, Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India
| | - Abhijit Chaudhury
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati 517507, Andhra Pradesh, India
| | | |
Collapse
|
6
|
Partial suppression of the respiratory defect of qrs1/her2 glutamyl-tRNA amidotransferase mutants by overexpression of the mitochondrial pentatricopeptide Msc6p. Curr Genet 2016; 62:607-17. [PMID: 26780366 DOI: 10.1007/s00294-016-0566-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 12/29/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
Abstract
Recently, a large body of evidences indicates the existence in the mitochondrial matrix of foci that contain different proteins involved in mitochondrial RNA metabolism. Some of these proteins have a pentatricopeptide repeat motif that constitutes their RNA-binding structures. Here we report that MSC6, a mitochondrial pentatricopeptide protein of unknown function, is a multi copy suppressor of mutations in QRS1/HER2 a component of the trimeric complex that catalyzes the transamidation of glutamyl-tRNAQ to glutaminyl-tRNAQ. This is an essential step in mitochondrial translation because of the lack of a specific mitochondrial aminoacyl glutaminyl-tRNA synthetase. MSC6 over-expression did not abolish translation of an aberrant variant form of Cox2p detected in QRS1/HER2 mutants, arguing against a suppression mechanism that bypasses Qrs1p function. A slight decrement of the mitochondrial translation capacity as well as diminished growth on respiratory carbon sources media for respiratory activity was observed in the msc6 null mutant. Additionally, the msc6 null mutant did not display any impairment in RNA transcription, processing or turnover. We concluded that Msc6p is a mitochondrial matrix protein and further studies are required to indicate the specific function of Msc6p in mitochondrial translation.
Collapse
|
7
|
Mailu BM, Li L, Arthur J, Nelson TM, Ramasamy G, Fritz-Wolf K, Becker K, Gardner MJ. Plasmodium Apicoplast Gln-tRNAGln Biosynthesis Utilizes a Unique GatAB Amidotransferase Essential for Erythrocytic Stage Parasites. J Biol Chem 2015; 290:29629-41. [PMID: 26318454 DOI: 10.1074/jbc.m115.655100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 01/25/2023] Open
Abstract
The malaria parasite Plasmodium falciparum apicoplast indirect aminoacylation pathway utilizes a non-discriminating glutamyl-tRNA synthetase to synthesize Glu-tRNA(Gln) and a glutaminyl-tRNA amidotransferase to convert Glu-tRNA(Gln) to Gln-tRNA(Gln). Here, we show that Plasmodium falciparum and other apicomplexans possess a unique heterodimeric glutamyl-tRNA amidotransferase consisting of GatA and GatB subunits (GatAB). We localized the P. falciparum GatA and GatB subunits to the apicoplast in blood stage parasites and demonstrated that recombinant GatAB converts Glu-tRNA(Gln) to Gln-tRNA(Gln) in vitro. We demonstrate that the apicoplast GatAB-catalyzed reaction is essential to the parasite blood stages because we could not delete the Plasmodium berghei gene encoding GatA in blood stage parasites in vivo. A phylogenetic analysis placed the split between Plasmodium GatB, archaeal GatE, and bacterial GatB prior to the phylogenetic divide between bacteria and archaea. Moreover, Plasmodium GatA also appears to have emerged prior to the bacterial-archaeal phylogenetic divide. Thus, although GatAB is found in Plasmodium, it emerged prior to the phylogenetic separation of archaea and bacteria.
Collapse
Affiliation(s)
- Boniface M Mailu
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Ling Li
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Jen Arthur
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Todd M Nelson
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Gowthaman Ramasamy
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Karin Fritz-Wolf
- the Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen 35392 Germany, and the Max-Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Katja Becker
- the Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen 35392 Germany, and
| | - Malcolm J Gardner
- From the Center for Infectious Disease Research, Seattle, Washington 98109, the Department of Global Health, University of Washington, Seattle, Washington 98195,
| |
Collapse
|
8
|
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: 2] [Impact Index Per Article: 0.2] [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
|
9
|
Mailu BM, Ramasamay G, Mudeppa DG, Li L, Lindner SE, Peterson MJ, DeRocher AE, Kappe SHI, Rathod PK, Gardner MJ. A nondiscriminating glutamyl-tRNA synthetase in the plasmodium apicoplast: the first enzyme in an indirect aminoacylation pathway. J Biol Chem 2013; 288:32539-32552. [PMID: 24072705 PMCID: PMC3820887 DOI: 10.1074/jbc.m113.507467] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/23/2013] [Indexed: 11/06/2022] Open
Abstract
The malaria parasite Plasmodium falciparum and related organisms possess a relict plastid known as the apicoplast. Apicoplast protein synthesis is a validated drug target in malaria because antibiotics that inhibit translation in prokaryotes also inhibit apicoplast protein synthesis and are sometimes used for malaria prophylaxis or treatment. We identified components of an indirect aminoacylation pathway for Gln-tRNA(Gln) biosynthesis in Plasmodium that we hypothesized would be essential for apicoplast protein synthesis. Here, we report our characterization of the first enzyme in this pathway, the apicoplast glutamyl-tRNA synthetase (GluRS). We expressed the recombinant P. falciparum enzyme in Escherichia coli, showed that it is nondiscriminating because it glutamylates both apicoplast tRNA(Glu) and tRNA(Gln), determined its kinetic parameters, and demonstrated its inhibition by a known bacterial GluRS inhibitor. We also localized the Plasmodium berghei ortholog to the apicoplast in blood stage parasites but could not delete the PbGluRS gene. These data show that Gln-tRNA(Gln) biosynthesis in the Plasmodium apicoplast proceeds via an essential indirect aminoacylation pathway that is reminiscent of bacteria and plastids.
Collapse
Affiliation(s)
- Boniface M Mailu
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | | | - Devaraja G Mudeppa
- the Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Ling Li
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Scott E Lindner
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Megan J Peterson
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Amy E DeRocher
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Stefan H I Kappe
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109,; the Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Pradipsinh K Rathod
- the Department of Chemistry, University of Washington, Seattle, Washington 98195-1700; the Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Malcolm J Gardner
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109,; the Department of Global Health, University of Washington, Seattle, Washington 98195.
| |
Collapse
|
10
|
Ferreira-Júnior JR, Bleicher L, Barros MH. Her2p molecular modeling, mutant analysis and intramitochondrial localization. Fungal Genet Biol 2013; 60:133-9. [DOI: 10.1016/j.fgb.2013.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 06/07/2013] [Accepted: 06/22/2013] [Indexed: 02/05/2023]
|
11
|
Kim J, Park W. Identification and characterization of genes regulated by AqsR, a LuxR-type regulator in Acinetobacter oleivorans DR1. Appl Microbiol Biotechnol 2013; 97:6967-78. [DOI: 10.1007/s00253-013-5006-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 05/09/2013] [Accepted: 05/17/2013] [Indexed: 12/25/2022]
|
12
|
Akochy PM, Lapointe J, Roy PH. Natural insertion of the bro-1 β-lactamase gene into the gatCAB operon affects Moraxella catarrhalis aspartyl-tRNAAsn amidotransferase activity. Microbiology (Reading) 2012; 158:2363-2371. [DOI: 10.1099/mic.0.060095-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Pierre-Marie Akochy
- Centre de Recherche en Infectiologie, CHUQ Pavillon CHUL, 2705 boul. Laurier, RC-709, QC G1V 4G2, Canada
- Institut Pasteur de Côte d’Ivoire, 01 BP 490 Abidjan, Côte d’Ivoire
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, QC G1V 0A6, Canada
| | - Jacques Lapointe
- Institut de biologie intégrative et des systèmes (IBIS), Pavillon Charles-Eugène-Marchand, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, QC G1V 0A6, Canada
| | - Paul H. Roy
- Centre de Recherche en Infectiologie, CHUQ Pavillon CHUL, 2705 boul. Laurier, RC-709, QC G1V 4G2, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, QC G1V 0A6, Canada
| |
Collapse
|
13
|
Kang J, Kuroyanagi S, Akisada T, Hagiwara Y, Tateno M. Unidirectional Mechanistic Valved Mechanisms for Ammonia Transport in GatCAB. J Chem Theory Comput 2012; 8:649-60. [PMID: 26596613 DOI: 10.1021/ct200387u] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glutamine amidotransferase CAB (GatCAB), a crucial enzyme involved in translational fidelity, catalyzes three reactions: (i) the glutaminase reaction to yield ammonia (NH3 or NH4(+)) from glutamine, (ii) the phosphorylation of Glu-tRNA(Gln), and (iii) the transamidase reaction to convert the phosphorylated Glu-tRNA(Gln) to Gln-tRNA(Gln). In the crystal structure of GatCAB, the two catalytic centers are far apart, and the presence of a hydrophilic channel to transport the molecules produced by the reaction (i) was proposed. We investigated the transport mechanisms of GatCAB by molecular dynamics (MD) simulations and free energy (PMF) calculations. In the MD simulations (in total ∼1.1 μs), the entrance of the previously proposed channel is closed, as observed in the crystal structure. Instead, a novel hydrophobic channel has been identified in this study: Since the newly identified entrance opened and closed repeatedly in the MD simulations, it may act as a gate. The calculated free energy difference revealed the significant preference of the newly identified gate/channel for NH3 transport (∼10(4)-fold). In contrast, with respect to NH4(+), the free energy barriers are significantly increased for both channels due to tight hydrogen-bonding with hydrophilic residues, which hinders efficient transport. The opening of the newly identified gate is modulated by Phe206, which acts as a "valve". For the backward flow of NH3, our PMF calculation revealed that the opening of the gate is hindered by Ala207, which acts as a mechanistic "stopper" against the motion of the "valve" (Phe206). This is the first report to elucidate the detailed mechanisms of unidirectional mechanistic valved transport inside proteins.
Collapse
Affiliation(s)
- Jiyoung Kang
- Graduate School of Pure and Applied Sciences, University of Tsukuba , Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8571, Japan
| | - Shigehide Kuroyanagi
- Graduate School of Pure and Applied Sciences, University of Tsukuba , Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8571, Japan
| | - Tomohiro Akisada
- Graduate School of Life Science, University of Hyogo , 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Yohsuke Hagiwara
- Graduate School of Pure and Applied Sciences, University of Tsukuba , Tennodai 1-1-1, Tsukuba Science City, Ibaraki 305-8571, Japan
| | - Masaru Tateno
- Graduate School of Life Science, University of Hyogo , 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| |
Collapse
|
14
|
Zhao L, Dewage SW, Bell MJ, Chang KM, Fatma S, Joshi N, Silva G, Cisneros GA, Hendrickson TL. The kinase activity of the Helicobacter pylori Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase is sensitive to distal mutations in its putative ammonia tunnel. Biochemistry 2012; 51:273-85. [PMID: 22229412 DOI: 10.1021/bi201143x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Helicobacter pylori (Hp) Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase (AdT) plays important roles in indirect aminoacylation and translational fidelity. AdT has two active sites, in two separate subunits. Kinetic studies have suggested that interdomain communication occurs between these subunits; however, this mechanism is not well understood. To explore domain-domain communication in AdT, we adapted an assay and optimized it to kinetically characterize the kinase activity of Hp AdT. This assay was applied to the analysis of a series of point mutations at conserved positions throughout the putative AdT ammonia tunnel that connects the two active sites. Several mutations that caused significant decreases in AdT's kinase activity (reduced by 55-75%) were identified. Mutations at Thr149 (37 Å distal to the GatB kinase active site) and Lys89 (located at the interface of GatA and GatB) were detrimental to AdT's kinase activity, suggesting that these mutations have disrupted interdomain communication between the two active sites. Models of wild-type AdT, a valine mutation at Thr149, and an arginine mutation at Lys89 were subjected to molecular dynamics simulations. A comparison of wild-type, T149V, and K89R AdT simulation results unmasks 59 common residues that are likely involved in connecting the two active sites.
Collapse
Affiliation(s)
- Liangjun Zhao
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
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: 18] [Impact Index Per Article: 1.4] [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
|
16
|
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: 22] [Impact Index Per Article: 1.7] [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
|
17
|
Barros MH, Rak M, Paulela JA, Tzagoloff A. Characterization of Gtf1p, the connector subunit of yeast mitochondrial tRNA-dependent amidotransferase. J Biol Chem 2011; 286:32937-47. [PMID: 21799017 DOI: 10.1074/jbc.m111.265371] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial GatCAB operon for tRNA-dependent amidotransferase (AdT) catalyzes the transamidation of mischarged glutamyl-tRNA(Gln) to glutaminyl-tRNA(Gln). Here we describe the phenotype of temperature-sensitive (ts) mutants of GTF1, a gene proposed to code for subunit F of mitochondrial AdT in Saccharomyces cerevisiae. The ts gtf1 mutants accumulate an electrophoretic variant of the mitochondrially encoded Cox2p subunit of cytochrome oxidase and an unstable form of the Atp8p subunit of the F(1)-F(0) ATP synthase that is degraded, thereby preventing assembly of the F(0) sector. Allotopic expression of recoded ATP8 and COX2 did not significantly improve growth of gtf1 mutants on respiratory substrates. However, ts gft1 mutants are partially rescued by overexpression of PET112 and HER2 that code for the yeast homologues of the catalytic subunits of bacterial AdT. Additionally, B66, a her2 point mutant has a phenotype similar to that of gtf1 mutants. These results provide genetic support for the essentiality, in vivo, of the GatF subunit of the heterotrimeric AdT that catalyzes formation of glutaminyl-tRNA(Gln) (Frechin, M., Senger, B., Brayé, M., Kern, D., Martin, R. P., and Becker, H. D. (2009) Genes Dev. 23, 1119-1130).
Collapse
Affiliation(s)
- Mario H Barros
- Department of Microbiology, University of São Paulo, 05508-900 São Paulo, Brazil
| | | | | | | |
Collapse
|
18
|
Blaise M, Fréchin M, Oliéric V, Charron C, Sauter C, Lorber B, Roy H, Kern D. Crystal structure of the archaeal asparagine synthetase: interrelation with aspartyl-tRNA and asparaginyl-tRNA synthetases. J Mol Biol 2011; 412:437-52. [PMID: 21820443 DOI: 10.1016/j.jmb.2011.07.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 07/19/2011] [Accepted: 07/21/2011] [Indexed: 11/28/2022]
Abstract
Asparagine synthetase A (AsnA) catalyzes asparagine synthesis using aspartate, ATP, and ammonia as substrates. Asparagine is formed in two steps: the β-carboxylate group of aspartate is first activated by ATP to form an aminoacyl-AMP before its amidation by a nucleophilic attack with an ammonium ion. Interestingly, this mechanism of amino acid activation resembles that used by aminoacyl-tRNA synthetases, which first activate the α-carboxylate group of the amino acid to form also an aminoacyl-AMP before they transfer the activated amino acid onto the cognate tRNA. In a previous investigation, we have shown that the open reading frame of Pyrococcus abyssi annotated as asparaginyl-tRNA synthetase (AsnRS) 2 is, in fact, an archaeal asparagine synthetase A (AS-AR) that evolved from an ancestral aspartyl-tRNA synthetase (AspRS). We present here the crystal structure of this AS-AR. The fold of this protein is similar to that of bacterial AsnA and resembles the catalytic cores of AspRS and AsnRS. The high-resolution structures of AS-AR associated with its substrates and end-products help to understand the reaction mechanism of asparagine formation and release. A comparison of the catalytic core of AS-AR with those of archaeal AspRS and AsnRS and with that of bacterial AsnA reveals a strong conservation. This study uncovers how the active site of the ancestral AspRS rearranged throughout evolution to transform an enzyme activating the α-carboxylate group into an enzyme that is able to activate the β-carboxylate group of aspartate, which can react with ammonia instead of tRNA.
Collapse
Affiliation(s)
- Mickaël Blaise
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, UPR 9002, 15 rue René Descartes, 67084 Strasbourg Cedex, France.
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Bhaskaran H, Perona JJ. Two-step aminoacylation of tRNA without channeling in Archaea. J Mol Biol 2011; 411:854-69. [PMID: 21726564 DOI: 10.1016/j.jmb.2011.06.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 06/21/2011] [Accepted: 06/22/2011] [Indexed: 10/18/2022]
Abstract
Catalysis of sequential reactions is often envisaged to occur by channeling of substrate between enzyme active sites without release into bulk solvent. However, while there are compelling physiological rationales for direct substrate transfer, proper experimental support for the hypothesis is often lacking, particularly for metabolic pathways involving RNA. Here, we apply transient kinetics approaches developed to study channeling in bienzyme complexes to an archaeal protein synthesis pathway featuring the misaminoacylated tRNA intermediate Glu-tRNA(Gln). Experimental and computational elucidation of a kinetic and thermodynamic framework for two-step cognate Gln-tRNA(Gln) synthesis demonstrates that the misacylating aminoacyl-tRNA synthetase (GluRS(ND)) and the tRNA-dependent amidotransferase (GatDE) function sequentially without channeling. Instead, rapid processing of the misacylated tRNA intermediate by GatDE and preferential elongation factor binding to the cognate Gln-tRNA(Gln) together permit accurate protein synthesis without formation of a binary protein-protein complex between GluRS(ND) and GatDE. These findings establish an alternate paradigm for protein quality control via two-step pathways for cognate aminoacyl-tRNA formation.
Collapse
Affiliation(s)
- Hari Bhaskaran
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106-9510, USA
| | | |
Collapse
|
20
|
Guth E, Thommen M, Weber-Ban E. Mycobacterial ubiquitin-like protein ligase PafA follows a two-step reaction pathway with a phosphorylated pup intermediate. J Biol Chem 2010; 286:4412-9. [PMID: 21081505 DOI: 10.1074/jbc.m110.189282] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Mycobacterium tuberculosis, the enzyme PafA is responsible for the activation and conjugation of the proteasome-targeting molecule Pup to protein substrates. As the proteasomal pathway has been shown to be vital to the persistence of M. tuberculosis, understanding the reaction mechanism of PafA is critical to the design of antituberculous agents. In this study, we have developed novel techniques to study the activity of PafA and have characterized fundamental features of the reaction mechanism. We show that PafA catalyzes a two-step reaction mechanism proceeding through a γ-glutamyl phosphate-mixed anhydride intermediate that is formed on the C-terminal glutamate of Pup before transfer of Pup to the substrate acceptor lysine. SDS-PAGE analysis of formation of the phosphorylated intermediate revealed that the rate of Pup activation matched the maximal steady-state rate of product formation in the overall reaction and suggested that Pup activation was rate-limiting when all substrates were present at saturating concentrations. Following activation, both ADP and the phosphorylated intermediate remained associated with the enzyme awaiting nucleophilic attack by a lysine residue of the target protein. The PafA reaction mechanism appeared to be noticeably biased toward the stable activation of Pup in the absence of additional substrate and required very low concentrations of ATP and Pup relative to other carboxylate-amine/ammonia ligase family members. The bona fide nucleophilic substrate PanB showed a 3 orders of magnitude stronger affinity than free lysine, promoting Pup conjugation to occur close to the rate limit of activation with physiologically relevant concentrations of substrate.
Collapse
Affiliation(s)
- Ethan Guth
- Institute of Molecular Biology & Biophysics, ETH Zurich, CH-8093 Zurich, Switzerland
| | | | | |
Collapse
|
21
|
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
|
22
|
tRNAs: cellular barcodes for amino acids. FEBS Lett 2009; 584:387-95. [PMID: 19903480 DOI: 10.1016/j.febslet.2009.11.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 10/29/2009] [Accepted: 11/05/2009] [Indexed: 01/06/2023]
Abstract
The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has also become increasingly clear that the ribosome is not the only destination to which tRNAs deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoacyl-tRNAs as substrates. Here we review examples of alternative functions for tRNA beyond translation, which together suggest that the role of tRNA is to deliver amino acids for a variety of processes that includes, but is not limited to, protein synthesis.
Collapse
|
23
|
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
|
24
|
Structure of a tRNA-dependent kinase essential for selenocysteine decoding. Proc Natl Acad Sci U S A 2009; 106:16215-20. [PMID: 19805283 DOI: 10.1073/pnas.0908861106] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Compared to bacteria, archaea and eukaryotes employ an additional enzyme for the biosynthesis of selenocysteine (Sec), the 21(st) natural amino acid (aa). An essential RNA-dependent kinase, O-phosphoseryl-tRNA(Sec) kinase (PSTK), converts seryl-tRNA(Sec) to O-phosphoseryl-tRNA(Sec), the immediate precursor of selenocysteinyl-tRNA(Sec). The sequence of Methanocaldococcus jannaschii PSTK (MjPSTK) suggests an N-terminal kinase domain (177 aa) followed by a presumed tRNA binding region (75 aa). The structures of MjPSTK complexed with ADP and AMPPNP revealed that this enzyme belongs to the P-loop kinase class, and that the kinase domain is closely related to gluconate kinase and adenylate kinase. ATP is bound by the P-loop domain (residues 11-18). Formed by antiparallel dimerization of two PSTK monomers, the enzyme structure shows a deep groove with positive electrostatic potential. Located in this groove is the enzyme's active site, which biochemical and genetic data suggest is composed of Asp-41, Arg-44, Glu-55, Tyr-82, Tyr-83, Met-86, and Met-132. Based on structural comparison with Escherichia coli adenylate kinase a docking model was generated that assigns these amino acids to the recognition of the terminal A76-Ser moieties of Ser-tRNA(Sec). The geometry and electrostatic environment of the groove in MjPSTK are perfectly complementary to the unusually long acceptor helix of tRNA(Sec).
Collapse
|
25
|
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
|
26
|
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
|
27
|
A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci U S A 2008; 105:8102-7. [PMID: 18535141 DOI: 10.1073/pnas.0801980105] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, "Candidatus Korarchaeum cryptofilum," which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.
Collapse
|
28
|
Hausmann CD, Ibba M. Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed. FEMS Microbiol Rev 2008; 32:705-21. [PMID: 18522650 DOI: 10.1111/j.1574-6976.2008.00119.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The accurate synthesis of proteins, dictated by the corresponding nucleotide sequence encoded in mRNA, is essential for cell growth and survival. Central to this process are the aminoacyl-tRNA synthetases (aaRSs), which provide amino acid substrates for the growing polypeptide chain in the form of aminoacyl-tRNAs. The aaRSs are essential for coupling the correct amino acid and tRNA molecules, but are also known to associate in higher order complexes with proteins involved in processes beyond translation. Multiprotein complexes containing aaRSs are found in all three domains of life playing roles in splicing, apoptosis, viral assembly, and regulation of transcription and translation. An overview of the complexes aaRSs form in all domains of life is presented, demonstrating the extensive network of connections between the translational machinery and cellular components involved in a myriad of essential processes beyond protein synthesis.
Collapse
Affiliation(s)
- Corinne D Hausmann
- Department of Microbiology, The Ohio State University, Columbus, OH 43210-1292, USA
| | | |
Collapse
|
29
|
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: 127] [Impact Index Per Article: 7.9] [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
|
30
|
Sheppard K, Akochy PM, Söll D. Assays for transfer RNA-dependent amino acid biosynthesis. Methods 2008; 44:139-45. [PMID: 18241795 PMCID: PMC2266967 DOI: 10.1016/j.ymeth.2007.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Accepted: 06/25/2007] [Indexed: 11/29/2022] Open
Abstract
Selenocysteinyl-tRNA(Sec), cysteinyl-tRNA(Cys), glutaminyl-tRNA(Gln), and asparaginyl-tRNA(Asn) in many organisms are formed in an indirect pathway in which a non-cognate amino acid is first attached to the tRNA. This non-cognate amino acid is then converted to the cognate amino acid by a tRNA-dependent modifying enzyme. The in vitro characterization of these modifying enzymes is challenging due to the fact the substrate, aminoacyl-tRNA, is labile and requires a prior enzymatic step to be synthesized. The need to separate product aa-tRNA from unreacted substrate is typically a labor- and time-intensive task; this adds another impediment in the investigation of these enzymes. Here, we review four different approaches for studying these tRNA-dependent amino acid modifications. In addition, we describe in detail a [32P]/nuclease P1 assay for glutaminyl-tRNA(Gln) and asparaginyl-tRNA(Asn) formation which is sensitive, enables monitoring of the aminoacyl state of the tRNA, and is less time consuming than some of the other techniques. This [32P]/nuclease P1 method should be adaptable to studying tRNA-dependent selenocysteine and cysteine synthesis.
Collapse
Affiliation(s)
- Kelly Sheppard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Pierre-Marie Akochy
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA
| |
Collapse
|
31
|
Mutations in the Drosophila mitochondrial tRNA amidotransferase, bene/gatA, cause growth defects in mitotic and endoreplicating tissues. Genetics 2008; 178:979-87. [PMID: 18245325 DOI: 10.1534/genetics.107.084376] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rapid larval growth is essential in the development of most metazoans. In this article, we show that bene, a gene previously identified on the basis of its oogenesis defects, is also required for larval growth and viability. We show that all bene alleles disrupt gatA, which encodes the Drosophila homolog of glutamyl-tRNA(Gln) amidotransferase subunit A (GatA). bene alleles are now referred to as gatA. GatA proteins are highly conserved throughout eukaryotes and many prokaryotes. These enzymes are required for proper translation of the proteins encoded by the mitochondrial genome and by many eubacterial genomes. Mitotic and endoreplicating tissues in Drosophila gatA loss-of-function mutants grow slowly and never achieve wild-type size, and gatA larvae die before pupariation. gatA mutant eye clones exhibit growth and differentiation defects, indicating that gatA expression is required cell autonomously for normal growth. The gatA gene is widely expressed in mitotic and endoreplicating tissues.
Collapse
|
32
|
Sheppard K, Sherrer RL, Söll D. Methanothermobacter thermautotrophicus tRNA Gln confines the amidotransferase GatCAB to asparaginyl-tRNA Asn formation. J Mol Biol 2008; 377:845-53. [PMID: 18291416 DOI: 10.1016/j.jmb.2008.01.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 01/15/2008] [Accepted: 01/16/2008] [Indexed: 10/22/2022]
Abstract
Many prokaryotes form the amide aminoacyl-tRNAs glutaminyl-tRNA and asparaginyl-tRNA by tRNA-dependent amidation of the mischarged tRNA species, glutamyl-tRNA(Gln) or aspartyl-tRNA(Asn). Archaea employ two such amidotransferases, GatCAB and GatDE, while bacteria possess only one, GatCAB. The Methanothermobacter thermautotrophicus GatDE is slightly more efficient using Asn as an amide donor than Gln (k(cat)/K(M) of 5.4 s(-1)/mM and 1.2 s(-1)/mM, respectively). Unlike the bacterial GatCAB enzymes studied to date, the M. thermautotrophicus GatCAB uses Asn almost as well as Gln as an amide donor (k(cat)/K(M) of 5.7 s(-1)/mM and 16.7 s(-1)/mM, respectively). In contrast to the initial characterization of the M. thermautotrophicus GatCAB as being able to form Asn-tRNA(Asn) and Gln-tRNA(Gln), our data demonstrate that while the enzyme is able to transamidate Asp-tRNA(Asn) (k(cat)/K(M) of 125 s(-1)/mM) it is unable to transamidate M. thermautotrophicus Glu-tRNA(Gln). However, M. thermautotrophicus GatCAB is capable of transamidating Glu-tRNA(Gln) from H. pylori or B. subtilis, and M. thermautotrophicus Glu-tRNA(Asn). Thus, M. thermautotrophicus encodes two amidotransferases, each with its own activity, GatDE for Gln-tRNA and GatCAB for Asn-tRNA synthesis.
Collapse
Affiliation(s)
- Kelly Sheppard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | | | | |
Collapse
|
33
|
Sheppard K, Söll D. On the evolution of the tRNA-dependent amidotransferases, GatCAB and GatDE. J Mol Biol 2008; 377:831-44. [PMID: 18279892 DOI: 10.1016/j.jmb.2008.01.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 12/21/2007] [Accepted: 01/02/2008] [Indexed: 11/19/2022]
Abstract
Glutaminyl-tRNA synthetase and asparaginyl-tRNA synthetase evolved from glutamyl-tRNA synthetase and aspartyl-tRNA synthetase, respectively, after the split in the last universal communal ancestor (LUCA). Glutaminyl-tRNA(Gln) and asparaginyl-tRNA(Asn) were likely formed in LUCA by amidation of the mischarged species, glutamyl-tRNA(Gln) and aspartyl-tRNA(Asn), by tRNA-dependent amidotransferases, as is still the case in most bacteria and all known archaea. The amidotransferase GatCAB is found in both domains of life, while the heterodimeric amidotransferase GatDE is found only in Archaea. The GatB and GatE subunits belong to a unique protein family that includes Pet112 that is encoded in the nuclear genomes of numerous eukaryotes. GatE was thought to have evolved from GatB after the emergence of the modern lines of decent. Our phylogenetic analysis though places the split between GatE and GatB, prior to the phylogenetic divide between Bacteria and Archaea, and Pet112 to be of mitochondrial origin. In addition, GatD appears to have emerged prior to the bacterial-archaeal phylogenetic divide. Thus, while GatDE is an archaeal signature protein, it likely was present in LUCA together with GatCAB. Archaea retained both amidotransferases, while Bacteria emerged with only GatCAB. The presence of GatDE has favored a unique archaeal tRNA(Gln) that may be preventing the acquisition of glutaminyl-tRNA synthetase in Archaea. Archaeal GatCAB, on the other hand, has not favored a distinct tRNA(Asn), suggesting that tRNA(Asn) recognition is not a major barrier to the retention of asparaginyl-tRNA synthetase in many Archaea.
Collapse
Affiliation(s)
- Kelly Sheppard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | | |
Collapse
|
34
|
Mouilleron S, Golinelli-Pimpaneau B. Conformational changes in ammonia-channeling glutamine amidotransferases. Curr Opin Struct Biol 2007; 17:653-64. [PMID: 17951049 DOI: 10.1016/j.sbi.2007.09.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Revised: 09/04/2007] [Accepted: 09/06/2007] [Indexed: 11/28/2022]
Abstract
Glutamine amidotransferases (GATs), which catalyze the synthesis of different aminated products, channel ammonia over 10-40 A from a glutamine substrate at the glutaminase site to an acceptor substrate at the synthase site. Ammonia production usually uses a cysteine-histidine-glutamate triad or a N-terminal cysteine residue. Crystal structures of several amidotransferase ligand complexes, mimicking intermediates along the catalytic cycle, have now been determined. In most cases, acceptor binding triggers glutaminase activation through domain-hinged movements and other conformational changes. Structural information shows how flexible loops of the synthase and glutaminase domains move to shield the two catalytic sites and anchor the substrates, and how the ammonia channel forms and opens or closes.
Collapse
Affiliation(s)
- Stéphane Mouilleron
- Laboratoire d'Enzymologie et Biochimie structurales, CNRS Bâtiment 34, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | | |
Collapse
|
35
|
Sheppard K, Akochy PM, Salazar JC, Söll D. The Helicobacter pylori amidotransferase GatCAB is equally efficient in glutamine-dependent transamidation of Asp-tRNAAsn and Glu-tRNAGln. J Biol Chem 2007; 282:11866-73. [PMID: 17329242 DOI: 10.1074/jbc.m700398200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The amide aminoacyl-tRNAs, Gln-tRNA(Gln) and Asn-tRNA(Asn), are formed in many bacteria by a pretranslational tRNA-dependent amidation of the mischarged tRNA species, Glu-tRNA(Gln) or Asp-tRNA(Asn). This conversion is catalyzed by a heterotrimeric amidotransferase GatCAB in the presence of ATP and an amide donor (Gln or Asn). Helicobacter pylori has a single GatCAB enzyme required in vivo for both Gln-tRNA(Gln) and Asn-tRNA(Asn) synthesis. In vitro characterization reveals that the enzyme transamidates Asp-tRNA(Asn) and Glu-tRNA(Gln) with similar efficiency (k(cat)/K(m) of 1368.4 s(-1)/mM and 3059.3 s(-1)/mM respectively). The essential glutaminase activity of the enzyme is a property of the A-subunit, which displays the characteristic amidase signature sequence. Mutations of the GatA catalytic triad residues (Lys(52), Ser(128), Ser(152)) abolished glutaminase activity and consequently the amidotransferase activity with glutamine as the amide donor. However, the latter activity was rescued when the mutant enzymes were presented with ammonium chloride. The presence of Asp-tRNA(Asn) and ATP enhances the glutaminase activity about 22-fold. H. pylori GatCAB uses the amide donor glutamine 129-fold more efficiently than asparagine, suggesting that GatCAB is a glutamine-dependent amidotransferase much like the unrelated asparagine synthetase B. Genomic analysis suggests that most bacteria synthesize asparagine in a glutamine-dependent manner, either by a tRNA-dependent or in a tRNA-independent route. However, all known bacteria that contain asparagine synthetase A form Asn-tRNA(Asn) by direct acylation catalyzed by asparaginyl-tRNA synthetase. Therefore, bacterial amide aminoacyl-tRNA formation is intimately tied to amide amino acid metabolism.
Collapse
Affiliation(s)
- Kelly Sheppard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
| | | | | | | |
Collapse
|
36
|
Namgoong S, Sheppard K, Sherrer RL, Söll D. Co-evolution of the archaeal tRNA-dependent amidotransferase GatCAB with tRNA(Asn). FEBS Lett 2007; 581:309-14. [PMID: 17214986 PMCID: PMC1808439 DOI: 10.1016/j.febslet.2006.12.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2006] [Revised: 12/12/2006] [Accepted: 12/13/2006] [Indexed: 12/01/2022]
Abstract
The important identity elements in tRNA(Gln) and tRNA(Asn) for bacterial GatCAB and in tRNA(Gln) for archaeal GatDE are the D-loop and the first base pair of the acceptor stem. Here we show that Methanothermobacter thermautotrophicus GatCAB, the archaeal enzyme, is different as it discriminates Asp-tRNA(Asp) and Asp-tRNA(Asn) by use of U49, the D-loop and to a lesser extent the variable loop. Since archaea possess the tRNA(Gln)-specific amidotransferase GatDE, the archaeal GatCAB enzyme evolved to recognize different elements in tRNA(Asn) than those recognized by GatDE or by the bacterial GatCAB enzyme in their tRNA substrates.
Collapse
Affiliation(s)
- Suk Namgoong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
| | | | | | | |
Collapse
|
37
|
Cathopoulis T, Chuawong P, Hendrickson TL. Novel tRNA aminoacylation mechanisms. MOLECULAR BIOSYSTEMS 2007; 3:408-18. [PMID: 17533454 DOI: 10.1039/b618899k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In nature, ribosomally synthesized proteins can contain at least 22 different amino acids: the 20 common amino acids as well as selenocysteine and pyrrolysine. Each of these amino acids is inserted into proteins codon-specifically via an aminoacyl-transfer RNA (aa-tRNA). In most cases, these aa-tRNAs are biosynthesized directly by a set of highly specific and accurate aminoacyl-tRNA synthetases (aaRSs). However, in some cases aaRSs with relaxed or novel substrate specificities cooperate with other enzymes to generate specific canonical and non-canonical aminoacyl-tRNAs.
Collapse
MESH Headings
- Amino Acyl-tRNA Synthetases/metabolism
- Aspartate-tRNA Ligase/metabolism
- Bacteria/enzymology
- RNA, Transfer, Amino Acyl/biosynthesis
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Asn/biosynthesis
- RNA, Transfer, Asn/chemistry
- RNA, Transfer, Cys/biosynthesis
- RNA, Transfer, Cys/chemistry
- RNA, Transfer, Gln/biosynthesis
- RNA, Transfer, Gln/chemistry
- Transfer RNA Aminoacylation
Collapse
Affiliation(s)
- Terry Cathopoulis
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | | | | |
Collapse
|
38
|
Bailly M, Giannouli S, Blaise M, Stathopoulos C, Kern D, Becker HD. A single tRNA base pair mediates bacterial tRNA-dependent biosynthesis of asparagine. Nucleic Acids Res 2006; 34:6083-94. [PMID: 17074748 PMCID: PMC1635274 DOI: 10.1093/nar/gkl622] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In many prokaryotes and in organelles asparagine and glutamine are formed by a tRNA-dependent amidotransferase (AdT) that catalyzes amidation of aspartate and glutamate, respectively, mischarged on tRNAAsn and tRNAGln. These pathways supply the deficiency of the organism in asparaginyl- and glutaminyl-tRNA synthtetases and provide the translational machinery with Asn-tRNAAsn and Gln-tRNAGln. So far, nothing is known about the structural elements that confer to tRNA the role of a specific cofactor in the formation of the cognate amino acid. We show herein, using aspartylated tRNAAsn and tRNAAsp variants, that amidation of Asp acylating tRNAAsn is promoted by the base pair U1-A72 whereas the G1-C72 pair and presence of the supernumerary nucleotide U20A in the D-loop of tRNAAsp prevent amidation. We predict, based on comparison of tRNAGln and tRNAGlu sequence alignments from bacteria using the AdT-dependent pathway to form Gln-tRNAGln, that the same combination of nucleotides also rules specific tRNA-dependent formation of Gln. In contrast, we show that the tRNA-dependent conversion of Asp into Asn by archaeal AdT is mainly mediated by nucleotides G46 and U47 of the variable region. In the light of these results we propose that bacterial and archaeal AdTs use kingdom-specific signals to catalyze the tRNA-dependent formations of Asn and Gln.
Collapse
MESH Headings
- Adenine/chemistry
- Asparagine/biosynthesis
- Base Sequence
- Kinetics
- Neisseria meningitidis/enzymology
- Nitrogenous Group Transferases/chemistry
- Nitrogenous Group Transferases/metabolism
- RNA, Archaeal/chemistry
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Asn/chemistry
- RNA, Transfer, Asn/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Gln/chemistry
- RNA, Transfer, Gln/metabolism
- RNA, Transfer, Glu/chemistry
- RNA, Transfer, Glu/metabolism
- Sequence Alignment
- Species Specificity
- Substrate Specificity
- Uridine/chemistry
Collapse
Affiliation(s)
| | - Stamatina Giannouli
- Department of Biochemistry and Biotechnology, University of Thessaly26 Ploutonos street, 41221 Larissa, Greece
| | | | - Constantinos Stathopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly26 Ploutonos street, 41221 Larissa, Greece
- To whom correspondence should be addressed. Tel: +33 3 88 41 70 92; Fax: +33 3 88 60 22 18;
| | - Daniel Kern
- To whom correspondence should be addressed. Tel: +33 3 88 41 70 92; Fax: +33 3 88 60 22 18;
| | | |
Collapse
|
39
|
Oshikane H, Sheppard K, Fukai S, Nakamura Y, Ishitani R, Numata T, Sherrer RL, Feng L, Schmitt E, Panvert M, Blanquet S, Mechulam Y, Söll D, Nureki O. Structural basis of RNA-dependent recruitment of glutamine to the genetic code. Science 2006; 312:1950-4. [PMID: 16809540 DOI: 10.1126/science.1128470] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Glutaminyl-transfer RNA (Gln-tRNA(Gln)) in archaea is synthesized in a pretranslational amidation of misacylated Glu-tRNA(Gln) by the heterodimeric Glu-tRNA(Gln) amidotransferase GatDE. Here we report the crystal structure of the Methanothermobacter thermautotrophicus GatDE complexed to tRNA(Gln) at 3.15 angstroms resolution. Biochemical analysis of GatDE and of tRNA(Gln) mutants characterized the catalytic centers for the enzyme's three reactions (glutaminase, kinase, and amidotransferase activity). A 40 angstrom-long channel for ammonia transport connects the active sites in GatD and GatE. tRNA(Gln) recognition by indirect readout based on shape complementarity of the D loop suggests an early anticodon-independent RNA-based mechanism for adding glutamine to the genetic code.
Collapse
MESH Headings
- Acylation
- Adenosine Triphosphate/metabolism
- Ammonia/metabolism
- Anticodon
- Binding Sites
- Catalytic Domain
- Computer Simulation
- Crystallography, X-Ray
- Dimerization
- Genetic Code
- Glutamine/metabolism
- Hydrogen Bonding
- Magnesium/metabolism
- Methanobacteriaceae/enzymology
- Methanobacteriaceae/genetics
- Models, Molecular
- Mutation
- Nitrogenous Group Transferases/chemistry
- Nitrogenous Group Transferases/metabolism
- Nucleic Acid Conformation
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Protein Structure, Tertiary
- RNA, Archaeal/chemistry
- RNA, Archaeal/metabolism
- RNA, Transfer, Gln/chemistry
- RNA, Transfer, Gln/metabolism
Collapse
Affiliation(s)
- Hiroyuki Oshikane
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Nakamura A, Yao M, Chimnaronk S, Sakai N, Tanaka I. Ammonia channel couples glutaminase with transamidase reactions in GatCAB. Science 2006; 312:1954-8. [PMID: 16809541 DOI: 10.1126/science.1127156] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The formation of glutaminyl transfer RNA (Gln-tRNA(Gln)) differs among the three domains of life. Most bacteria employ an indirect pathway to produce Gln-tRNA(Gln) by a heterotrimeric glutamine amidotransferase CAB (GatCAB) that acts on the misacylated Glu-tRNA(Gln). Here, we describe a series of crystal structures of intact GatCAB from Staphylococcus aureus in the apo form and in the complexes with glutamine, asparagine, Mn2+, and adenosine triphosphate analog. Two identified catalytic centers for the glutaminase and transamidase reactions are markedly distant but connected by a hydrophilic ammonia channel 30 A in length. Further, we show that the first U-A base pair in the acceptor stem and the D loop of tRNA(Gln) serve as identity elements essential for discrimination by GatCAB and propose a complete model for the overall concerted reactions to synthesize Gln-tRNA(Gln).
Collapse
MESH Headings
- Adenosine Diphosphate/metabolism
- Amino Acid Sequence
- Aminoacyltransferases/metabolism
- Ammonia/metabolism
- Apoenzymes/chemistry
- Apoenzymes/metabolism
- Asparagine/metabolism
- Base Pairing
- Catalytic Domain
- Crystallography, X-Ray
- Glutaminase/metabolism
- Glutamine/chemistry
- Glutamine/metabolism
- Hydrogen Bonding
- Hydrophobic and Hydrophilic Interactions
- Magnesium/metabolism
- Manganese/metabolism
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Protein Subunits
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Gln/chemistry
- RNA, Transfer, Gln/metabolism
- Staphylococcus aureus/enzymology
- Staphylococcus aureus/genetics
- Staphylococcus aureus/metabolism
Collapse
Affiliation(s)
- Akiyoshi Nakamura
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | | | | | | | | |
Collapse
|
41
|
Abstract
The 3.0 Angstrom crystal structure of a tRNA-dependent amidotransferase from the hyperthermophilic archaeon Pyrococcus abyssi provides the first detailed insight into how cells lacking canonical tRNA synthetases nonetheless carry out protein synthesis with high fidelity.
Collapse
MESH Headings
- Adenosine Diphosphate/metabolism
- Binding Sites
- Crystallography, X-Ray
- Glutamate-tRNA Ligase/metabolism
- Nitrogenous Group Transferases/chemistry
- Nitrogenous Group Transferases/genetics
- Nitrogenous Group Transferases/metabolism
- Protein Biosynthesis
- Pyrococcus abyssi/enzymology
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Gln/metabolism
Collapse
Affiliation(s)
- John J Perona
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, USA
| |
Collapse
|
42
|
Schmitt E, Panvert M, Blanquet S, Mechulam Y. Structural Basis for tRNA-Dependent Amidotransferase Function. Structure 2005; 13:1421-33. [PMID: 16216574 DOI: 10.1016/j.str.2005.06.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Revised: 06/20/2005] [Accepted: 06/30/2005] [Indexed: 11/26/2022]
Abstract
Besides direct charging of tRNAs by aminoacyl-tRNA synthetases, indirect routes also ensure attachment of some amino acids onto tRNA. Such routes may explain how new amino acids entered into protein synthesis. In archaea and in most bacteria, tRNA(Gln) is first misaminoacylated by glutamyl-tRNA synthetase. Glu-tRNA(Gln) is then matured into Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. We report the structure of a tRNA-dependent amidotransferase-that of GatDE from Pyrococcus abyssi. The 3.0 A resolution crystal structure shows a tetramer with two GatD molecules as the core and two GatE molecules at the periphery. The fold of GatE cannot be related to that of any tRNA binding enzyme. The ammonium donor site on GatD and the tRNA site on GatE are markedly distant. Comparison of GatD and L-asparaginase structures shows how the motion of a beta hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE.
Collapse
MESH Headings
- Amino Acid Sequence
- Amino Acyl-tRNA Synthetases/chemistry
- Amino Acyl-tRNA Synthetases/metabolism
- Binding Sites
- Conserved Sequence
- Crystallography, X-Ray
- Dimerization
- Glutamate-tRNA Ligase/chemistry
- Glutamate-tRNA Ligase/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nitrogenous Group Transferases/chemistry
- Nitrogenous Group Transferases/genetics
- Nitrogenous Group Transferases/metabolism
- Protein Biosynthesis
- Protein Folding
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Protein Subunits/chemistry
- Pyrococcus abyssi/enzymology
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Gln/metabolism
- Sequence Homology, Amino Acid
- Threonine/chemistry
- X-Ray Diffraction
Collapse
Affiliation(s)
- Emmanuelle Schmitt
- Laboratoire de Biochimie, Unité Mixte de Recherche 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France.
| | | | | | | |
Collapse
|