1
|
Sangsuwan W, Taweesablamlert A, Boonkerd A, Isarangkool Na Ayutthaya C, Yoo S, Javid B, Faikhruea K, Vilaivan T, Aonbangkhen C, Chuawong P. A quest for novel antimicrobial targets: Inhibition of Asp-tRNA Asn/Glu-tRNA Gln amidotransferase (GatCAB) by synthetic analogs of aminoacyl-adenosine in vitro and live bacteria. Bioorg Chem 2024; 150:107530. [PMID: 38852310 DOI: 10.1016/j.bioorg.2024.107530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/25/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
The Asp-tRNAAsn/Glu-tRNAGln amidotransferase (GatCAB) has been proposed as a novel antibacterial drug target due to its indispensability in prominent human pathogens. While several inhibitors with in vitro activity have been identified, none have been demonstrated to have potent activity against live bacteria. In this work, seven non-hydrolyzable transition state mimics of GatCAB were synthesized and tested as the transamidase inhibitors against GatCAB from the human pathogen Helicobacter pylori. Notably, the methyl sulfone analog of glutamyl-adenosine significantly reduced GatCAB's transamination rate. Additionally, four lipid-conjugates of these mimics displayed antibacterial activity against Bacillus subtilis, likely due to enhanced cell permeability. Inhibitory activity against GatCAB in live bacteria was confirmed using a sensitive gain-of-function dual luciferase reporter in Mycobacterium bovis-BCG. Only the lipid-conjugated methyl sulfone analog exhibited a significant increase in mistranslation rate, highlighting its cell permeability and inhibitory potential. This study provides insights for developing urgently needed novel antibacterial agents amidst emerging antimicrobial drug resistance.
Collapse
Affiliation(s)
- Withsakorn Sangsuwan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Amata Taweesablamlert
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Anon Boonkerd
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Chawarat Isarangkool Na Ayutthaya
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand
| | - Sion Yoo
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Babak Javid
- Division of Experimental Medicine, University of California, San Francisco, CA, USA
| | - Kriangsak Faikhruea
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand; Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Pitak Chuawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Special Research Unit for Advanced Magnetic Resonance (AMR), Kasetsart University, Bangkok 10900, Thailand.
| |
Collapse
|
2
|
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
|
3
|
Indirect tRNA aminoacylation during accurate translation and phenotypic mistranslation. Curr Opin Chem Biol 2017; 41:114-122. [DOI: 10.1016/j.cbpa.2017.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/03/2017] [Accepted: 10/08/2017] [Indexed: 11/18/2022]
|
4
|
Zhao L, Rathnayake UM, Dewage SW, Wood WN, Veltri AJ, Cisneros GA, Hendrickson TL. Characterization of tunnel mutants reveals a catalytic step in ammonia delivery by an aminoacyl-tRNA amidotransferase. FEBS Lett 2016; 590:3122-32. [DOI: 10.1002/1873-3468.12347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Liangjun Zhao
- Department of Chemistry; Wayne State University; Detroit MI USA
| | | | | | - Whitney N. Wood
- Department of Chemistry; Wayne State University; Detroit MI USA
| | | | | | | |
Collapse
|
5
|
Dewage SW, Cisneros GA. Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB). J Phys Chem B 2015; 119:3669-77. [PMID: 25654336 DOI: 10.1021/jp5123568] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most bacteria and all archaea misacylate the tRNAs corresponding to Asn and Gln with Asp and Glu (Asp-tRNA(Asn) and Glu-tRNA(Gln)).The GatCAB enzyme of most bacteria converts misacylated Glu-tRNA(Gln) to Gln-tRNA(Gln) in order to enable the incorporation of glutamine during protein synthesis. The conversion process involves the intramolecular transfer of ammonia between two spatially separated active sites. This study presents a computational analysis of the two putative intramolecular tunnels that have been suggested to describe the ammonia transfer between the two active sites. Molecular dynamics simulations have been performed for wild-type GatCAB of S. aureus and its mutants: T175(A)V, K88(B)R, E125(B)D, and E125(B)Q. The two tunnels have been analyzed in terms of free energy of ammonia transfer along them. The probability of occurrence of each type of tunnel and the variation of the probability for wild-type GatCAB and its mutants is also discussed.
Collapse
Affiliation(s)
- Sajeewa Walimuni Dewage
- Department of Chemistry, Wayne State University , 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | | |
Collapse
|
6
|
Araiso Y, Huot JL, Sekiguchi T, Frechin M, Fischer F, Enkler L, Senger B, Ishitani R, Becker HD, Nureki O. Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases. Nucleic Acids Res 2014; 42:6052-63. [PMID: 24692665 PMCID: PMC4027206 DOI: 10.1093/nar/gku234] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Yeast mitochondrial Gln-mtRNAGln is synthesized by the transamidation of mischarged Glu-mtRNAGln by a non-canonical heterotrimeric tRNA-dependent amidotransferase (AdT). The GatA and GatB subunits of the yeast AdT (GatFAB) are well conserved among bacteria and eukaryota, but the GatF subunit is a fungi-specific ortholog of the GatC subunit found in all other known heterotrimeric AdTs (GatCAB). Here we report the crystal structure of yeast mitochondrial GatFAB at 2.0 Å resolution. The C-terminal region of GatF encircles the GatA–GatB interface in the same manner as GatC, but the N-terminal extension domain (NTD) of GatF forms several additional hydrophobic and hydrophilic interactions with GatA. NTD-deletion mutants displayed growth defects, but retained the ability to respire. Truncation of the NTD in purified mutants reduced glutaminase and transamidase activities when glutamine was used as the ammonia donor, but increased transamidase activity relative to the full-length enzyme when the donor was ammonium chloride. Our structure-based functional analyses suggest the NTD is a trans-acting scaffolding peptide for the GatA glutaminase active site. The positive surface charge and novel fold of the GatF–GatA interface, shown in this first crystal structure of an organellar AdT, stand in contrast with the more conventional, negatively charged bacterial AdTs described previously.
Collapse
Affiliation(s)
- Yuhei Araiso
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Jonathan L Huot
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Takuya Sekiguchi
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Mathieu Frechin
- Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Frédéric Fischer
- Unité Propre de Recherche Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, F-67084 Strasbourg, France
| | - Ludovic Enkler
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Bruno Senger
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Ryuichiro Ishitani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 113-0033 Tokyo, Japan
| | - Hubert D Becker
- Unité Mixte de Recherche 7156 Génétique Moléculaire Génomique Microbiologie, Centre National de la Recherche Scientifique, Université de Strasbourg, F-67084 Strasbourg, France
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 113-0033 Tokyo, Japan
| |
Collapse
|
7
|
Silva GN, Fatma S, Floyd AM, Fischer F, Chuawong P, Cruz AN, Simari RM, Joshi N, Kern D, Hendrickson TL. A tRNA-independent mechanism for transamidosome assembly promotes aminoacyl-tRNA transamidation. J Biol Chem 2012; 288:3816-22. [PMID: 23258533 DOI: 10.1074/jbc.m112.441394] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many bacteria lack genes encoding asparaginyl- and/or glutaminyl-tRNA synthetase and consequently rely on an indirect path for the synthesis of both Asn-tRNA(Asn) and Gln-tRNA(Gln). In some bacteria such as Thermus thermophilus, efficient delivery of misacylated tRNA to the downstream amidotransferase (AdT) is ensured by formation of a stable, tRNA-dependent macromolecular complex called the Asn-transamidosome. This complex enables direct delivery of Asp-tRNA(Asn) from the non-discriminating aspartyl-tRNA synthetase to AdT, where it is converted into Asn-tRNA(Asn). Previous characterization of the analogous Helicobacter pylori Asn-transamidosome revealed that it is dynamic and cannot be stably isolated, suggesting the possibility of an alternative mechanism to facilitate assembly of a stable complex. We have identified a novel protein partner called Hp0100 as a component of a stable, tRNA-independent H. pylori Asn-transamidosome; this complex contains a non-discriminating aspartyl-tRNA synthetase, AdT, and Hp0100 but does not require tRNA(Asn) for assembly. Hp0100 also enhances the capacity of AdT to convert Asp-tRNA(Asn) into Asn-tRNA(Asn) by ∼35-fold. Our results demonstrate that bacteria have adopted multiple divergent methods for transamidosome assembly and function.
Collapse
Affiliation(s)
- Gayathri N Silva
- Department of Chemistry, Wayne State University, Detroit, Michigan 48230, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|