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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] [MESH Headings] [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.
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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.
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2
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Yu XX, Chen KX, Yuan PP, Wang YH, Li HX, Zhao YX, Dai YJ. Asp-tRNA Asn/Glu-tRNA Gln amidotransferase A subunit-like amidase mediates the degradation of insecticide flonicamid by Variovorax boronicumulans CGMCC 4969. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172479. [PMID: 38621543 DOI: 10.1016/j.scitotenv.2024.172479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The main metabolic product of the pyridinecarboxamide insecticide flonicamid, N-(4-trifluoromethylnicotinyl)glycinamide (TFNG-AM), has been shown to have very high mobility in soil, leading to its accumulation in the environment. Catabolic pathways of flonicamid have been widely reported, but few studies have focused on the metabolism of TFNG-AM. Here, the rapid transformation of TFNG-AM and production of the corresponding acid product N-(4-trifluoromethylnicotinoyl) glycine (TFNG) by the plant growth-promoting bacterium Variovorax boronicumulans CGMCC 4969 were investigated. With TFNG-AM at an initial concentration of 0.86 mmol/L, 90.70 % was transformed by V. boronicumulans CGMCC 4969 resting cells within 20 d, with a degradation half-life of 4.82 d. A novel amidase that potentially mediated this transformation process, called AmiD, was identified by bioinformatic analyses. The gene encoding amiD was cloned and expressed recombinantly in Escherichia coli, and the enzyme AmiD was characterized. Key amino acid residue Val154, which is associated with the catalytic activity and substrate specificity of signature family amidases, was identified for the first time by homology modeling, structural alignment, and site-directed mutagenesis analyses. When compared to wild-type recombinant AmiD, the mutant AmiD V154G demonstrated a 3.08-fold increase in activity toward TFNG-AM. The activity of AmiD V154G was greatly increased toward aromatic L-phenylalanine amides, heterocyclic TFNG-AM and IAM, and aliphatic asparagine, whereas it was dramatically lowered toward benzamide, phenylacetamide, nicotinamide, acetamide, acrylamide, and hexanamid. Quantitative PCR analysis revealed that AmiD may be a substrate-inducible enzyme in V. boronicumulans CGMCC 4969. The mechanism of transcriptional regulation of AmiD by a member of the AraC family of regulators encoded upstream of the amiD gene was preliminarily investigated. This study deepens our understanding of the mechanisms of metabolism of toxic amides in the environment, providing new ideas for microbial bioremediation.
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Affiliation(s)
- Xue-Xiu Yu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Ke-Xin Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Pan-Pan Yuan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Yu-He Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Hua-Xiao Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Yun-Xiu Zhao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Jiangsu Synthetic Innovation Center for Coastal Bioagriculture, Yancheng Teachers University, Yancheng 224007, People's Republic of China.
| | - Yi-Jun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China.
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3
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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.
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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
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4
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Meng K, Chung CZ, Söll D, Krahn N. Unconventional genetic code systems in archaea. Front Microbiol 2022; 13:1007832. [PMID: 36160229 PMCID: PMC9499178 DOI: 10.3389/fmicb.2022.1007832] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Archaea constitute the third domain of life, distinct from bacteria and eukaryotes given their ability to tolerate extreme environments. To survive these harsh conditions, certain archaeal lineages possess unique genetic code systems to encode either selenocysteine or pyrrolysine, rare amino acids not found in all organisms. Furthermore, archaea utilize alternate tRNA-dependent pathways to biosynthesize and incorporate members of the 20 canonical amino acids. Recent discoveries of new archaeal species have revealed the co-occurrence of these genetic code systems within a single lineage. This review discusses the diverse genetic code systems of archaea, while detailing the associated biochemical elements and molecular mechanisms.
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Affiliation(s)
- Kexin Meng
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Christina Z. Chung
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Natalie Krahn
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, United States
- *Correspondence: Natalie Krahn,
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5
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Deghadi RG, Elsharkawy AE, Ashmawy AM, Mohamed GG. Antibacterial and anticorrosion behavior of bioactive complexes of selected transition metal ions with new 2‐acetylpyridine Schiff base. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6579] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Reem G. Deghadi
- Chemistry Department, Faculty of Science Cairo University Giza Egypt
| | | | - Ashraf M. Ashmawy
- Chemistry Department, Faculty of Science (Boys) Al‐Azhar University Cairo Egypt
| | - Gehad G. Mohamed
- Chemistry Department, Faculty of Science Cairo University Giza Egypt
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6
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Mukai T, Amikura K, Fu X, Söll D, Crnković A. Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems. Front Genet 2022; 12:794509. [PMID: 35047015 PMCID: PMC8762117 DOI: 10.3389/fgene.2021.794509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/18/2021] [Indexed: 01/23/2023] Open
Abstract
Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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7
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Nolan LM, Cain AK, Clamens T, Furniss RCD, Manoli E, Sainz-Polo MA, Dougan G, Albesa-Jové D, Parkhill J, Mavridou DA, Filloux A. Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells. Nat Microbiol 2021; 6:1199-1210. [PMID: 34413503 PMCID: PMC7611593 DOI: 10.1038/s41564-021-00950-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
The Type VI secretion system (T6SS) is a bacterial nanomachine that delivers toxic effectors to kill competitors or subvert some of their key functions. Here, we use transposon directed insertion-site sequencing to identify T6SS toxins associated with the H1-T6SS, one of the three T6SS machines found in Pseudomonas aeruginosa. This approach identified several putative toxin-immunity pairs, including Tse8-Tsi8. Full characterization of this protein pair demonstrated that Tse8 is delivered by the VgrG1a spike complex into prey cells where it targets the transamidosome, a multiprotein complex involved in protein synthesis in bacteria that lack either one, or both, of the asparagine and glutamine transfer RNA synthases. Biochemical characterization of the interactions between Tse8 and the transamidosome components GatA, GatB and GatC suggests that the presence of Tse8 alters the fine-tuned stoichiometry of the transamidosome complex, and in vivo assays demonstrate that Tse8 limits the ability of prey cells to synthesize proteins. These data expand the range of cellular components targeted by the T6SS by identifying a T6SS toxin affecting protein synthesis and validate the use of a transposon directed insertion site sequencing-based global genomics approach to expand the repertoire of T6SS toxins in T6SS-encoding bacteria.
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Affiliation(s)
- Laura M. Nolan
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Amy K. Cain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas Clamens
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - R. Christopher D. Furniss
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Eleni Manoli
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Maria A. Sainz-Polo
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - David Albesa-Jové
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Despoina A.I. Mavridou
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom,Department of Molecular Biosciences, University of Texas at Austin, Austin, 78712, Texas, USA,Correspondence to Alain Filloux: ; Despoina Mavridou:
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection (CMBI), Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom,Correspondence to Alain Filloux: ; Despoina Mavridou:
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8
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Deghadi RG, Elsharkawy AE, Ashmawy AM, Mohamed GG. Can One Novel Series of Transition Metal Complexes of Oxy-dianiline Schiff Base Afford Advances in Both Biological Inorganic Chemistry and Materials Science? COMMENT INORG CHEM 2021. [DOI: 10.1080/02603594.2021.1962310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Reem G. Deghadi
- Chemistry Department, Faculty of Science, Cairo University, 12613, Giza, Egypt
| | - Ahmed E. Elsharkawy
- Chemical Treatment Department, Qarun Petroleum Company, 1160, Cairo, Maadi, Egypt
| | - Ashraf M. Ashmawy
- Chemistry Department, Faculty of Science (Boys), Al-Azhar University, 11884, Egypt
| | - Gehad G. Mohamed
- Chemistry Department, Faculty of Science, Cairo University, 12613, Giza, Egypt
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9
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Abstract
Most bacteria employ a two-step indirect tRNA aminoacylation pathway for the synthesis of aminoacylated tRNAGln and tRNAAsn. The heterotrimeric enzyme GatCAB performs a critical amidotransferase reaction in the second step of this pathway. We have previously demonstrated in mycobacteria that this two-step pathway is error prone and translational errors contribute to adaptive phenotypes such as antibiotic tolerance. Furthermore, we identified clinical isolates of the globally important pathogen Mycobacterium tuberculosis with partial loss-of-function mutations in gatA, and demonstrated that these mutations result in high, specific rates of translational error and increased rifampin tolerance. However, the mechanisms by which these clinically derived mutations in gatA impact GatCAB function were unknown. Here, we describe biochemical and biophysical characterization of M. tuberculosis GatCAB, containing either wild-type gatA or one of two gatA mutants from clinical strains. We show that these mutations have minimal impact on enzymatic activity of GatCAB; however, they result in destabilization of the GatCAB complex as well as that of the ternary asparaginyl-transamidosome. Stabilizing complex formation with the solute trehalose increases specific translational fidelity of not only the mutant strains but also of wild-type mycobacteria. Therefore, our data suggest that alteration of GatCAB stability may be a mechanism for modulation of translational fidelity. IMPORTANCE Most bacteria use a two-step indirect pathway to aminoacylate tRNAGln and tRNAAsn, despite the fact that the indirect pathway consumes more energy and is error prone. We have previously shown that the higher protein synthesis errors from this indirect pathway in mycobacteria allow adaptation to hostile environments such as antibiotic treatment through generation of novel alternate proteins not coded by the genome. However, the precise mechanisms of how translational fidelity is tuned were not known. Here, we biochemically and biophysically characterize the critical enzyme of the Mycobacterium tuberculosis indirect pathway, GatCAB, as well as two mutant enzymes previously identified from clinical isolates that were associated with increased mistranslation. We show that the mutants dysregulate the pathway via destabilizing the enzyme complex. Importantly, increasing stability improves translational fidelity in both wild-type and mutant bacteria, demonstrating a mechanism by which mycobacteria may tune mistranslation rates.
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10
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González-Magaña A, Sainz-Polo MÁ, Pretre G, Çapuni R, Lucas M, Altuna J, Montánchez I, Fucini P, Albesa-Jové D. Structural insights into Pseudomonas aeruginosaType six secretion system exported effector 8. J Struct Biol 2020; 212:107651. [PMID: 33096229 DOI: 10.1016/j.jsb.2020.107651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Recent reports indicate that the Type six secretion system exported effector 8 (Tse8) is a cytoactive effector secreted by the Type VI secretion system (T6SS) of the human pathogen Pseudomonas aeruginosa. The T6SS is a nanomachine that assembles inside of the bacteria and injects effectors/toxins into target cells, providing a fitness advantage over competing bacteria and facilitating host colonisation. Here we present the first crystal structure of Tse8 revealing that it conserves the architecture of the catalytic triad Lys84-transSer162-Ser186 that characterises members of the Amidase Signature superfamily. Furthermore, using binding affinity experiments, we show that the interaction of phenylmethylsulfonyl fluoride (PMSF) to Tse8 is dependent on the putative catalytic residue Ser186, providing support for its nucleophilic reactivity. This work thus demonstrates that Tse8 belongs to the Amidase Signature (AS) superfamily. Furthermore, it highlights Tse8 similarity to two family members: the Stenotrophomonas maltophilia Peptide Amidase and the Glutamyl-tRNAGln amidotransferase subunit A from Staphylococcus aureus.
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Affiliation(s)
- Amaia González-Magaña
- Instituto Biofisika (UPV/EHU, CSIC), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940 Leioa, Spain
| | - M Ángela Sainz-Polo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Gabriela Pretre
- Instituto Biofisika (UPV/EHU, CSIC), Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB) and Departamento de Bioquímica y Biología Molecular, University of the Basque Country, 48940 Leioa, Spain
| | - Retina Çapuni
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - María Lucas
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria. Santander, 39011 Cantabria, Spain
| | - Jon Altuna
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
| | - Itxaso Montánchez
- Departamento de Inmunología, Microbiología y Parasitología, University of the Basque Country, 48940 Leioa, Spain
| | - Paola Fucini
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - David Albesa-Jové
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.
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11
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Cai RJ, Su HW, Li YY, Javid B. Forward Genetics Reveals a gatC-gatA Fusion Polypeptide Causes Mistranslation and Rifampicin Tolerance in Mycobacterium smegmatis. Front Microbiol 2020; 11:577756. [PMID: 33072044 PMCID: PMC7541841 DOI: 10.3389/fmicb.2020.577756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 12/26/2022] Open
Abstract
Most bacteria, including mycobacteria, utilize a two-step indirect tRNA aminoacylation pathway to generate correctly aminoacylated glutaminyl and asparaginyl tRNAs. This involves an initial step in which a non-discriminatory aminoacyl tRNA synthetase misacylates the tRNA, followed by a second step in which the essential amidotransferase, GatCAB, amidates the misacylated tRNA to its correct, cognate form. It had been previously demonstrated that mutations in gatA can mediate increased error rates specifically of glutamine to glutamate or asparagine to aspartate in protein synthesis. However, the role of mutations in gatB or gatC in mediating mistranslation are unknown. Here, we applied a forward genetic screen to enrich for mistranslating mutants of Mycobacterium smegmatis. The majority (57/67) of mutants had mutations in one of the gatCAB genes. Intriguingly, the most common mutation identified was an insertion in the 3' of gatC, abolishing its stop codon, and resulting in a fused GatC-GatA polypeptide. Modeling the effect of the fusion on GatCAB structure suggested a disruption of the interaction of GatB with the CCA-tail of the misacylated tRNA, suggesting a potential mechanism by which this mutation may mediate increased translational errors. Furthermore, we confirm that the majority of mutations in gatCAB that result in increased mistranslation also cause increased tolerance to rifampicin, although there was not a perfect correlation between mistranslation rates and degree of tolerance. Overall, our study identifies that mutations in all three gatCAB genes can mediate adaptive mistranslation and that mycobacteria are extremely tolerant to perturbation in the indirect tRNA aminoacylation pathway.
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Affiliation(s)
- Rong-Jun Cai
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Hong-Wei Su
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Yang-Yang Li
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China
| | - Babak Javid
- Centre for Global Health and Infectious Diseases, Collaborative Innovation Centre for the Diagnosis and Treatment of Infectious Diseases, Tsinghua University School of Medicine, Beijing, China.,Beijing Advanced Innovation Center in Structural Biology, Beijing, China.,Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
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12
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Chew BLA, Tanoto FR, Luo D. LC-MS assay targeting the mycobacterial indirect aminoacylation pathway uncovers glutaminase activities of the nondiscriminating aspartyl-synthetase. FEBS Lett 2020; 594:2159-2167. [PMID: 32279326 DOI: 10.1002/1873-3468.13786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/28/2020] [Accepted: 03/26/2020] [Indexed: 11/08/2022]
Abstract
The synthesis of asparagine (Asn)-tRNAAsn in most prokaryotes uses an indirect aminoacylation pathway involving a nondiscriminating aspartyl synthetase (ND-AspRS) and a glutamine amidotransferase (GatCAB). This was recently implicated as an adaptive mistranslation mechanism for antimicrobial resistance in Mycobacterium tuberculosis, but it remains poorly understood. We report an accessible liquid chromatography-mass spectrometry method with unparalleled chemical specificity, sensitivity, and quantification over the current assays to enable the direct analysis and drug screening campaigns of this pathway. Through this method, we show that the mycobacterial ND-AspRS stimulates the glutaminase activity of GatCAB. We further uncover novel glutaminase activity of the synthetase. These biological insights help better understand the indirect aminoacylation biology and allude to new roles beyond protein translation.
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Affiliation(s)
- Bing Liang Alvin Chew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
- NTU Institute of Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore City, Singapore
| | | | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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13
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Chuawong P, Likittrakulwong W, Suebka S, Wiriyatanakorn N, Saparpakorn P, Taweesablamlert A, Sudprasert W, Hendrickson T, Svasti J. Anticodon-binding domain swapping in a nondiscriminating aspartyl-tRNA synthetase reveals contributions to tRNA specificity and catalytic activity. Proteins 2020; 88:1133-1142. [PMID: 32067260 DOI: 10.1002/prot.25881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/15/2019] [Accepted: 02/12/2020] [Indexed: 11/10/2022]
Abstract
The nondiscriminating aspartyl-tRNA synthetase (ND-AspRS), found in many archaea and bacteria, covalently attaches aspartic acid to tRNAAsp and tRNAAsn generating a correctly charged Asp-tRNAAsp and an erroneous Asp-tRNAAsn . This relaxed tRNA specificity is governed by interactions between the tRNA and the enzyme. In an effort to assess the contributions of the anticodon-binding domain to tRNA specificity, we constructed two chimeric enzymes, Chimera-D and Chimera-N, by replacing the native anticodon-binding domain in the Helicobacter pylori ND-AspRS with that of a discriminating AspRS (Chimera-D) and an asparaginyl-tRNA synthetase (AsnRS, Chimera-N), both from Escherichia coli. Both chimeric enzymes showed similar secondary structure compared to wild-type (WT) ND-AspRS and maintained the ability to form dimeric complexes in solution. Although less catalytically active than WT, Chimera-D was more discriminating as it aspartylated tRNAAsp over tRNAAsn with a specificity ratio of 7.0 compared to 2.9 for the WT enzyme. In contrast, Chimera-N exhibited low catalytic activity toward tRNAAsp and was unable to aspartylate tRNAAsn . The observed catalytic activities for the two chimeras correlate with their heterologous toxicity when expressed in E. coli. Molecular dynamics simulations show a reduced hydrogen bond network at the interface between the anticodon-binding domain and the catalytic domain in Chimera-N compared to Chimera-D or WT, explaining its lower stability and catalytic activity.
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Affiliation(s)
- Pitak Chuawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Wirot Likittrakulwong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Faculty of Agricultural Technology, Pibulsongkram Rajabhat University, Phitsanulok, Thailand
| | - Suwimon Suebka
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Faculty of Science and Technology, Valaya Alongkorn Rajabhat University, Pathum Thani, Thailand
| | | | | | - Amata Taweesablamlert
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Wanwisa Sudprasert
- Department of Applied Radiation and Isotopes, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Jisnuson Svasti
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok, Thailand
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14
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Andi B, Soares AS, Shi W, Fuchs MR, McSweeney S, Liu Q. Structure of the dihydrolipoamide succinyltransferase catalytic domain from Escherichia coli in a novel crystal form: a tale of a common protein crystallization contaminant. Acta Crystallogr F Struct Biol Commun 2019; 75:616-624. [PMID: 31475929 PMCID: PMC6718150 DOI: 10.1107/s2053230x19011488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/15/2019] [Indexed: 12/12/2022] Open
Abstract
The crystallization of amidase, the ultimate enzyme in the Trp-dependent auxin-biosynthesis pathway, from Arabidopsis thaliana was attempted using protein samples with at least 95% purity. Cube-shaped crystals that were assumed to be amidase crystals that belonged to space group I4 (unit-cell parameters a = b = 128.6, c = 249.7 Å) were obtained and diffracted to 3.0 Å resolution. Molecular replacement using structures from the PDB containing the amidase signature fold as search models was unsuccessful in yielding a convincing solution. Using the Sequence-Independent Molecular replacement Based on Available Databases (SIMBAD) program, it was discovered that the structure corresponded to dihydrolipoamide succinyltransferase from Escherichia coli (PDB entry 1c4t), which is considered to be a common crystallization contaminant protein. The structure was refined to an Rwork of 23.0% and an Rfree of 27.2% at 3.0 Å resolution. The structure was compared with others of the same protein deposited in the PDB. This is the first report of the structure of dihydrolipoamide succinyltransferase isolated without an expression tag and in this novel crystal form.
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Affiliation(s)
- Babak Andi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Wuxian Shi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Martin R. Fuchs
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Sean McSweeney
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Qun Liu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
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15
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Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL. 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. F1000Res 2019; 8:ISCB Comm J-287. [PMID: 31069053 PMCID: PMC6480952 DOI: 10.12688/f1000research.18458.2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/04/2019] [Indexed: 01/01/2023] Open
Abstract
We present forgi, a Python library to analyze the tertiary structure of RNA secondary structure elements. Our representation of an RNA molecule is centered on secondary structure elements (stems, bulges and loops). By fitting a cylinder to the helix axis, these elements are carried over into a coarse-grained 3D structure representation. Integration with Biopython allows for handling of all-atom 3D information. forgi can deal with a variety of file formats including dotbracket strings, PDB and MMCIF files. We can handle modified residues, missing residues, cofold and multifold structures as well as nucleotide numbers starting at arbitrary positions. We apply this library to the study of stacking helices in junctions and pseudoknots and investigate how far stacking helices in solved experimental structures can divert from coaxial geometries.
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Affiliation(s)
- Bernhard C. Thiel
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Irene K. Beckmann
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Peter Kerpedjiev
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Ivo L. Hofacker
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, 1090, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, 1090, Austria
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16
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Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL. 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. F1000Res 2019; 8:ISCB Comm J-287. [PMID: 31069053 PMCID: PMC6480952 DOI: 10.12688/f1000research.18458.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/06/2019] [Indexed: 10/12/2023] Open
Abstract
We present forgi, a Python library to analyze the tertiary structure of RNA secondary structure elements. Our representation of an RNA molecule is centered on secondary structure elements (stems, bulges and loops). By fitting a cylinder to the helix axis, these elements are carried over into a coarse-grained 3D structure representation. Integration with Biopython allows for handling of all-atom 3D information. forgi can deal with a variety of file formats including dotbracket strings, PDB and MMCIF files. We can handle modified residues, missing residues, cofold and multifold structures as well as nucleotide numbers starting at arbitrary positions. We apply this library to the study of stacking helices in junctions and pseudo knots and investigate how far stacking helices in solved experimental structures can divert from coaxial geometries.
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Affiliation(s)
- Bernhard C. Thiel
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Irene K. Beckmann
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Peter Kerpedjiev
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Ivo L. Hofacker
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, 1090, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, 1090, Austria
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17
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Ruan JJ, Yu Y, Hou W, Chen Z, Fang J, Zhang J, Ni M, Li D, Lu S, Rui J, Wu R, Zhang W, Ruan BH. Kidney-Type Glutaminase Inhibitor Hexylselen Selectively Kills Cancer Cells via a Three-Pronged Mechanism. ACS Pharmacol Transl Sci 2019; 2:18-30. [PMID: 32219214 DOI: 10.1021/acsptsci.8b00047] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Indexed: 12/26/2022]
Abstract
Tumor metabolism has been deeply investigated for cancer therapeutics. Here, we demonstrate that glutamine deficiency alone could not completely inhibit cancer cell growth and that many potent kidney-type glutaminase (KGA) inhibitors did not show satisfying in vivo efficacy. The potent KGA allosteric inhibitor, CB-839, resulted in up to 80% growth inhibition of all tested cell lines, whereas Hexylselen (CPD-3B), a KGA/glutamate dehydrogenase (GDH) inhibitor, showed essentially no toxicity to normal cells up to a 10 μM concentration and could completely inhibit the growth of many aggressive cell lines. Further analyses showed that CPD-3B targets not only KGA and GDH but also thioredoxin reductase (TrxR) and amidotransferase (GatCAB), which results in corresponding regulation of Akt/Erk/caspase-9 signaling pathways. In an aggressive liver cancer xenograft model, CPD-3B significantly reduced tumor size, caused massive tumor tissue damage, and prolonged survival rate. These provide important information for furthering the drug design of an effective anticancer KGA allosteric inhibitor.
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Affiliation(s)
- Jennifer Jin Ruan
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yan Yu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Hou
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zhao Chen
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jinzhang Fang
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jingjing Zhang
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Muowei Ni
- Center for Cancer Research, Zhejiang Cancer Hospital, Hangzhou 310022, PR China
| | - Di Li
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shiying Lu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jingjing Rui
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Rui Wu
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Zhang
- Department of Urology, Tongde Hospital of Zhejiang Province, Hangzhou 310012, China
| | - Benfang Helen Ruan
- College of Pharmaceutical Science, Collaborative Innovation Center of Yangtza River Delta Region Green Pharmaceuticals, IDD & CB, Zhejiang University of Technology, Hangzhou 310014, China
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18
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Esquirol L, Peat TS, Wilding M, Liu JW, French NG, Hartley CJ, Onagi H, Nebl T, Easton CJ, Newman J, Scott C. An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme. J Biol Chem 2018. [PMID: 29523689 DOI: 10.1074/jbc.ra118.001996] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyanuric acid is a metabolic intermediate of s-triazines, such as atrazine (a common herbicide) and melamine (used in resins and plastics). Cyanuric acid is mineralized to ammonia and carbon dioxide by the soil bacterium Pseudomonas sp. strain ADP via three hydrolytic enzymes (AtzD, AtzE, and AtzF). Here, we report the purification and biochemical and structural characterization of AtzE. Contrary to previous reports, we found that AtzE is not a biuret amidohydrolase, but instead it catalyzes the hydrolytic deamination of 1-carboxybiuret. X-ray crystal structures of apo AtzE and AtzE bound with the suicide inhibitor phenyl phosphorodiamidate revealed that the AtzE enzyme complex consists of two independent molecules in the asymmetric unit. We also show that AtzE forms an α2β2 heterotetramer with a previously unidentified 68-amino acid-long protein (AtzG) encoded in the cyanuric acid mineralization operon from Pseudomonas sp. strain ADP. Moreover, we observed that AtzG is essential for the production of soluble, active AtzE and that this obligate interaction is a vestige of their shared evolutionary origin. We propose that AtzEG was likely recruited into the cyanuric acid-mineralizing pathway from an ancestral glutamine transamidosome that required protein-protein interactions to enforce the exclusion of solvent from the transamidation reaction.
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Affiliation(s)
- Lygie Esquirol
- From the Biocatalysis and Synthetic Biology Team and.,the Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, and
| | - Thomas S Peat
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria 3052, Australia
| | - Matthew Wilding
- the Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, and.,CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria 3052, Australia
| | - Jian-Wei Liu
- From the Biocatalysis and Synthetic Biology Team and
| | | | | | - Hideki Onagi
- the Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, and
| | - Thomas Nebl
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria 3052, Australia
| | - Christopher J Easton
- the Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, and
| | - Janet Newman
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria 3052, Australia
| | - Colin Scott
- From the Biocatalysis and Synthetic Biology Team and .,Synthetic Biology Future Science Platform, CSIRO Land and Water, Canberra, Australian Capital Territory 2601
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19
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Abstract
We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code.
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Affiliation(s)
- Daewoo Pak
- a Center for Statistical Training and Consulting , Michigan State University , E. Lansing , MI 48824 , USA
| | - Nan Du
- b Computer Science and Engineering , Michigan State University , E. Lansing , MI 48824
| | | | - Yanni Sun
- b Computer Science and Engineering , Michigan State University , E. Lansing , MI 48824
| | - Zachary F Burton
- d Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI 48824-1319
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20
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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]
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21
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Corona A, Palmer SO, Zamacona R, Mendez B, Dean FB, Bullard JM. Discovery and Characterization of Chemical Compounds That Inhibit the Function of Aspartyl-tRNA Synthetase from Pseudomonas aeruginosa. SLAS DISCOVERY 2017; 23:294-301. [PMID: 29186665 DOI: 10.1177/2472555217744559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pseudomonas aeruginosa, an opportunistic pathogen, is highly susceptible to developing resistance to multiple antibiotics. The gene encoding aspartyl-tRNA synthetase (AspRS) from P. aeruginosa was cloned and the resulting protein characterized. AspRS was kinetically evaluated, and the KM values for aspartic acid, ATP, and tRNA were 170, 495, and 0.5 μM, respectively. AspRS was developed into a screening platform using scintillation proximity assay (SPA) technology and used to screen 1690 chemical compounds, resulting in the identification of two inhibitory compounds, BT02A02 and BT02C05. The minimum inhibitory concentrations (MICs) were determined against nine clinically relevant bacterial strains, including efflux pump mutant and hypersensitive strains of P. aeruginosa. The compounds displayed broad-spectrum antibacterial activity and inhibited growth of the efflux and hypersensitive strains with MICs of 16 μg/mL. Growth of wild-type strains were unaffected, indicating that efflux was likely responsible for this lack of activity. BT02A02 did not inhibit growth of human cell cultures at any concentration. However, BT02C05 did inhibit human cell cultures with a cytotoxicity concentration (CC50) of 61.6 μg/mL. The compounds did not compete with either aspartic acid or ATP for binding AspRS, indicating that the mechanism of action of the compound occurs outside the active site of aminoacylation.
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Affiliation(s)
- Araceli Corona
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | | | - Regina Zamacona
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - Benjamin Mendez
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - Frank B Dean
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
| | - James M Bullard
- 1 Chemistry Department, The University of Texas-RGV, Edinburg, TX, USA
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22
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Structural basis for tRNA-dependent cysteine biosynthesis. Nat Commun 2017; 8:1521. [PMID: 29142195 PMCID: PMC5688128 DOI: 10.1038/s41467-017-01543-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/26/2017] [Indexed: 11/25/2022] Open
Abstract
Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNACys followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNACys, respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNACys between SepRS and SepCysS distant active sites. This channeling mechanism could facilitate the consecutive reactions of the two-step indirect pathway of Cys-tRNACys synthesis (tRNA-dependent cysteine biosynthesis) to prevent challenge of translational fidelity, and may reflect the mechanism that cysteine was originally added into genetic code. tRNA-dependent cysteine biosynthesis is catalyzed by the transsulfursome protein complex. Here, the authors use a multidisciplinary approach to structurally characterize the archaeal transsulfursome and propose a model for tRNA channeling in the complex.
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23
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Songsiriritthigul C, Suebka S, Chen CJ, Fuengfuloy P, Chuawong P. Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori. Acta Crystallogr F Struct Biol Commun 2017; 73:62-69. [PMID: 28177315 PMCID: PMC5297925 DOI: 10.1107/s2053230x16020586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/28/2016] [Indexed: 01/25/2023] Open
Abstract
The N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) plays a crucial role in the recognition of both tRNAAsp and tRNAAsn. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS1-104) from the human-pathogenic bacterium Helicobacter pylori is reported at 2.0 Å resolution. The apo form of H. pylori ND-AspRS1-104 shares high structural similarity with the N-terminal anticodon-binding domains of the discriminating aspartyl-tRNA synthetase (D-AspRS) from Escherichia coli and ND-AspRS from Pseudomonas aeruginosa, allowing recognition elements to be proposed for tRNAAsp and tRNAAsn. It is proposed that a long loop (Arg77-Lys90) in this H. pylori domain influences its relaxed tRNA specificity, such that it is classified as nondiscriminating. A structural comparison between D-AspRS from E. coli and ND-AspRS from P. aeruginosa suggests that turns E and F (78GAGL81 and 83NPKL86) in H. pylori ND-AspRS play a crucial role in anticodon recognition. Accordingly, the conserved Pro84 in turn F facilitates the recognition of the anticodons of tRNAAsp (34GUC36) and tRNAAsn (34GUU36). The absence of the amide H atom allows both C and U bases to be accommodated in the tRNA-recognition site.
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MESH Headings
- Amino Acid Sequence
- Anticodon/chemistry
- Anticodon/metabolism
- Apoproteins/chemistry
- Apoproteins/genetics
- Apoproteins/metabolism
- Aspartate-tRNA Ligase/chemistry
- Aspartate-tRNA Ligase/genetics
- Aspartate-tRNA Ligase/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Binding Sites
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Gene Expression
- Helicobacter pylori/chemistry
- Helicobacter pylori/enzymology
- Models, Molecular
- Plasmids/chemistry
- Plasmids/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Pseudomonas aeruginosa/enzymology
- Pseudomonas aeruginosa/genetics
- RNA, Transfer, Asn/chemistry
- RNA, Transfer, Asn/genetics
- RNA, Transfer, Asn/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Structural Homology, Protein
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Affiliation(s)
- Chomphunuch Songsiriritthigul
- Synchrotron Light Research Institute (Public Organization), 111 University Avenue, Nakhon Ratchasima 30000, Thailand
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Suwimon Suebka
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, and Special Research Unit for Advanced Magnetic Resonance, Kasetsart University, 50 Ngamwongwan Road, Chatuchak, Bangkok 10900, Thailand
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Pitchayada Fuengfuloy
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, and Special Research Unit for Advanced Magnetic Resonance, Kasetsart University, 50 Ngamwongwan Road, Chatuchak, Bangkok 10900, Thailand
| | - Pitak Chuawong
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, and Special Research Unit for Advanced Magnetic Resonance, Kasetsart University, 50 Ngamwongwan Road, Chatuchak, Bangkok 10900, Thailand
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24
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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
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25
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Baker JA, Simkovic F, Taylor HMC, Rigden DJ. Potential DNA binding and nuclease functions of ComEC domains characterized in silico. Proteins 2016; 84:1431-42. [PMID: 27318187 PMCID: PMC5031224 DOI: 10.1002/prot.25088] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/25/2016] [Accepted: 06/13/2016] [Indexed: 12/15/2022]
Abstract
Bacterial competence, which can be natural or induced, allows the uptake of exogenous double stranded DNA (dsDNA) into a competent bacterium. This process is known as transformation. A multiprotein assembly binds and processes the dsDNA to import one strand and degrade another yet the underlying molecular mechanisms are relatively poorly understood. Here distant relationships of domains in Competence protein EC (ComEC) of Bacillus subtilis (Uniprot: P39695) were characterized. DNA-protein interactions were investigated in silico by analyzing models for structural conservation, surface electrostatics and structure-based DNA binding propensity; and by data-driven macromolecular docking of DNA to models. Our findings suggest that the DUF4131 domain contains a cryptic DNA-binding OB fold domain and that the β-lactamase-like domain is the hitherto cryptic competence nuclease. Proteins 2016; 84:1431-1442. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
- James A Baker
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Felix Simkovic
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Helen M C Taylor
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Daniel J Rigden
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom.
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Chen M, Nakazawa Y, Kubo Y, Asano N, Kato K, Tanaka I, Yao M. Crystallographic analysis of a subcomplex of the transsulfursome with tRNA for Cys-tRNA(Cys) synthesis. Acta Crystallogr F Struct Biol Commun 2016; 72:569-72. [PMID: 27380375 PMCID: PMC4933008 DOI: 10.1107/s2053230x16009559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/14/2016] [Indexed: 11/10/2022] Open
Abstract
In most organisms, Cys-tRNA(Cys) is directly synthesized by cysteinyl-tRNA synthetase (CysRS). Many methanogenic archaea, however, use a two-step, indirect pathway to synthesize Cys-tRNA(Cys) owing to a lack of CysRS and cysteine-biosynthesis systems. This reaction is catalyzed by O-phosphoseryl-tRNA synthetase (SepRS), Sep-tRNA:Cys-tRNA synthase (SepCysS) and SepRS/SepCysS pathway enhancer (SepCysE) as the transsulfursome, in which SepCysE connects both SepRS and SepCysS. On the transsulfursome, SepRS first ligates an O-phosphoserine to tRNA(Cys), and the mischarged intermediate Sep-tRNA(Cys) is then transferred to SepCysS, where it is further modified to Cys-tRNA(Cys). In this study, a subcomplex of the transsulfursome with tRNA(Cys) (SepCysS-SepCysE-tRNA(Cys)), which is involved in the second reaction step of the indirect pathway, was constructed and then crystallized. The crystals diffracted X-rays to a resolution of 2.6 Å and belonged to space group P6522, with unit-cell parameters a = b = 107.2, c = 551.1 Å. The structure determined by molecular replacement showed that the complex consists of a SepCysS dimer, a SepCysE dimer and one tRNA(Cys) in the asymmetric unit.
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Affiliation(s)
- Meirong Chen
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yuto Nakazawa
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yume Kubo
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Nozomi Asano
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Koji Kato
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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27
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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28
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Pham VH, Maaroufi H, Levesque RC, Lapointe J. Cyclic peptides identified by phage display are competitive inhibitors of the tRNA-dependent amidotransferase of Helicobacter pylori. Peptides 2016; 79:8-15. [PMID: 26976271 DOI: 10.1016/j.peptides.2016.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 02/07/2023]
Abstract
In Helicobacter pylori, the heterotrimeric tRNA-dependent amidotransferase (GatCAB) is essential for protein biosynthesis because it catalyzes the conversion of misacylated Glu-tRNA(Gln) and Asp-tRNA(Asn) into Gln-tRNA(Gln) and Asn-tRNA(Asn), respectively. In this study, we used a phage library to identify peptide inhibitors of GatCAB. A library displaying loop-constrained heptapeptides was used to screen for phages binding to the purified GatCAB. To optimize the probability of obtaining competitive inhibitors of GatCAB with respect to its substrate Glu-tRNA(Gln), we used that purified substrate in the biopanning process of the phage-display technique to elute phages bound to GatCAB at the third round of the biopanning process. Among the eluted phages, we identified several that encode cyclic peptides rich in Trp and Pro that inhibit H. pylori GatCAB in vitro. Peptides P10 and P9 were shown to be competitive inhibitors of GatCAB with respect to its substrate Glu-tRNA(Gln), with Ki values of 126 and 392μM, respectively. The docking models revealed that the Trp residues of these peptides form π-π stacking interactions with Tyr81 of the synthetase active site, as does the 3'-terminal A76 of tRNA, supporting their competitive behavior with respect to Glu-tRNA(Gln) in the transamidation reaction. These peptides can be used as scaffolds in the search for novel antibiotics against the pathogenic bacteria that require GatCAB for Gln-tRNA(Gln) and/or Asn-tRNA(Asn) formation.
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Affiliation(s)
- Van Hau Pham
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada; The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec G1V 0A6, Canada.
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada; Département de Biologie Médicale, Faculté de Médicine, Université Laval, Québec G1V 0A6, Canada
| | - Jacques Lapointe
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec G1V 0A6, Canada; The Quebec Network for Research on Protein Function, Structure, and Engineering (PROTEO), Québec G1V 0A6, Canada.
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29
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Nair N, Raff H, Islam MT, Feen M, Garofalo DM, Sheppard K. The Bacillus subtilis and Bacillus halodurans Aspartyl-tRNA Synthetases Retain Recognition of tRNA(Asn). J Mol Biol 2016; 428:618-630. [PMID: 26804570 DOI: 10.1016/j.jmb.2016.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 12/19/2022]
Abstract
Synthesis of asparaginyl-tRNA (Asn-tRNA(Asn)) in bacteria can be formed either by directly ligating Asn to tRNA(Asn) using an asparaginyl-tRNA synthetase (AsnRS) or by synthesizing Asn on the tRNA. In the latter two-step indirect pathway, a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) attaches Asp to tRNA(Asn) and the amidotransferase GatCAB transamidates the Asp to Asn on the tRNA. GatCAB can be similarly used for Gln-tRNA(Gln) formation. Most bacteria are predicted to use only one route for Asn-tRNA(Asn) formation. Given that Bacillus halodurans and Bacillus subtilis encode AsnRS for Asn-tRNA(Asn) formation and Asn synthetases to synthesize Asn and GatCAB for Gln-tRNA(Gln) synthesis, their AspRS enzymes were thought to be specific for tRNA(Asp). However, we demonstrate that the AspRSs are non-discriminating and can be used with GatCAB to synthesize Asn. The results explain why B. subtilis with its Asn synthetase genes knocked out is still an Asn prototroph. Our phylogenetic analysis suggests that this may be common among Firmicutes and 30% of all bacteria. In addition, the phylogeny revealed that discrimination toward tRNA(Asp) by AspRS has evolved independently multiple times. The retention of the indirect pathway in B. subtilis and B. halodurans likely reflects the ancient link between Asn biosynthesis and its use in translation that enabled Asn to be added to the genetic code.
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Affiliation(s)
- Nilendra Nair
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA
| | - Hannah Raff
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA
| | | | - Melanie Feen
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA
| | - Denise M Garofalo
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA
| | - Kelly Sheppard
- Chemistry Department, Skidmore College, Saratoga Springs, NY 12866, USA.
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