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Ivanesthi IR, Latifah E, Amrullah LF, Tseng YK, Chuang TH, Pan HC, Yang CS, Liu SY, Wang CC. Adaptation of a eukaryote-like ProRS to a prokaryote-like tRNAPro. Nucleic Acids Res 2024; 52:7158-7170. [PMID: 38842939 PMCID: PMC11229370 DOI: 10.1093/nar/gkae483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024] Open
Abstract
Prolyl-tRNA synthetases (ProRSs) are unique among aminoacyl-tRNA synthetases (aaRSs) in having two distinct structural architectures across different organisms: prokaryote-like (P-type) and eukaryote/archaeon-like (E-type). Interestingly, Bacillus thuringiensis harbors both types, with P-type (BtProRS1) and E-type ProRS (BtProRS2) coexisting. Despite their differences, both enzymes are constitutively expressed and functional in vivo. Similar to BtProRS1, BtProRS2 selectively charges the P-type tRNAPro and displays higher halofuginone tolerance than canonical E-type ProRS. However, these two isozymes recognize the primary identity elements of the P-type tRNAPro-G72 and A73 in the acceptor stem-through distinct mechanisms. Moreover, BtProRS2 exhibits significantly higher tolerance to stresses (such as heat, hydrogen peroxide, and dithiothreitol) than BtProRS1 does. This study underscores how an E-type ProRS adapts to a P-type tRNAPro and how it may contribute to the bacterium's survival under stress conditions.
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Affiliation(s)
- Indira Rizqita Ivanesthi
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Emi Latifah
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Luqman Fikri Amrullah
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Yi-Kuan Tseng
- Graduate Institute of Statistics, National Central University, Zhongli District, Taoyuan320317, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan Town, Miaoli 35053, Taiwan
| | - Hung-Chuan Pan
- Department of Neurosurgery, Taichung Veterans General Hospital, Taichung 407219, Taiwan
| | - Chih-Shiang Yang
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Shih-Yang Liu
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan 320317, Taiwan
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Nasim F, Kumar MS, Alvala M, Qureshi IA. Unraveling the peculiarities and development of novel inhibitors of leishmanial arginyl-tRNA synthetase. FEBS J 2024; 291:2955-2979. [PMID: 38525644 DOI: 10.1111/febs.17122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/22/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
Aminoacylation by tRNA synthetase is a crucial part of protein synthesis and is widely recognized as a therapeutic target for drug development. Unlike the arginyl-tRNA synthetases (ArgRSs) reported previously, here, we report an ArgRS of Leishmania donovani (LdArgRS) that can follow the canonical two-step aminoacylation process. Since a previously uncharacterized insertion region is present within its catalytic domain, we implemented the splicing by overlap extension PCR (SOE-PCR) method to create a deletion mutant (ΔIns-LdArgRS) devoid of this region to investigate its function. Notably, the purified LdArgRS and ΔIns-LdArgRS exhibited different oligomeric states along with variations in their enzymatic activity. The full-length protein showed better catalytic efficiency than ΔIns-LdArgRS, and the insertion region was identified as the tRNA binding domain. In addition, a benzothiazolo-coumarin derivative (Comp-7j) possessing high pharmacokinetic properties was recognized as a competitive and more specific inhibitor of LdArgRS than its human counterpart. Removal of the insertion region altered the mode of inhibition for ΔIns-LdArgRS and caused a reduction in the inhibitor's binding affinity. Both purified proteins depicted variances in the secondary structural content upon ligand binding and thus, thermostability. Apart from the trypanosomatid-specific insertion and Rossmann fold motif, LdArgRS revealed typical structural characteristics of ArgRSs, and Comp-7j was found to bind within the ATP binding pocket. Furthermore, the placement of tRNAArg near the insertion region enhanced the stability and compactness of LdArgRS compared to other ligands. This study thus reports a unique ArgRS with respect to catalytic as well as structural properties, which can be considered a plausible drug target for the derivation of novel anti-leishmanial agents.
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Affiliation(s)
- Fouzia Nasim
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Muppidi Shravan Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | - Mallika Alvala
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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Latifah E, Ivanesthi IR, Tseng Y, Pan H, Wang C. Adaptive evolution: Eukaryotic enzyme's specificity shift to a bacterial substrate. Protein Sci 2024; 33:e5028. [PMID: 38757396 PMCID: PMC11099734 DOI: 10.1002/pro.5028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/18/2024]
Abstract
Prolyl-tRNA synthetase (ProRS), belonging to the family of aminoacyl-tRNA synthetases responsible for pairing specific amino acids with their respective tRNAs, is categorized into two distinct types: the eukaryote/archaeon-like type (E-type) and the prokaryote-like type (P-type). Notably, these types are specific to their corresponding cognate tRNAs. In an intriguing paradox, Thermus thermophilus ProRS (TtProRS) aligns with the E-type ProRS but selectively charges the P-type tRNAPro, featuring the bacterium-specific acceptor-stem elements G72 and A73. This investigation reveals TtProRS's notable resilience to the inhibitor halofuginone, a synthetic derivative of febrifugine emulating Pro-A76, resembling the characteristics of the P-type ProRS. Furthermore, akin to the P-type ProRS, TtProRS identifies its cognate tRNA through recognition of the acceptor-stem elements G72/A73, along with the anticodon elements G35/G36. However, in contrast to the P-type ProRS, which relies on a strictly conserved R residue within the bacterium-like motif 2 loop for recognizing G72/A73, TtProRS achieves this through a non-conserved sequence, RTR, within the otherwise non-interacting eukaryote-like motif 2 loop. This investigation sheds light on the adaptive capacity of a typically conserved housekeeping enzyme to accommodate a novel substrate.
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Affiliation(s)
- Emi Latifah
- Department of Life SciencesNational Central UniversityTaoyuanTaiwan
| | | | - Yi‐Kuan Tseng
- Graduate Institute of StatisticsNational Central UniversityTaoyuanTaiwan
| | - Hung‐Chuan Pan
- Department of NeurosurgeryTaichung Veterans General HospitalTaichungTaiwan
| | - Chien‐Chia Wang
- Department of Life SciencesNational Central UniversityTaoyuanTaiwan
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Chakraborty N, Das BK, Bera AK, Borah S, Mohanty D, Yadav AK, Kumar J, Koushlesh SK, Chanu TN, Panda SP, Vallangi R. Co-Prevalence of Virulence and Pathogenic Potential in Multiple Antibiotic Resistant Aeromonas spp. from Diseased Fishes with In Silico Insight on the Virulent Protein Network. Life (Basel) 2022; 12:life12121979. [PMID: 36556344 PMCID: PMC9781969 DOI: 10.3390/life12121979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Aeromonas species exhibit widespread presence in food, poultry, and aquaculture. They are major multi-drug-resistant fish pathogens. This study aims to identify Aeromonas species harbouring virulence genes aerolysin, flagellin, and lipase from diseased fishes of Assam wetlands with association with antibiotic resistance and in vivo pathogenicity. One hundred and thirty-four Aeromonas strains were isolated and thirty representative species identified using genus-specific 16S rRNA gene amplification. A. veronii was most prevalent (53.7%) followed by A. hydrophila (40.2%), A. caviae (4.47%), and A. dhakensis (1.49%). Ninety percent (90%) of strains harboured at least one of the studied virulence genes: aerA (73.3%), lip (46.6%), and flaA (26.6%). The highest multiple antibiotic resistance (MAR) index 0.8 corresponded to A. hydrophila DBTNE1 (MZ723069), containing all the studied genes. The lowest LD50 values (1.6 × 106 CFU/fish) corresponded to isolates having both aerA and lip. β-lactams showed utmost resistance and lowest for aminoglycosides. There was a significant (p < 0.05) Pearson chi-square test of association between the occurrence of virulence and antibiotic resistance. The in silico protein−protein interaction revealed important drug targets, such as σ28 transcription factor, aminoacyl-tRNA synthetase, and diacylglycerol kinase, with significant (p < 0.05) enrichment. This study suggests that fish-isolate Aeromonas strains represent potential threat to aquaculture with subsequent risk of transferring antibiotic resistance to human pathogens.
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Affiliation(s)
- Nabanita Chakraborty
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Guwahati 781006, India
| | - Basanta Kumar Das
- Central Inland Fisheries Research Institute (ICAR), Barrackpore 700120, India
- Correspondence: ; Tel.: +91-033-2592-1190; Fax: +91-033-2592-0388
| | - Asit Kumar Bera
- Central Inland Fisheries Research Institute (ICAR), Barrackpore 700120, India
| | - Simanku Borah
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Guwahati 781006, India
| | - Debasmita Mohanty
- Central Inland Fisheries Research Institute (ICAR), Barrackpore 700120, India
| | - Anil Kumar Yadav
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Guwahati 781006, India
| | - Jeetendra Kumar
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Prayagraj 211002, India
| | | | | | - Soumya Prasad Panda
- Central Inland Fisheries Research Institute (ICAR), Barrackpore 700120, India
| | - Ravali Vallangi
- Regional Centre, Central Inland Fisheries Research Institute (ICAR), Guwahati 781006, India
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Jani J, Pappachan A. A review on quality control agents of protein translation - The role of Trans-editing proteins. Int J Biol Macromol 2022; 199:252-263. [PMID: 34995670 DOI: 10.1016/j.ijbiomac.2021.12.176] [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: 10/23/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Translation of RNA to protein is a key feature of cellular life. The fidelity of this process mainly depends on the availability of correctly charged tRNAs. Different domains of tRNA synthetase (aaRS) maintain translation quality by ensuring the proper attachment of particular amino acid with respective tRNA, thus it establishes the rule of genetic code. However occasional errors by aaRS generate mischarged tRNAs, which can become lethal to the cells. Accurate protein synthesis necessitates hydrolysis of mischarged tRNAs. Various cis and trans-editing proteins are identified which recognize these mischarged products and correct them by hydrolysis. Trans-editing proteins are homologs of cis-editing domains of aaRS. The trans-editing proteins work in close association with aaRS, Ef-Tu, and ribosome to prevent global mistranslation and ensures correct charging of tRNA. In this review, we discuss the major trans-editing proteins and compared them with their cis-editing counterparts. We also discuss their structural features, biochemical activity and role in maintaining cellular protein homeostasis.
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Affiliation(s)
- Jaykumar Jani
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India
| | - Anju Pappachan
- School of Life Sciences, Central University of Gujarat, Sector 30, Gandhinagar 382030, Gujarat, India.
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Kuzmishin Nagy AB, Bakhtina M, Musier-Forsyth K. Trans-editing by aminoacyl-tRNA synthetase-like editing domains. Enzymes 2020; 48:69-115. [PMID: 33837712 DOI: 10.1016/bs.enz.2020.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRS) are ubiquitous enzymes responsible for aminoacyl-tRNA (aa-tRNA) synthesis. Correctly formed aa-tRNAs are necessary for proper decoding of mRNA and accurate protein synthesis. tRNAs possess specific nucleobases that promote selective recognition by cognate aaRSs. Selecting the cognate amino acid can be more challenging because all amino acids share the same peptide backbone and several are isosteric or have similar side chains. Thus, aaRSs can misactivate non-cognate amino acids and produce mischarged aa-tRNAs. If left uncorrected, mischarged aa-tRNAs deliver their non-cognate amino acid to the ribosome resulting in misincorporation into the nascent polypeptide chain. This changes the primary protein sequence and potentially causes misfolding or formation of non-functional proteins that impair cell survival. A variety of proofreading or editing pathways exist to prevent and correct mistakes in aa-tRNA formation. Editing may occur before the amino acid transfer step of aminoacylation via hydrolysis of the aminoacyl-adenylate. Alternatively, post-transfer editing, which occurs after the mischarged aa-tRNA is formed, may be carried out via a distinct editing site on the aaRS where the mischarged aa-tRNA is deacylated. In recent years, it has become clear that most organisms also encode factors that lack aminoacylation activity but resemble aaRS editing domains and function to clear mischarged aa-tRNAs in trans. This review focuses on these trans-editing factors, which are encoded in all three domains of life and function together with editing domains present within aaRSs to ensure that the accuracy of protein synthesis is sufficient for cell survival.
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Affiliation(s)
- Alexandra B Kuzmishin Nagy
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, United States.
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Hughes CA, Gorabi V, Escamilla Y, Dean FB, Bullard JM. Two Forms of Tyrosyl-tRNA Synthetase from Pseudomonas aeruginosa: Characterization and Discovery of Inhibitory Compounds. SLAS DISCOVERY 2020; 25:1072-1086. [PMID: 32583746 DOI: 10.1177/2472555220934793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Pseudomonas aeruginosa is a multidrug-resistant (MDR) pathogen and a causative agent of both nosocomial and community-acquired infections. The genes (tyrS and tyrZ) encoding both forms of P. aeruginosa tyrosyl-tRNA synthetase (TyrRS-S and TyrRS-Z) were cloned and the resulting proteins purified. TyrRS-S and TyrRS-Z were kinetically evaluated and the Km values for interaction with Tyr, ATP, and tRNATyr were 172, 204, and 1.5 μM and 29, 496, and 1.9 μM, respectively. The kcatobs values for interaction with Tyr, ATP, and tRNATyr were calculated to be 3.8, 1.0, and 0.2 s-1 and 3.1, 3.8, and 1.9 s-1, respectively. Using scintillation proximity assay (SPA) technology, a druglike 2000-compound library was screened to identify inhibitors of the enzymes. Four compounds (BCD37H06, BCD38C11, BCD49D09, and BCD54B04) were identified with inhibitory activity against TyrRS-S. BCD38C11 also inhibited TyrRS-Z. The IC50 values for BCD37H06, BCD38C11, BCD49D09, and BCD54B04 against TyrRS-S were 24, 71, 65, and 50 μM, respectively, while the IC50 value for BCD38C11 against TyrRS-Z was 241 μM. Minimum inhibitory concentrations (MICs) were determined against a panel of clinically important pathogens. All four compounds were observed to inhibit the growth of cultures of both Gram-positive and Gram-negative bacteria organisms with a bacteriostatic mode of action. When tested against human cell cultures, none of the compounds were toxic at concentrations up to 400 μg/mL. In mechanism of inhibition studies, BCD38C11 and BCD49D09 selectively inhibited TyrRS activity by competing with ATP for binding. BCD37H06 and BCD54B04 inhibited TyrRS activity by a mechanism other than substrate competition.
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Affiliation(s)
- Casey A Hughes
- The University of Texas-RGV, Edinburg, TX, USA.,Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX, USA
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