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Kushwaha V, Capalash N. Aminoacyl-tRNA synthetase (AARS) as an attractive drug target in neglected tropical trypanosomatid diseases-Leishmaniasis, Human African Trypanosomiasis and Chagas disease. Mol Biochem Parasitol 2022; 251:111510. [PMID: 35988745 DOI: 10.1016/j.molbiopara.2022.111510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 10/15/2022]
Abstract
TriTryp diseases (Leishmaniasis, Human African Trypanosomiasis (HAT), and Chagas disease) are devastating parasitic neglected tropical diseases (NTDs) that affect billions of people in developing countries, cause high mortality in humans, and impose a large socio-economic burden. The current treatment options against tritryp diseases are suboptimal and challenging due to the emergence of resistance against available tritryp drugs. Hence, designing and developing effective anti-tritryp drugs with novel targets are required. Aminoacyl-tRNA synthetases (AARSs) involved in specific aminoacylation of transfer RNAs (tRNAs), interrupt protein synthesis through inhibitors, and retard the parasite growth. AaRSs have long been studied as therapeutic targets in bacteria, and three aaRS inhibitors, mupirocin (against IleRS), tavaborole AN2690 (against LeuRS), and halofuginone (against ProRS), are already in clinical practice. The structural differences between tritryp and human aaRSs and the presence of unique sequences (N-terminal domain/C-terminal domain/catalytic domain) make them potential target for developing selective inhibitors. Drugs based on a single aaRS target developed by high-throughput screening (HTS) are less effective due to the emergence of resistance. However, designing multi-targeted drugs may be a better strategy for resistance development. In this perspective, we discuss the characteristics of tritryp aaRSs, sequence conservation in their orthologs and their peculiarities, recent advancements towards the single-target and multi-target aaRS inhibitors developed through rational design.
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Affiliation(s)
- Vikas Kushwaha
- Department of Biotechnology, Panjab University, Sector-25, South Campus, Chandigarh 160025, India.
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Sector-25, South Campus, Chandigarh 160025, India.
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2
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Lassak J, Sieber A, Hellwig M. Exceptionally versatile take II: post-translational modifications of lysine and their impact on bacterial physiology. Biol Chem 2022; 403:819-858. [PMID: 35172419 DOI: 10.1515/hsz-2021-0382] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 01/16/2023]
Abstract
Among the 22 proteinogenic amino acids, lysine sticks out due to its unparalleled chemical diversity of post-translational modifications. This results in a wide range of possibilities to influence protein function and hence modulate cellular physiology. Concomitantly, lysine derivatives form a metabolic reservoir that can confer selective advantages to those organisms that can utilize it. In this review, we provide examples of selected lysine modifications and describe their role in bacterial physiology.
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Affiliation(s)
- Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Alina Sieber
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Michael Hellwig
- Technische Universität Braunschweig - Institute of Food Chemistry, Schleinitzstraße 20, D-38106 Braunschweig, Germany
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3
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Pfab M, Kielkowski P, Krafczyk R, Volkwein W, Sieber SA, Lassak J, Jung K. Synthetic post-translational modifications of elongation factor P using the ligase EpmA. FEBS J 2020; 288:663-677. [PMID: 32337775 DOI: 10.1111/febs.15346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/24/2020] [Accepted: 04/23/2020] [Indexed: 12/20/2022]
Abstract
Canonically, tRNA synthetases charge tRNA. However, the lysyl-tRNA synthetase paralog EpmA catalyzes the attachment of (R)-β-lysine to the ε-amino group of lysine 34 of the translation elongation factor P (EF-P) in Escherichia coli. This modification is essential for EF-P-mediated translational rescue of ribosomes stalled at consecutive prolines. In this study, we determined the kinetics of EpmA and its variant EpmA_A298G to catalyze the post-translational modification of K34 in EF-P with eight noncanonical substrates. In addition, acetylated EF-P was generated using an amber suppression system. The impact of these synthetically modified EF-P variants on in vitro translation of a polyproline-containing NanoLuc luciferase reporter was analyzed. Our results show that natural (R)-β-lysylation was more effective in rescuing stalled ribosomes than any other synthetic modification tested. Thus, our work not only provides new biochemical insights into the function of EF-P, but also opens a new route to post-translationally modify proteins using EpmA.
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Affiliation(s)
- Miriam Pfab
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Pavel Kielkowski
- Organic Chemistry II, Technical University of Munich, Garching, Germany
| | - Ralph Krafczyk
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Wolfram Volkwein
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Stephan A Sieber
- Organic Chemistry II, Technical University of Munich, Garching, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
| | - Kirsten Jung
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Germany
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4
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Vivijs B, Aertsen A, Michiels CW. Identification of Genes Required for Growth of Escherichia coli MG1655 at Moderately Low pH. Front Microbiol 2016; 7:1672. [PMID: 27826291 PMCID: PMC5078493 DOI: 10.3389/fmicb.2016.01672] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/06/2016] [Indexed: 01/27/2023] Open
Abstract
The survival of some pathotypes of Escherichia coli in very low pH environments like highly acidic foods and the stomach has been well documented and contributes to their success as foodborne pathogens. In contrast, the ability of E. coli to grow at moderately low pH has received less attention, although this property can be anticipated to be also very important for the safety of mildly acidic foods. Therefore, the objective of this study was to identify cellular functions required for growth of the non-pathogenic strain E. coli MG1655 at low pH. First, the role of the four E. coli amino acid decarboxylase systems, which are the major cellular mechanisms allowing extreme acid survival, was investigated using mutants defective in each of the systems. Only the lysine decarboxylase (CadA) was required for low pH growth. Secondly, a screening of 8544 random transposon insertion mutants resulted in the identification of six genes affecting growth in LB broth acidified to pH 4.50 with HCl. Two of the genes, encoding the transcriptional regulator LeuO and the elongation factor P-β-lysine ligase EpmA, can be linked to CadA production. Two other genes, encoding the diadenosine tetraphosphatase ApaH and the tRNA modification GTPase MnmE, have been previously implicated in the bacterial response to stresses other than low pH. A fifth gene encodes the LPS heptosyltransferase WaaC, and its mutant has a deep rough colony phenotype, which has been linked to reduced acid tolerance in earlier work. Finally, tatC encodes a secA-independent protein translocase that exports a few dozen proteins and thus is likely to have a pleiotropic phenotype. For mnmE, apaH, epmA, and waaC, de novo in frame deletion and genetic complementation confirmed their role in low pH growth, and these deletion mutants were also affected in growth in apple juice and tomato juice. However, the mutants were not affected in survival in gastric simulation medium at pH 2.5, indicating that growth at moderately low pH and survival of extremely low pH depend mostly on different cellular functions.
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Affiliation(s)
| | | | - Chris W. Michiels
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU LeuvenLeuven, Belgium
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5
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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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6
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Doerfel LK, Rodnina MV. Elongation factor P: Function and effects on bacterial fitness. Biopolymers 2016; 99:837-45. [PMID: 23828669 DOI: 10.1002/bip.22341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 06/19/2013] [Indexed: 12/22/2022]
Abstract
The elongation phase of translation is promoted by three universal elongation factors, EF-Tu, EF-Ts, and EF-G in bacteria and their homologs in archaea and eukaryotes. Recent findings demonstrate that the translation of a subset of mRNAs requires a fourth elongation factor, EF-P in bacteria or the homologs factors a/eIF5A in other kingdoms of life. EF-P prevents the ribosome from stalling during the synthesis of proteins containing consecutive Pro residues, such as PPG, PPP, or longer Pro clusters. The efficient and coordinated synthesis of such proteins is required for bacterial growth, motility, virulence, and stress response. EF-P carries a unique post-translational modification, which contributes to its catalytic proficiency. The modification enzymes, which are lacking in higher eukaryotes, provide attractive new targets for the development of new, highly specific antimicrobials.
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Affiliation(s)
- Lili K Doerfel
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Goettingen, Germany
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7
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Doerfel LK, Wohlgemuth I, Kubyshkin V, Starosta AL, Wilson DN, Budisa N, Rodnina MV. Entropic Contribution of Elongation Factor P to Proline Positioning at the Catalytic Center of the Ribosome. J Am Chem Soc 2015; 137:12997-3006. [DOI: 10.1021/jacs.5b07427] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lili K. Doerfel
- Department
of Physical Biochemistry, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Ingo Wohlgemuth
- Department
of Physical Biochemistry, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Vladimir Kubyshkin
- Institut
für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Agata L. Starosta
- Gene
Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany
| | - Daniel N. Wilson
- Gene
Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany
- Center
for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Nediljko Budisa
- Institut
für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Marina V. Rodnina
- Department
of Physical Biochemistry, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
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8
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Bullwinkle T, Lazazzera B, Ibba M. Quality Control and Infiltration of Translation by Amino Acids Outside of the Genetic Code. Annu Rev Genet 2014; 48:149-66. [DOI: 10.1146/annurev-genet-120213-092101] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tammy Bullwinkle
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
| | - Beth Lazazzera
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, Ohio 43210
- Ohio State Biochemistry Program and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210;
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9
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Starosta AL, Lassak J, Jung K, Wilson DN. The bacterial translation stress response. FEMS Microbiol Rev 2014; 38:1172-201. [PMID: 25135187 DOI: 10.1111/1574-6976.12083] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 07/18/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022] Open
Abstract
Throughout their life, bacteria need to sense and respond to environmental stress. Thus, such stress responses can require dramatic cellular reprogramming, both at the transcriptional as well as the translational level. This review focuses on the protein factors that interact with the bacterial translational apparatus to respond to and cope with different types of environmental stress. For example, the stringent factor RelA interacts with the ribosome to generate ppGpp under nutrient deprivation, whereas a variety of factors have been identified that bind to the ribosome under unfavorable growth conditions to shut-down (RelE, pY, RMF, HPF and EttA) or re-program (MazF, EF4 and BipA) translation. Additional factors have been identified that rescue ribosomes stalled due to stress-induced mRNA truncation (tmRNA, ArfA, ArfB), translation of unfavorable protein sequences (EF-P), heat shock-induced subunit dissociation (Hsp15), or antibiotic inhibition (TetM, FusB). Understanding the mechanism of how the bacterial cell responds to stress will not only provide fundamental insight into translation regulation, but will also be an important step to identifying new targets for the development of novel antimicrobial agents.
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Affiliation(s)
- Agata L Starosta
- Gene Center, Department for Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany; Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
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10
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Manhas R, Tripathi P, Khan S, Sethu Lakshmi B, Lal SK, Gowri VS, Sharma A, Madhubala R. Identification and functional characterization of a novel bacterial type asparagine synthetase A: a tRNA synthetase paralog from Leishmania donovani. J Biol Chem 2014; 289:12096-12108. [PMID: 24610810 DOI: 10.1074/jbc.m114.554642] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asparagine is formed by two structurally distinct asparagine synthetases in prokaryotes. One is the ammonia-utilizing asparagine synthetase A (AsnA), and the other is asparagine synthetase B (AsnB) that uses glutamine or ammonia as a nitrogen source. In a previous investigation using sequence-based analysis, we had shown that Leishmania spp. possess asparagine-tRNA synthetase paralog asparagine synthetase A (LdASNA) that is ammonia-dependent. Here, we report the cloning, expression, and kinetic analysis of ASNA from Leishmania donovani. Interestingly, LdASNA was both ammonia- and glutamine-dependent. To study the physiological role of ASNA in Leishmania, gene deletion mutations were attempted via targeted gene replacement. Gene deletion of LdASNA showed a growth delay in mutants. However, chromosomal null mutants of LdASNA could not be obtained as the double transfectant mutants showed aneuploidy. These data suggest that LdASNA is essential for survival of the Leishmania parasite. LdASNA enzyme was recalcitrant toward crystallization so we instead crystallized and solved the atomic structure of its close homolog from Trypanosoma brucei (TbASNA) at 2.2 Å. A very significant conservation in active site residues is observed between TbASNA and Escherichia coli AsnA. It is evident that the absence of an LdASNA homolog from humans and its essentiality for the parasites make LdASNA a novel drug target.
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Affiliation(s)
- Reetika Manhas
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pankaj Tripathi
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sameena Khan
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | | | - Shambhu Krishan Lal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Amit Sharma
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Rentala Madhubala
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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11
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Rossi D, Kuroshu R, Zanelli CF, Valentini SR. eIF5A and EF-P: two unique translation factors are now traveling the same road. WILEY INTERDISCIPLINARY REVIEWS. RNA 2014; 5:209-22. [PMID: 24402910 DOI: 10.1002/wrna.1211] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/01/2013] [Accepted: 11/06/2013] [Indexed: 11/09/2022]
Abstract
Translational control is extremely important in all organisms, and some of its aspects are highly conserved among all primary kingdoms, such as those related to the translation elongation step. The previously classified translation initiation factor 5A (eIF5A) and its bacterial homologue elongation factor P (EF-P) were discovered in the late 70's and have recently been the object of many studies. eIF5A and EF-P are the only cellular proteins that undergo hypusination and lysinylation, respectively, both of which are unique posttranslational modifications. Herein, we review all the important discoveries related to the biochemical and functional characterization of these factors, highlighting the implication of eIF5A in translation elongation instead of initiation. The findings that eIF5A and EF-P are important for specific cellular processes and play a role in the relief of ribosome stalling caused by specific amino acid sequences, such as those containing prolines reinforce the hypothesis that these factors are involved in specialized translation. Although there are some divergences between these unique factors, recent studies have clarified that they act similarly during protein synthesis. Further studies may reveal their precise mechanism of ribosome activity modulation as well as the mRNA targets that require eIF5A and EF-P for their proper translation.
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Affiliation(s)
- Danuza Rossi
- Department of Biological Sciences, School of Pharmaceutical Sciences, Univ Estadual Paulista (UNESP), Araraquara, SP, Brazil
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12
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Gowri VS, Ghosh I, Sharma A, Madhubala R. Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major. BMC Genomics 2012; 13:621. [PMID: 23151081 PMCID: PMC3532385 DOI: 10.1186/1471-2164-13-621] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 10/30/2012] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Leishmania major, a protozoan parasite, is the causative agent of cutaneous leishmaniasis. Due to the development of resistance against the currently available anti-leishmanial drugs, there is a growing need for specific inhibitors and novel drug targets. In this regards, aminoacyl tRNA synthetases, the linchpins of protein synthesis, have received recent attention among the kinetoplastid research community. This is the first comprehensive survey of the aminoacyl tRNA synthetases, their paralogs and other associated proteins from L. major. RESULTS A total of 26 aminoacyl tRNA synthetases were identified using various computational and bioinformatics tools. Phylogenetic analysis and domain architectures of the L. major aminoacyl tRNA synthetases suggest a probable archaeal/eukaryotic origin. Presence of additional domains or N- or C-terminal extensions in 11 aminoacyl tRNA synthetases from L. major suggests possibilities such as additional tRNA binding or oligomerization or editing activity. Five freestanding editing domains were identified in L. major. Domain assignment revealed a novel asparagine tRNA synthetase paralog, asparagine synthetase A which has been so far reported from prokaryotes and archaea. CONCLUSIONS A comprehensive bioinformatic analysis revealed 26 aminoacyl tRNA synthetases and five freestanding editing domains in L. major. Identification of two EMAP (endothelial monocyte-activating polypeptide) II-like proteins similar to human EMAP II-like proteins suggests their participation in multisynthetase complex formation. While the phylogeny of tRNA synthetases suggests a probable archaeal/eukaryotic origin, phylogeny of asparagine synthetase A strongly suggests a bacterial origin. The unique features identified in this work provide rationale for designing inhibitors against parasite aminoacyl tRNA synthetases and their paralogs.
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Affiliation(s)
- V S Gowri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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13
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Abstract
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally 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 hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (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 betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview 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 accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall 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 pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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14
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Park JH, Johansson HE, Aoki H, Huang BX, Kim HY, Ganoza MC, Park MH. Post-translational modification by β-lysylation is required for activity of Escherichia coli elongation factor P (EF-P). J Biol Chem 2011; 287:2579-90. [PMID: 22128152 DOI: 10.1074/jbc.m111.309633] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical β-lysyl-lysine. Here we present biochemical evidence for β-lysyl-lysine modification in Escherichia coli EF-P and for its role in EF-P activity by characterizing native and recombinant EF-P proteins for their modification status and activity in vitro. Mass spectrometric analyses confirmed the lysyl modification at lysine 34 in native and recombinant EF-P proteins. The β-lysyl-lysine isopeptide was identified in the exhaustive Pronase digests of native EF-P and recombinant EF-P isolated from E. coli coexpressing EF-P, YjeA, and YjeK but not in the digests of proteins derived from the vectors encoding EF-P alone or EF-P together with YjeA, indicating that both enzymes, YjeA and YjeK, are required for β-lysylation of EF-P. Endogenous EF-P as well as the recombinant EF-P preparation containing β-lysyl-EF-P stimulated N-formyl-methionyl-puromycin synthesis ∼4-fold over the preparations containing unmodified EF-P and/or α-lysyl-EF-P. The mutant lacking the modification site lysine (K34A) was inactive. This is the first report of biochemical evidence for the β-lysylation of EF-P in vivo and the requirement for this modification for the activity of EF-P.
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Affiliation(s)
- Jong-Hwan Park
- Oral and Pharyngeal Cancer Branch, NIDCR, National Institutes of Health, Bethesda, Maryland 20892, USA
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15
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Abstract
Elongation factor P (EF-P) is posttranslationally modified at a conserved lysyl residue by the coordinated action of two enzymes, PoxA and YjeK. We have previously established the importance of this modification in Salmonella stress resistance. Here we report that, like poxA and yjeK mutants, Salmonella strains lacking EF-P display increased susceptibility to hypoosmotic conditions, antibiotics, and detergents and enhanced resistance to the compound S-nitrosoglutathione. The susceptibility phenotypes are largely explained by the enhanced membrane permeability of the efp mutant, which exhibits increased uptake of the hydrophobic dye 1-N-phenylnaphthylamine (NPN). Analysis of the membrane proteomes of wild-type and efp mutant Salmonella strains reveals few changes, including the prominent overexpression of a single porin, KdgM, in the efp mutant outer membrane. Removal of KdgM in the efp mutant background ameliorates the detergent, antibiotic, and osmosensitivity phenotypes and restores wild-type permeability to NPN. Our data support a role for EF-P in the translational regulation of a limited number of proteins that, when perturbed, renders the cell susceptible to stress by the adventitious overexpression of an outer membrane porin.
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16
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Roy H, Zou SB, Bullwinkle TJ, Wolfe BS, Gilreath MS, Forsyth CJ, Navarre WW, Ibba M. The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine. Nat Chem Biol 2011; 7:667-9. [PMID: 21841797 PMCID: PMC3177975 DOI: 10.1038/nchembio.632] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 06/17/2011] [Indexed: 11/09/2022]
Abstract
The lysyl-tRNA synthetase paralog PoxA modifies elongation factor P (EF-P) with α-lysine at low efficiency. Cell-free extracts contained non-α-lysine substrates of PoxA that modified EF-P by a change in mass consistent with β–lysine, a substrate also predicted by genomic analyses. EF-P was efficiently, functionally, modified with (R)-β-lysine but not (S)-β-lysine or genetically encoded α-amino acids, indicating that PoxA has evolved an activity orthogonal to that of the canonical aminoacyl-tRNA synthetases.
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Affiliation(s)
- Hervé Roy
- Department of Microbiology, Center for RNA Biology, Ohio State University, Columbus, Ohio, USA
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