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Journal articles on the topic 'Cysteine tRNA'

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Published: 28 June 2021
Last updated: 11 February 2022

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1

Ida, Tomoaki, Akira Nishimura, Masanobu Morita, Hozumi Motohashi, and Takaaki Akaike. "Cysteine Hydropersulfide Production Catalyzed by Cysteinyl-tRNA Synthetases." Free Radical Biology and Medicine 112 (November 2017): 189–90. http://dx.doi.org/10.1016/j.freeradbiomed.2017.10.297.

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2

Jakubowski, Hieronim. "Editing function ofEscherichia coli cysteinyl-tRNA synthetase: cyclization of cysteine to cysteine thiolactone." Nucleic Acids Research 22, no. 7 (1994): 1155–60. http://dx.doi.org/10.1093/nar/22.7.1155.

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3

Liu, Yuchen, David J. Vinyard, Megan E. Reesbeck, Tateki Suzuki, Kasidet Manakongtreecheep, Patrick L. Holland, Gary W. Brudvig, and Dieter Söll. "A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes." Proceedings of the National Academy of Sciences 113, no. 45 (October 24, 2016): 12703–8. http://dx.doi.org/10.1073/pnas.1615732113.

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The sulfur-containing nucleosides in transfer RNA (tRNAs) are present in all three domains of life; they have critical functions for accurate and efficient translation, such as tRNA structure stabilization and proper codon recognition. The tRNA modification enzymes ThiI (in bacteria and archaea) and Ncs6 (in archaea and eukaryotic cytosols) catalyze the formation of 4-thiouridine (s4U) and 2-thiouridine (s2U), respectively. The ThiI homologs were proposed to transfer sulfur via cysteine persulfide enzyme adducts, whereas the reaction mechanism of Ncs6 remains unknown. Here we show that ThiI from the archaeon Methanococcus maripaludis contains a [3Fe-4S] cluster that is essential for its tRNA thiolation activity. Furthermore, the archaeal and eukaryotic Ncs6 homologs as well as phosphoseryl-tRNA (Sep-tRNA):Cys-tRNA synthase (SepCysS), which catalyzes the Sep-tRNA to Cys-tRNA conversion in methanogens, also possess a [3Fe-4S] cluster similar to the methanogenic archaeal ThiI. These results suggest that the diverse tRNA thiolation processes in archaea and eukaryotic cytosols share a common mechanism dependent on a [3Fe-4S] cluster for sulfur transfer.
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4

Hamann, Christian S., Kevin R. Sowers, Richard S. A. Lipman, and Ya-Ming Hou. "An Archaeal Aminoacyl-tRNA Synthetase Missing from Genomic Analysis." Journal of Bacteriology 181, no. 18 (September 15, 1999): 5880–84. http://dx.doi.org/10.1128/jb.181.18.5880-5884.1999.

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ABSTRACT The complete genomic sequencing of Methanococcus jannaschii cannot identify the gene for the cysteine-specific member of aminoacyl-tRNA synthetases. However, we show here that enzyme activity is present in the cell lysate of M. jannaschii. The demonstration of this activity suggests a direct pathway for the synthesis of cysteinyl-tRNACys during protein synthesis.
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5

Ambrogelly, Alexandre, Ivan Ahel, Carla Polycarpo, Shipra Bunjun-Srihari, Bethany Krett, Clarisse Jacquin-Becker, Benfang Ruan, et al. "Methanocaldococcus jannaschiiProlyl-tRNA Synthetase Charges tRNAProwith Cysteine." Journal of Biological Chemistry 277, no. 38 (July 18, 2002): 34749–54. http://dx.doi.org/10.1074/jbc.m206929200.

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6

Leimkühler, Silke. "The Biosynthesis of the Molybdenum Cofactor in Escherichia coli and Its Connection to FeS Cluster Assembly and the Thiolation of tRNA." Advances in Biology 2014 (April 29, 2014): 1–21. http://dx.doi.org/10.1155/2014/808569.

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The thiolation of biomolecules is a complex process that involves the activation of sulfur. The L-cysteine desulfurase IscS is the main sulfur mobilizing protein in Escherichia coli that provides the sulfur from L-cysteine to several important biomolecules in the cell such as iron sulfur (FeS) clusters, molybdopterin (MPT), thiamine, and thionucleosides of tRNA. Various proteins mediate the transfer of sulfur from IscS to various biomolecules using different interaction partners. A direct connection between the sulfur-containing molecules FeS clusters, thiolated tRNA, and the molybdenum cofactor (Moco) has been identified. The first step of Moco biosynthesis involves the conversion of 5′GTP to cyclic pyranopterin monophosphate (cPMP), a reaction catalyzed by a FeS cluster containing protein. Formed cPMP is further converted to MPT by insertion of two sulfur atoms. The sulfur for this reaction is provided by the L-cysteine desulfurase IscS in addition to the involvement of the TusA protein. TusA is also involved in the sulfur transfer for the thiolation of tRNA. This review will describe the biosynthesis of Moco in E. coli in detail and dissects the sulfur transfer pathways for Moco and tRNA and their connection to FeS cluster biosynthesis.
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7

Helgadóttir, Sunna, Guillermina Rosas-Sandoval, Dieter Söll, and David E. Graham. "Biosynthesis of Phosphoserine in the Methanococcales." Journal of Bacteriology 189, no. 2 (October 27, 2006): 575–82. http://dx.doi.org/10.1128/jb.01269-06.

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ABSTRACT Methanococcus maripaludis and Methanocaldococcus jannaschii produce cysteine for protein synthesis using a tRNA-dependent pathway. These methanogens charge tRNACys with l-phosphoserine, which is also an intermediate in the predicted pathways for serine and cystathionine biosynthesis. To establish the mode of phosphoserine production in Methanococcales, cell extracts of M. maripaludis were shown to have phosphoglycerate dehydrogenase and phosphoserine aminotransferase activities. The heterologously expressed and purified phosphoglycerate dehydrogenase from M. maripaludis had enzymological properties similar to those of its bacterial homologs but was poorly inhibited by serine. While bacterial enzymes are inhibited by micromolar concentrations of serine bound to an allosteric site, the low sensitivity of the archaeal protein to serine is consistent with phosphoserine's position as a branch point in several pathways. A broad-specificity class V aspartate aminotransferase from M. jannaschii converted the phosphohydroxypyruvate product to phosphoserine. This enzyme catalyzed the transamination of aspartate, glutamate, phosphoserine, alanine, and cysteate. The M. maripaludis homolog complemented a serC mutation in the Escherichia coli phosphoserine aminotransferase. All methanogenic archaea apparently share this pathway, providing sufficient phosphoserine for the tRNA-dependent cysteine biosynthetic pathway.
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8

Sawa, Tomohiro, Hozumi Motohashi, Hideshi Ihara, and Takaaki Akaike. "Enzymatic Regulation and Biological Functions of Reactive Cysteine Persulfides and Polysulfides." Biomolecules 10, no. 9 (August 27, 2020): 1245. http://dx.doi.org/10.3390/biom10091245.

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Cysteine persulfide (CysSSH) and cysteine polysulfides (CysSSnH, n > 1) are cysteine derivatives that have sulfane sulfur atoms bound to cysteine thiol. Advances in analytical methods that detect and quantify persulfides and polysulfides have shown that CysSSH and related species such as glutathione persulfide occur physiologically and are prevalent in prokaryotes, eukaryotes, and mammals in vivo. The chemical properties and abundance of these compounds suggest a central role for reactive persulfides in cell-regulatory processes. CysSSH and related species have been suggested to act as powerful antioxidants and cellular protectants and may serve as redox signaling intermediates. It was recently shown that cysteinyl-tRNA synthetase (CARS) is a new cysteine persulfide synthase. In addition, we discovered that CARS is involved in protein polysulfidation that is coupled with translation. Mitochondrial activity in biogenesis and bioenergetics is supported and upregulated by CysSSH derived from mitochondrial CARS. In this review article, we discuss the mechanisms of the biosynthesis of CysSSH and related persulfide species, with a particular focus on the roles of CARS. We also review the antioxidative and anti-inflammatory actions of persulfides.
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9

Lipman, Richard S. A., Kevin R. Sowers, and Ya-Ming Hou. "Synthesis of Cysteinyl-tRNACysby a Genome That Lacks the Normal Cysteine-tRNA Synthetase†." Biochemistry 39, no. 26 (July 2000): 7792–98. http://dx.doi.org/10.1021/bi0004955.

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10

Yuan, Jing, Michael J. Hohn, R. Lynn Sherrer, Sotiria Palioura, Dan Su, and Dieter Söll. "A tRNA-dependent cysteine biosynthesis enzyme recognizes the selenocysteine-specific tRNA in Escherichia coli." FEBS Letters 584, no. 13 (May 21, 2010): 2857–61. http://dx.doi.org/10.1016/j.febslet.2010.05.028.

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11

Lauhon, Charles T. "Requirement for IscS in Biosynthesis of All Thionucleosides in Escherichia coli." Journal of Bacteriology 184, no. 24 (December 15, 2002): 6820–29. http://dx.doi.org/10.1128/jb.184.24.6820-6829.2002.

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ABSTRACT Escherichia coli tRNA contains four naturally occurring nucleosides modified with sulfur. Cysteine is the intracellular sulfur source for each of these modified bases. We previously found that the iscS gene, a member of the nifS cysteine desulfurase gene family, is required for 4-thiouridine biosynthesis in E. coli. Since IscS does not bind tRNA, its role is the mobilization and distribution of sulfur to enzymes that catalyze the sulfur insertion steps. In addition to iscS, E. coli contains two other nifS homologs, csdA and csdB, each of which has cysteine desulfurase activity and could potentially donate sulfur for thionucleoside biosynthesis. Double csdA csdB and iscS csdA mutants were prepared or obtained, and all mutants were analyzed for thionucleoside content. It was found that unfractionated tRNA isolated from the iscS mutant strain contained <5% of the level of sulfur found in the parent strain. High-pressure liquid chromatography analysis of tRNA nuclease digests from the mutant strain grown in the presence of [35S]cysteine showed that only a small fraction of 2-thiocytidine was present, while the other thionucleosides were absent when cells were isolated during log phase. As expected, digests from the iscS mutant strain contained 6-N-dimethylallyl adenosine (i6A) in place of 6-N-dimethylallyl-2-methylthioadenosine and 5-methylaminomethyl uridine (mnm5U) instead of 5-methylaminomethyl-2-thiouridine. Prolonged growth of the iscS and iscS csdA mutant strains revealed a gradual increase in levels of 2-thiocytidine and 6-N-dimethylallyl-2-methylthioadenosine with extended incubation (>24 h), while the thiouridines remained absent. This may be due to a residual level of Fe-S cluster biosynthesis in iscS deletion strains. An overall scheme for thionucleoside biosynthesis in E. coli is discussed.
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12

Chen, Meirong, Yuto Nakazawa, Yume Kubo, Nozomi Asano, Koji Kato, Isao Tanaka, and Min Yao. "Crystallographic analysis of a subcomplex of the transsulfursome with tRNA for Cys-tRNACyssynthesis." Acta Crystallographica Section F Structural Biology Communications 72, no. 7 (June 28, 2016): 569–72. http://dx.doi.org/10.1107/s2053230x16009559.

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In most organisms, Cys-tRNACysis directly synthesized by cysteinyl-tRNA synthetase (CysRS). Many methanogenic archaea, however, use a two-step, indirect pathway to synthesize Cys-tRNACysowing to a lack of CysRS and cysteine-biosynthesis systems. This reaction is catalyzed byO-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 anO-phosphoserine to tRNACys, and the mischarged intermediate Sep-tRNACysis then transferred to SepCysS, where it is further modified to Cys-tRNACys. In this study, a subcomplex of the transsulfursome with tRNACys(SepCysS–SepCysE–tRNACys), 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 groupP6522, with unit-cell parametersa=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 tRNACysin the asymmetric unit.
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13

Helgadóttir, Sunna, Sylvie Sinapah, Dieter Söll, and Jiqiang Ling. "Mutational analysis of Sep-tRNA:Cys-tRNA synthase reveals critical residues for tRNA-dependent cysteine formation." FEBS Letters 586, no. 1 (December 9, 2011): 60–63. http://dx.doi.org/10.1016/j.febslet.2011.11.024.

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14

Döring, Volker, and Philippe Marlière. "Reassigning Cysteine in the Genetic Code of Escherichia coli." Genetics 150, no. 2 (October 1, 1998): 543–51. http://dx.doi.org/10.1093/genetics/150.2.543.

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Abstract We investigated directed deviations from the universal genetic code. Mutant tRNAs that incorporate cysteine at positions corresponding to the isoleucine AUU, AUC, and AUA and methionine AUG codons were introduced in Escherichia coli K12. Missense mutations at the cysteine catalytic site of thymidylate synthase were systematically crossed with synthetic suppressor tRNACys genes coexpressed from compatible plasmids. Strains harboring complementary codon/anticodon associations could be stably propagated as thymidine prototrophs. A plasmid-encoded tRNACys reading the codon AUA persisted for more than 500 generations in a strain requiring its suppressor activity for thymidylate biosynthesis, but was eliminated from a strain not requiring it. Cysteine miscoding at the codon AUA was also enforced in the active site of amidase, an enzyme found in Helicobacter pylori and not present in wild-type E. coli. Propagating the amidase missense mutation in E. coli with an aliphatic amide as nitrogen source required the overproduction of Cys-tRNA synthetase together with the complementary suppressor tRNACys. The toxicity of cysteine miscoding was low in all our strains. The small size and amphiphilic character of this amino acid may render it acceptable as a replacement at most protein positions and thus apt to overcome the steric and polar constraints that limit evolution of the genetic code.
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15

Ahel, Ivan, Constantinos Stathopoulos, Alexandre Ambrogelly, Anselm Sauerwald, Helen Toogood, Thomas Hartsch, and Dieter Söll. "Cysteine Activation Is an Inherentin VitroProperty of Prolyl-tRNA Synthetases." Journal of Biological Chemistry 277, no. 38 (July 18, 2002): 34743–48. http://dx.doi.org/10.1074/jbc.m206928200.

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16

Black, Katherine A., and Patricia C. Dos Santos. "Abbreviated Pathway for Biosynthesis of 2-Thiouridine in Bacillus subtilis." Journal of Bacteriology 197, no. 11 (March 30, 2015): 1952–62. http://dx.doi.org/10.1128/jb.02625-14.

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ABSTRACTThe 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine, and lysine tRNA molecules serves to stabilize the anticodon structure, improving ribosomal binding and overall efficiency of the translational process. Biosynthesis of s2U inEscherichia colirequires a cysteine desulfurase (IscS), a thiouridylase (MnmA), and five intermediate sulfur-relay enzymes (TusABCDE). TheE. coliMnmA adenylates and subsequently thiolates tRNA to form the s2U modification.Bacillus subtilislacks IscS and the intermediate sulfur relay proteins, yet its genome contains a cysteine desulfurase gene,yrvO, directly adjacent tomnmA. The genomic synteny ofyrvOandmnmAcombined with the absence of the Tus proteins indicated a potential functionality of these proteins in s2U formation. Here, we provide evidence that theB. subtilisYrvO and MnmA are sufficient for s2U biosynthesis. A conditionalB. subtilisknockout strain showed that s2U abundance correlates with MnmA expression, andin vivocomplementation studies inE. coliIscS- or MnmA-deficient strains revealed the competency of these proteins in s2U biosynthesis.In vitroexperiments demonstrated s2U formation by YrvO and MnmA, and kinetic analysis established a partnership between theB. subtilisproteins that is contingent upon the presence of ATP. Furthermore, we observed that the slow-growth phenotype ofE. coliΔiscSand ΔmnmAstrains associated with s2U depletion is recovered byB. subtilis yrvOandmnmA. These results support the proposal that the involvement of a devoted cysteine desulfurase, YrvO, in s2U synthesis bypasses the need for a complex biosynthetic pathway by direct sulfur transfer to MnmA.IMPORTANCEThe 2-thiouridine (s2U) modification of the wobble position in glutamate, glutamine, and lysine tRNA is conserved in all three domains of life and stabilizes the anticodon structure, thus guaranteeing fidelity in translation. The biosynthesis of s2U inEscherichia colirequires seven proteins: the cysteine desulfurase IscS, the thiouridylase MnmA, and five intermediate sulfur-relay enzymes (TusABCDE).Bacillus subtilisand most Gram-positive bacteria lack a complete set of biosynthetic components. Interestingly, themnmAcoding sequence is located adjacent toyrvO, encoding a cysteine desulfurase. In this work, we provide evidence that theB. subtilisYrvO is able to transfer sulfur directly to MnmA. Both proteins are sufficient for s2U biosynthesis in a pathway independent of the one used inE. coli.
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17

Ruan, Benfang, Hiroaki Nakano, Masashi Tanaka, Jonathan A. Mills, Joseph A. DeVito, Bokkee Min, K. Brooks Low, John R. Battista, and Dieter Söll. "Cysteinyl-tRNACys Formation in Methanocaldococcus jannaschii: the Mechanism Is Still Unknown." Journal of Bacteriology 186, no. 1 (January 1, 2004): 8–14. http://dx.doi.org/10.1128/jb.186.1.8-14.2004.

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ABSTRACT Most organisms form Cys-tRNACys, an essential component for protein synthesis, through the action of cysteinyl-tRNA synthetase (CysRS). However, the genomes of Methanocaldococcus jannaschii, Methanothermobacter thermautotrophicus, and Methanopyrus kandleri do not contain a recognizable cysS gene encoding CysRS. It was reported that M. jannaschii prolyl-tRNA synthetase (C. Stathopoulos, T. Li, R. Longman, U. C. Vothknecht, H. D. Becker, M. Ibba, and D. Söll, Science 287:479-482, 2000; R. S. Lipman, K. R. Sowers, and Y. M. Hou, Biochemistry 39:7792-7798, 2000) or the M. jannaschii MJ1477 protein (C. Fabrega, M. A. Farrow, B. Mukhopadhyay, V. de Crécy-Lagard, A. R. Ortiz, and P. Schimmel, Nature 411:110-114, 2001) provides the “missing” CysRS activity for in vivo Cys-tRNACys formation. These conclusions were supported by complementation of temperature-sensitive Escherichia coli cysS(Ts) strain UQ818 with archaeal proS genes (encoding prolyl-tRNA synthetase) or with the Deinococcus radiodurans DR0705 gene, the ortholog of the MJ1477 gene. Here we show that E. coli UQ818 harbors a mutation (V27E) in CysRS; the largest differences compared to the wild-type enzyme are a fourfold increase in the Km for cysteine and a ninefold reduction in the k cat for ATP. While transformants of E. coli UQ818 with archaeal and bacterial cysS genes grew at a nonpermissive temperature, growth was also supported by elevated intracellular cysteine levels, e.g., by transformation with an E. coli cysE allele (encoding serine acetyltransferase) or by the addition of cysteine to the culture medium. An E. coli cysS deletion strain permitted a stringent complementation test; growth could be supported only by archaeal or bacterial cysS genes and not by archaeal proS genes or the D. radiodurans DR0705 gene. Construction of a D. radiodurans DR0705 deletion strain showed this gene to be dispensable. However, attempts to delete D. radiodurans cysS failed, suggesting that this is an essential Deinococcus gene. These results imply that it is not established that proS or MJ1477 gene products catalyze Cys-tRNACys synthesis in M. jannaschii. Thus, the mechanism of Cys-tRNACys formation in M. jannaschii still remains to be discovered.
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18

Wakasugi, Keisuke. "An Exposed Cysteine Residue of Human Angiostatic Mini Tryptophanyl-tRNA Synthetase." Biochemistry 49, no. 14 (April 13, 2010): 3156–60. http://dx.doi.org/10.1021/bi1000239.

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19

Hussain, Tahir, Manickam Yogavel, and Amit Sharma. "Inhibition of Protein Synthesis and Malaria Parasite Development by Drug Targeting of Methionyl-tRNA Synthetases." Antimicrobial Agents and Chemotherapy 59, no. 4 (January 12, 2015): 1856–67. http://dx.doi.org/10.1128/aac.02220-13.

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ABSTRACTAminoacyl-tRNA synthetases (aaRSs) are housekeeping enzymes that couple cognate tRNAs with amino acids to transmit genomic information for protein translation. ThePlasmodium falciparumnuclear genome encodes twoP. falciparummethionyl-tRNA synthetases (PfMRS), termed PfMRScytand PfMRSapi. Phylogenetic analyses revealed that the two proteins are of primitive origin and are related to heterokonts (PfMRScyt) or proteobacteria/primitive bacteria (PfMRSapi). We show that PfMRScytlocalizes in parasite cytoplasm, while PfMRSapilocalizes to apicoplasts in asexual stages of malaria parasites. Two known bacterial MRS inhibitors, REP3123 and REP8839, hamperedPlasmodiumgrowth very effectively in the early and late stages of parasite development. Small-molecule drug-like libraries were screened against modeled PfMRS structures, and several “hit” compounds showed significant effects on parasite growth. We then tested the effects of the hit compounds on protein translation by labeling nascent proteins with35S-labeled cysteine and methionine. Three of the tested compounds reduced protein synthesis and also blocked parasite growth progression from the ring stage to the trophozoite stage. Drug docking studies suggested distinct modes of binding for the three compounds, compared with the enzyme product methionyl adenylate. Therefore, this study provides new targets (PfMRSs) and hit compounds that can be explored for development as antimalarial drugs.
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20

Rauch, Benjamin Julius, and John J. Perona. "Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein." Journal of Bacteriology 198, no. 14 (May 2, 2016): 1974–83. http://dx.doi.org/10.1128/jb.00141-16.

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ABSTRACTConserved genes essential to sulfur assimilation and trafficking in aerobic organisms are missing in many methanogens, most of which inhabit highly sulfidic, anaerobic environmental niches. This suggests that methanogens possess distinct pathways for the synthesis of key metabolites and intermediates, including cysteine, homocysteine, and protein persulfide groups. Prior work identified a novel tRNA-dependent two-step pathway for cysteine biosynthesis and a new metabolic transformation by which sulfur is inserted into aspartate semialdehyde to produce homocysteine. Homocysteine biosynthesis requires two of the three proteins previously identified in our laboratory by a comprehensive bioinformatics approach. Here, we show that the third protein identifiedin silico, the ApbE-like protein COG2122, facilitates sulfide assimilation inMethanosarcina acetivorans. Knockout strains lacking the gene encoding COG2122 are severely impaired for growth when sulfide is provided as the sole sulfur source. However, rapid growth is recovered upon supplementation with cysteine, homocysteine, or cystathionine, suggesting that COG2122 is required for efficient biosynthesis of both cysteine and homocysteine. Deletion of the gene encoding COG2122 does not influence the extent of sulfur modifications in tRNA or the prevalence of iron-sulfur clusters, indicating that the function of COG2122 could be limited to sulfide assimilation for cysteine and homocysteine biosynthesis alone.IMPORTANCEWe have found that the conservedM. acetivoransma1715gene, which encodes an ApbE-like protein, is required for optimal growth with sulfide as the sole sulfur source and supports both cysteine and homocysteine biosynthesisin vivo. Together with related functional-genomics studies in methanogens, these findings make a key contribution to elucidating the novel pathways of sulfide assimilation and sulfur trafficking in anaerobic microorganisms that existed before the advent of oxygenic photosynthesis. The data suggest that the MA1715 protein is particularly important to sustaining robust physiological function when ambient sulfide concentrations are low. Phylogenetic analysis shows that MA1715 and other recently discovered methanogen sulfur-trafficking proteins share an evolutionary history with enzymes in the methanogenesis pathway. The newly characterized genes thus likely formed an essential part of the core metabolic machinery of the ancestral euryarchaeote.
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21

Kamtekar, S., W. D. Kennedy, J. Wang, C. Stathopoulos, D. Soll, and T. A. Steitz. "The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases." Proceedings of the National Academy of Sciences 100, no. 4 (February 10, 2003): 1673–78. http://dx.doi.org/10.1073/pnas.0437911100.

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22

Rajakovich, Lauren J., John Tomlinson, and Patricia C. Dos Santos. "Functional Analysis of Bacillus subtilis Genes Involved in the Biosynthesis of 4-Thiouridine in tRNA." Journal of Bacteriology 194, no. 18 (July 6, 2012): 4933–40. http://dx.doi.org/10.1128/jb.00842-12.

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ABSTRACTThiI has been identified as an essential enzyme involved in the biosynthesis of thiamine and the tRNA thionucleoside modification, 4-thiouridine. InEscherichia coliandSalmonella enterica, ThiI acts as a sulfurtransferase, receiving the sulfur donated from the cysteine desulfurase IscS and transferring it to the target molecule or additional sulfur carrier proteins. However, inBacillus subtilisand most species from theFirmicutesphylum, ThiI lacks the rhodanese domain that contains the site responsible for the sulfurtransferase activity. The lack of the gene encoding for a canonical IscS cysteine desulfurase and the presence of a short sequence of ThiI in these bacteria pointed to mechanistic differences involving sulfur trafficking reactions in both biosynthetic pathways. Here, we have carried out functional analysis ofB. subtilisthiIand the adjacent gene,nifZ, encoding for a cysteine desulfurase. Gene inactivation experiments inB. subtilisindicate the requirement of ThiI and NifZ for the biosynthesis of 4-thiouridine, but not thiamine.In vitrosynthesis of 4-thiouridine by ThiI and NifZ, along with labeling experiments, suggests the occurrence of an alternate transient site for sulfur transfer, thus obviating the need for a rhodanese domain.In vivocomplementation studies inE. coliIscS- or ThiI-deficient strains provide further support for specific interactions between NifZ and ThiI. These results are compatible with the proposal thatB. subtilisNifZ and ThiI utilize mechanistically distinct and mutually specific sulfur transfer reactions.
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Hertz, Rivi, Ayala Tovy, Michael Kirschenbaum, Meirav Geffen, Tomoyoshi Nozaki, Noam Adir, and Serge Ankri. "The Entamoeba histolytica Dnmt2 Homolog (Ehmeth) Confers Resistance to Nitrosative Stress." Eukaryotic Cell 13, no. 4 (February 21, 2014): 494–503. http://dx.doi.org/10.1128/ec.00031-14.

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ABSTRACT Nitric oxide (NO) has antimicrobial properties against many pathogens due to its reactivity as an S-nitrosylating agent. It inhibits many of the key enzymes that are involved in the metabolism and virulence of the parasite Entamoeba histolytica through S-nitrosylation of essential cysteine residues. Very little information is available on the mechanism of resistance to NO by pathogens in general and by this parasite in particular. Here, we report that exposure of the parasites to S -nitrosoglutathione (GSNO), an NO donor molecule, strongly reduces their viability and protein synthesis. However, the deleterious effects of NO were significantly reduced in trophozoites overexpressing Ehmeth, the cytosine-5 methyltransferase of the Dnmt2 family. Since these trophozoites also exhibited high levels of tRNA Asp methylation, the high levels suggested that Ehmeth-mediated tRNA Asp methylation is part of the resistance mechanism to NO. We previously reported that enolase, another glycolytic enzyme, binds to Ehmeth and inhibits its activity. We observed that the amount of Ehmeth-enolase complex was significantly reduced in GSNO-treated E. histolytica , which explains the aforementioned increase of tRNA methylation. Specifically, we demonstrated via site-directed mutagenesis that cysteine residues 228 and 229 of Ehmeth are susceptible to S-nitrosylation and are crucial for Ehmeth binding to enolase and for Ehmeth-mediated resistance to NO. These results indicate that Ehmeth has a central role in the response of the parasite to NO, and they contribute to the growing evidence that NO is a regulator of epigenetic mechanisms.
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Lauhon, Charles T., Elizabeth Skovran, Hugo D. Urbina, Diana M. Downs, and Larry E. Vickery. "Substitutions in an Active Site Loop ofEscherichia coliIscS Result in Specific Defects in Fe-S Cluster and Thionucleoside Biosynthesisin Vivo." Journal of Biological Chemistry 279, no. 19 (February 21, 2004): 19551–58. http://dx.doi.org/10.1074/jbc.m401261200.

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IscS catalyzes the fragmentation ofl-cysteine tol-alanine and sulfane sulfur in the form of a cysteine persulfide in the active site of the enzyme. InEscherichia coliIscS, the active site cysteine Cys328resides in a flexible loop that potentially influences both the formation and stability of the cysteine persulfide as well as the specificity of sulfur transfer to protein substrates. Alanine-scanning substitution of this 14 amino acid region surrounding Cys328identified additional residues important for IscS functionin vivo. Two mutations, S326A and L333A, resulted in strains that were severely impaired in Fe-S cluster synthesisin vivo. The mutant strains were deficient in Fe-S cluster-dependent tRNA thionucleosides (s2C and ms2i6A) yet showed wild type levels of Fe-S-independent thionucleosides (s4U and mnm5s2U) that require persulfide formation and transfer.In vitro, the mutant proteins were similar to wild type in both cysteine desulfurase activity and sulfur transfer to IscU. These results indicate that residues in the active site loop can selectively affect Fe-S cluster biosynthesisin vivowithout detectably affecting persulfide delivery and suggest that additional assays may be necessary to fully represent the functions of IscS in Fe-S cluster formation.
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25

Leipuviene, Ramune, Qiang Qian, and Glenn R. Björk. "Formation of Thiolated Nucleosides Present in tRNA from Salmonella enterica serovar Typhimurium Occurs in Two Principally Distinct Pathways." Journal of Bacteriology 186, no. 3 (February 1, 2004): 758–66. http://dx.doi.org/10.1128/jb.186.3.758-766.2004.

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ABSTRACT tRNA from Salmonella enterica serovar Typhimurium contains five thiolated nucleosides, 2-thiocytidine (s2C), 4-thiouridine (s4U), 5-methylaminomethyl-2-thiouridine (mnm5s2U), 5-carboxymethylaminomethyl-2-thiouridine (cmnm5s2U), and N-6-(4-hydroxyisopentenyl)-2-methylthioadenosine (ms2io6A). The levels of all of them are significantly reduced in cells with a mutated iscS gene, which encodes the cysteine desulfurase IscS, a member of the ISC machinery that is responsible for [Fe-S] cluster formation in proteins. A mutant (iscU52) was isolated that carried an amino acid substitution (S107T) in the IscU protein, which functions as a major scaffold in the formation of [Fe-S] clusters. In contrast to the iscS mutant, the iscU52 mutant showed reduced levels of only two of the thiolated nucleosides, ms2io6A (10-fold) and s2C (more than 2-fold). Deletions of the iscU, hscA, or fdx genes from the isc operon lead to a similar tRNA thiolation pattern to that seen for the iscU52 mutant. Unexpectedly, deletion of the iscA gene, coding for an alternative scaffold protein for the [Fe-S] clusters, showed a novel tRNA thiolation pattern, where the synthesis of only one thiolated nucleoside, ms2io6A, was decreased twofold. Based on our results, we suggest two principal distinct routes for thiolation of tRNA: (i) a direct sulfur transfer from IscS to the tRNA modifying enzymes ThiI and MnmA, which form s4U and the s2U moiety of (c)mnm5s2U, respectively; and (ii) an involvement of [Fe-S] proteins (an unidentified enzyme in the synthesis of s2C and MiaB in the synthesis of ms2io6A) in the transfer of sulfur to the tRNA.
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26

Liu, Mofang, Yiwei Huang, Jinfu Wu, Enduo Wang, and Yinglai Wang. "Effect of Cysteine Residues on the Activity of Arginyl-tRNA Synthetase fromEscherichia coli†." Biochemistry 38, no. 34 (August 1999): 11006–11. http://dx.doi.org/10.1021/bi990392q.

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27

Klipcan, Liron, Milana Frenkel-Morgenstern, and Mark G. Safro. "Presence of tRNA-dependent pathways correlates with high cysteine content in methanogenic Archaea." Trends in Genetics 24, no. 2 (February 2008): 59–63. http://dx.doi.org/10.1016/j.tig.2007.11.007.

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28

Liu, Y., A. Nakamura, Y. Nakazawa, N. Asano, K. A. Ford, M. J. Hohn, I. Tanaka, M. Yao, and D. Soll. "Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea." Proceedings of the National Academy of Sciences 111, no. 29 (July 7, 2014): 10520–25. http://dx.doi.org/10.1073/pnas.1411267111.

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29

Johnson, Parker M., Christina M. Beck, Robert P. Morse, Fernando Garza-Sánchez, David A. Low, Christopher S. Hayes, and Celia W. Goulding. "Unraveling the essential role of CysK in CDI toxin activation." Proceedings of the National Academy of Sciences 113, no. 35 (August 16, 2016): 9792–97. http://dx.doi.org/10.1073/pnas.1607112113.

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Contact-dependent growth inhibition (CDI) is a widespread mechanism of bacterial competition. CDI+ bacteria deliver the toxic C-terminal region of contact-dependent inhibition A proteins (CdiA-CT) into neighboring target bacteria and produce CDI immunity proteins (CdiI) to protect against self-inhibition. The CdiA-CTEC536 deployed by uropathogenic Escherichia coli 536 (EC536) is a bacterial toxin 28 (Ntox28) domain that only exhibits ribonuclease activity when bound to the cysteine biosynthetic enzyme O-acetylserine sulfhydrylase A (CysK). Here, we present crystal structures of the CysK/CdiA-CTEC536 binary complex and the neutralized ternary complex of CysK/CdiA-CT/CdiIEC536. CdiA-CTEC536 inserts its C-terminal Gly-Tyr-Gly-Ile peptide tail into the active-site cleft of CysK to anchor the interaction. Remarkably, E. coli serine O-acetyltransferase uses a similar Gly-Asp-Gly-Ile motif to form the “cysteine synthase” complex with CysK. The cysteine synthase complex is found throughout bacteria, protozoa, and plants, indicating that CdiA-CTEC536 exploits a highly conserved protein–protein interaction to promote its toxicity. CysK significantly increases CdiA-CTEC536 thermostability and is required for toxin interaction with tRNA substrates. These observations suggest that CysK stabilizes the toxin fold, thereby organizing the nuclease active site for substrate recognition and catalysis. By contrast, Ntox28 domains from Gram-positive bacteria lack C-terminal Gly-Tyr-Gly-Ile motifs, suggesting that they do not interact with CysK. We show that the Ntox28 domain from Ruminococcus lactaris is significantly more thermostable than CdiA-CTEC536, and its intrinsic tRNA-binding properties support CysK-independent nuclease activity. The striking differences between related Ntox28 domains suggest that CDI toxins may be under evolutionary pressure to maintain low global stability.
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30

Hendrickson, Tamara L., Whitney N. Wood, and Udumbara M. Rathnayake. "Did Amino Acid Side Chain Reactivity Dictate the Composition and Timing of Aminoacyl-tRNA Synthetase Evolution?" Genes 12, no. 3 (March 12, 2021): 409. http://dx.doi.org/10.3390/genes12030409.

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The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA synthetases (aaRSs). In this conceptual paper, we propose that the chemical reactivity of some amino acid side chains (e.g., lysine, cysteine, homocysteine, ornithine, homoserine, and selenocysteine) delayed or prohibited the emergence of the corresponding aaRSs and helped define the amino acids in the standard genetic code. We also consider the possibility that amino acid chemistry delayed the emergence of the glutaminyl- and asparaginyl-tRNA synthetases, neither of which are ubiquitous in extant organisms. We argue that fundamental chemical principles played critical roles in fixation of some aspects of the genetic code pre- and post-LUCA.
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31

Lundgren, Hans K., and Glenn R. Björk. "Structural Alterations of the Cysteine Desulfurase IscS of Salmonella enterica Serovar Typhimurium Reveal Substrate Specificity of IscS in tRNA Thiolation." Journal of Bacteriology 188, no. 8 (April 15, 2006): 3052–62. http://dx.doi.org/10.1128/jb.188.8.3052-3062.2006.

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ABSTRACT The cysteine desulfurase IscS in Salmonella enterica serovar Typhimurium is required for the formation of all four thiolated nucleosides in tRNA, which is thought to occur via two principally different biosynthetic pathways. The synthesis of 4-thiouridine (s4U) and 5-methylaminomethyl-2-thiouridine (mnm5s2U) occurs by a transfer of sulfur from IscS via various proteins to the target nucleoside in the tRNA, and no iron-sulfur cluster protein participates, whereas the synthesis of 2-thiocytidine (s2C) and N 6-(4-hydroxyisopentenyl)-2-methylthioadenosine (ms2io6A) is dependent on iron-sulfur cluster proteins, whose formation and maintenance depend on IscS. Accordingly, inactivation of IscS should result in decreased synthesis of all thiolated nucleosides. We selected mutants defective either in the synthesis of a thiolated nucleoside (mnm5s2U) specific for the iron-sulfur protein-independent pathway or in the synthesis of a thiolated nucleoside (ms2io6A) specific for the iron-sulfur protein-dependent pathway. Although we found altered forms of IscS that influenced the synthesis of all thiolated nucleosides, consistent with the model, we also found mutants defective in subsets of thiolated nucleosides. Alterations in the C-terminal region of IscS reduced the level of only ms2io6A, suggesting that the synthesis of this nucleoside is especially sensitive to minor aberrations in iron-sulfur cluster transfer activity. Our results suggest that IscS has an intrinsic substrate specificity in how it mediates sulfur mobilization and/or iron-sulfur cluster formation and maintenance required for thiolation of tRNA.
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32

Kameoka, Masanori, Max Morgan, Marc Binette, Rodney S. Russell, Liwei Rong, Xiaofeng Guo, Andrew Mouland, Lawrence Kleiman, Chen Liang, and Mark A. Wainberg. "The Tat Protein of Human Immunodeficiency Virus Type 1 (HIV-1) Can Promote Placement of tRNA Primer onto Viral RNA and Suppress Later DNA Polymerization in HIV-1 Reverse Transcription." Journal of Virology 76, no. 8 (April 15, 2002): 3637–45. http://dx.doi.org/10.1128/jvi.76.8.3637-3645.2002.

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ABSTRACT Human immunodeficiency virus type-1 Tat has been proposed to play a role in the regulation of reverse transcription. We previously demonstrated that wild-type Tat can augment viral infectivity by suppressing the reverse transcriptase (RT) reaction at late stages of the viral life cycle in order to prevent the premature synthesis of potentially deleterious viral DNA products. Here we have performed a detailed analysis of the cell-free reverse transcription reaction to elucidate the mechanism(s) whereby Tat can affect this process. Our results show that Tat can suppress nonspecific DNA elongation while moderately affecting the specific initiation stage of reverse transcription. In addition, Tat has an RNA-annealing activity and can promote the placement of tRNA onto viral RNA. This points to a functional homology between Tat and the viral nucleocapsid (NC) protein that is known to be directly involved in this process. Experiments using a series of mutant Tat proteins revealed that the cysteine-rich and core domains of Tat are responsible for suppression of DNA elongation, while each of the cysteine-rich, core, and basic domains, as well as a glutamine-rich region in the C-terminal domain, are important for the placement of tRNA onto the viral RNA genome. These results suggest that Tat can play at least two different roles in the RT reaction, i.e., suppression of DNA polymerization and placement of tRNA onto viral RNA. We believe that the first of these activities of Tat may contribute to the overall efficiency of reverse transcription of the viral genome during a new round of infection as well as to enhanced production of infectious viral particles. We hypothesize that the second activity, illustrating functional homology between Tat and NC, suggests a potential role for NC in the displacement of Tat during viral maturation.
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33

Das, Mayashree, Arshiya Dewan, Somnath Shee, and Amit Singh. "The Multifaceted Bacterial Cysteine Desulfurases: From Metabolism to Pathogenesis." Antioxidants 10, no. 7 (June 23, 2021): 997. http://dx.doi.org/10.3390/antiox10070997.

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Living cells have developed a relay system to efficiently transfer sulfur (S) from cysteine to various thio-cofactors (iron-sulfur (Fe-S) clusters, thiamine, molybdopterin, lipoic acid, and biotin) and thiolated tRNA. The presence of such a transit route involves multiple protein components that allow the flux of S to be precisely regulated as a function of environmental cues to avoid the unnecessary accumulation of toxic concentrations of soluble sulfide (S2−). The first enzyme in this relay system is cysteine desulfurase (CSD). CSD catalyzes the release of sulfane S from L-cysteine by converting it to L-alanine by forming an enzyme-linked persulfide intermediate on its conserved cysteine residue. The persulfide S is then transferred to diverse acceptor proteins for its incorporation into the thio-cofactors. The thio-cofactor binding-proteins participate in essential and diverse cellular processes, including DNA repair, respiration, intermediary metabolism, gene regulation, and redox sensing. Additionally, CSD modulates pathogenesis, antibiotic susceptibility, metabolism, and survival of several pathogenic microbes within their hosts. In this review, we aim to comprehensively illustrate the impact of CSD on bacterial core metabolic processes and its requirement to combat redox stresses and antibiotics. Targeting CSD in human pathogens can be a potential therapy for better treatment outcomes.
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34

Pallanck, L., S. Li, and L. H. Schulman. "The anticodon and discriminator base are major determinants of cysteine tRNA identity in vivo." Journal of Biological Chemistry 267, no. 11 (April 1992): 7221–23. http://dx.doi.org/10.1016/s0021-9258(18)42508-2.

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35

Ming, Xiaotian, Kristina Smith, Hiroaki Suga, and Ya-Ming Hou. "Recognition of tRNA Backbone for Aminoacylation with Cysteine: Evolution from Escherichia coli to Human." Journal of Molecular Biology 318, no. 5 (May 2002): 1207–20. http://dx.doi.org/10.1016/s0022-2836(02)00232-2.

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36

Tanaka, Masashi, Toshihiro Obayashi, Makoto Yoneda, Sergey A. Kovalenko, Satoru Sugiyama, and Takayuki Ozawa. "Mitochondrial DNA mutations in cardiomyopathy: Combination of replacements yielding cysteine residues and tRNA mutations." Muscle & Nerve 18, S14 (1995): S165—S169. http://dx.doi.org/10.1002/mus.880181432.

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37

Brustad, Eric, Mark L. Bushey, Ansgar Brock, Johnathan Chittuluru, and Peter G. Schultz. "A promiscuous aminoacyl-tRNA synthetase that incorporates cysteine, methionine, and alanine homologs into proteins." Bioorganic & Medicinal Chemistry Letters 18, no. 22 (November 2008): 6004–6. http://dx.doi.org/10.1016/j.bmcl.2008.09.050.

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38

Lee, Jeong-In, John E. Dominy, Angelos K. Sikalidis, Lawrence L. Hirschberger, Wei Wang, and Martha H. Stipanuk. "HepG2/C3A cells respond to cysteine deprivation by induction of the amino acid deprivation/integrated stress response pathway." Physiological Genomics 33, no. 2 (April 2008): 218–29. http://dx.doi.org/10.1152/physiolgenomics.00263.2007.

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To further define genes that are differentially expressed during cysteine deprivation and to evaluate the roles of amino acid deprivation vs. oxidative stress in the response to cysteine deprivation, we assessed gene expression in human hepatoma cells cultured in complete or cysteine-deficient medium. Overall, C3A cells responded to cysteine deprivation by activation of the eukaryotic initiation factor (eIF)2α kinase-mediated integrated stress response to inhibit global protein synthesis; increased expression of genes containing amino acid response elements ( ASNS, ATF3, CEBPB, SLC7A11, and TRIB3); increased expression of genes for amino acid transporters ( SLC7A11, SLC1A4, and SLC3A2), aminoacyl-tRNA synthetases ( CARS), and, to a limited extent, amino acid metabolism ( ASNS and CTH); increased expression of genes that act to suppress growth ( STC2, FOXO3A, GADD45A, LNK, and INHBE); and increased expression of several enzymes that favor glutathione synthesis and maintenance of protein thiol groups ( GCLC, GCLM, SLC7A11, and TXNRD1). Although GCLC, GCLM, SLC7A11, HMOX, and TXNRD1 were upregulated, most genes known to be upregulated via oxidative stress were not affected by cysteine deprivation. Because most genes known to be upregulated in response to eIF2α phosphorylation and activating transcription factor 4 (ATF4) synthesis were differentially expressed in response to cysteine deprivation, it is likely that many responses to cysteine deprivation are mediated, at least in part, by the general control nondepressible 2 (GCN2)/ATF4-dependent integrated stress response. This conclusion was supported by the observation of similar differential expression of a subset of genes in response to leucine deprivation. A consequence of sulfur amino acid restriction appears to be the upregulation of the cellular capacity to cope with oxidative and chemical stresses via the integrated stress response.
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39

Osawa, Takuo, Koichi Ito, Hideko Inanaga, Osamu Nureki, Kozo Tomita, and Tomoyuki Numata. "Conserved Cysteine Residues of GidA Are Essential for Biogenesis of 5-Carboxymethylaminomethyluridine at tRNA Anticodon." Structure 17, no. 5 (May 2009): 713–24. http://dx.doi.org/10.1016/j.str.2009.03.013.

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40

Hamann, Christian S., and Ya-Ming Hou. "Enzymic Aminoacylation of tRNA Acceptor Stem Helixes with Cysteine Is Dependent on a Single Nucleotide." Biochemistry 34, no. 19 (May 16, 1995): 6527–32. http://dx.doi.org/10.1021/bi00019a034.

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41

Walbott, H., C. Husson, S. Auxilien, and B. Golinelli-Pimpaneau. "Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase." RNA 13, no. 7 (July 1, 2007): 967–73. http://dx.doi.org/10.1261/rna.515707.

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42

Qu, Ge, Wei Wang, Ling-Ling Chen, Shao-Song Qian, and Hong-Yu Zhang. "tRNA-dependent Cysteine Biosynthetic Pathway Represents a Strategy to Increase Cysteine Contents by Preventing it from Thermal Degradation: Thermal Adaptation of Methanogenic Archaea Ancestor." Journal of Biomolecular Structure and Dynamics 27, no. 2 (October 1, 2009): 111–14. http://dx.doi.org/10.1080/07391102.2009.10507301.

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43

Chen, Minghao, Shin-ichi Asai, Shun Narai, Shusuke Nambu, Naoki Omura, Yuriko Sakaguchi, Tsutomu Suzuki, et al. "Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA." Proceedings of the National Academy of Sciences 114, no. 19 (April 24, 2017): 4954–59. http://dx.doi.org/10.1073/pnas.1615585114.

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Two-thiouridine (s2U) at position 54 of transfer RNA (tRNA) is a posttranscriptional modification that enables thermophilic bacteria to survive in high-temperature environments. s2U is produced by the combined action of two proteins, 2-thiouridine synthetase TtuA and 2-thiouridine synthesis sulfur carrier protein TtuB, which act as a sulfur (S) transfer enzyme and a ubiquitin-like S donor, respectively. Despite the accumulation of biochemical data in vivo, the enzymatic activity by TtuA/TtuB has rarely been observed in vitro, which has hindered examination of the molecular mechanism of S transfer. Here we demonstrate by spectroscopic, biochemical, and crystal structure analyses that TtuA requires oxygen-labile [4Fe-4S]-type iron (Fe)-S clusters for its enzymatic activity, which explains the previously observed inactivation of this enzyme in vitro. The [4Fe-4S] cluster was coordinated by three highly conserved cysteine residues, and one of the Fe atoms was exposed to the active site. Furthermore, the crystal structure of the TtuA-TtuB complex was determined at a resolution of 2.5 Å, which clearly shows the S transfer of TtuB to tRNA using its C-terminal thiocarboxylate group. The active site of TtuA is connected to the outside by two channels, one occupied by TtuB and the other used for tRNA binding. Based on these observations, we propose a molecular mechanism of S transfer by TtuA using the ubiquitin-like S donor and the [4Fe-4S] cluster.
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44

Nilsson, Kristina, Hans K. Lundgren, Tord G. Hagervall, and Glenn R. Björk. "The Cysteine Desulfurase IscS Is Required for Synthesis of All Five Thiolated Nucleosides Present in tRNA from Salmonella enterica Serovar Typhimurium." Journal of Bacteriology 184, no. 24 (December 15, 2002): 6830–35. http://dx.doi.org/10.1128/jb.184.24.6830-6835.2002.

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ABSTRACT Deficiency of a modified nucleoside in tRNA often mediates suppression of +1 frameshift mutations. In Salmonella enterica serovar Typhimurium strain TR970 (hisC3737), which requires histidine for growth, a potential +1 frameshifting site, CCC-CAA-UAA, exists within the frameshifting window created by insertion of a C in the hisC gene. This site may be suppressed by peptidyl-tRNAProcmo5UGG (cmo5U is uridine-5-oxyacetic acid), making a frameshift when decoding the near-cognate codon CCC, provided that a pause occurs by, e.g., a slow entry of the tRNAGlnmnm5s2UUG (mnm5s2U is 5-methylaminomethyl-2-thiouridine) to the CAA codon located in the A site. We selected mutants of strain TR970 that were able to grow without histidine, and one such mutant (iscS51) was shown to have an amino acid substitution in the l-cysteine desulfurase IscS. Moreover, the levels of all five thiolated nucleosides 2-thiocytidine, mnm5s2U, 5-carboxymethylaminomethyl-2-thiouridine, 4-thiouridine, and N-6-(4-hydroxyisopentenyl)-2-methylthioadenosine present in the tRNA of S. enterica were reduced in the iscS51 mutant. In logarithmically growing cells of Escherichia coli, a deletion of the iscS gene resulted in nondetectable levels of all thiolated nucleosides in tRNA except N-6-(4-hydroxyisopentenyl)-2-methylthioadenosine, which was present at only 1.6% of the wild-type level. After prolonged incubation of cells in stationary phase, a 20% level of 2-thiocytidine and a 2% level of N-6-(4-hydroxyisopentenyl)-2-methylthioadenosine was observed, whereas no 4-thiouridine, 5-carboxymethylaminomethyl-2-thiouridine, or mnm5s2U was found. We attribute the frameshifting ability mediated by the iscS51 mutation to a slow decoding of CAA by the tRNAGlnmnm5s2UUG due to mnm5s2U deficiency. Since the growth rate of the iscS deletion mutant in rich medium was similar to that of a mutant (mnmA) lacking only mnm5s2U, we suggest that the major cause for the reduced growth rate of the iscS deletion mutant is the lack of mnm5s2U and 5-carboxymethylaminomethyl-2-thiouridine and not the lack of any of the other three thiolated nucleosides that are also absent in the iscS deletion mutant.
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45

Wu, Min-Xian, Shelby J. Filley, Jie Xiong, Jerome J. Lee, and Kelvin A. W. Hill. "A cysteine in the C-terminal region of alanyl-tRNA synthetase is important for aminoacylation activity." Biochemistry 33, no. 40 (October 11, 1994): 12260–66. http://dx.doi.org/10.1021/bi00206a032.

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46

Miller, W. Todd, Kelvin A. W. Hill, and Paul Schimmel. "Evidence for a "cysteine-histidine box" metal-binding site in an Escherichia coli aminoacyl-tRNA synthetase." Biochemistry 30, no. 28 (July 16, 1991): 6970–76. http://dx.doi.org/10.1021/bi00242a023.

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47

Mueller, Eugene G., Peter M. Palenchar, and Christopher J. Buck. "The Role of the Cysteine Residues of ThiI in the Generation of 4-Thiouridine in tRNA." Journal of Biological Chemistry 276, no. 36 (July 6, 2001): 33588–95. http://dx.doi.org/10.1074/jbc.m104067200.

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48

Nakai, Yumi, Masato Nakai, Roland Lill, Tsutomu Suzuki, and Hideyuki Hayashi. "Thio Modification of Yeast Cytosolic tRNA Is an Iron-Sulfur Protein-Dependent Pathway." Molecular and Cellular Biology 27, no. 8 (February 5, 2007): 2841–47. http://dx.doi.org/10.1128/mcb.01321-06.

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ABSTRACT Defects in the yeast cysteine desulfurase Nfs1 cause a severe impairment in the 2-thio modification of uridine of mitochondrial tRNAs (mt-tRNAs) and cytosolic tRNAs (cy-tRNAs). Nfs1 can also provide the sulfur atoms of the iron-sulfur (Fe/S) clusters generated by the mitochondrial and cytosolic Fe/S cluster assembly machineries, termed ISC and CIA, respectively. Therefore, a key question remains as to whether the biosynthesis of Fe/S clusters is a prerequisite for the 2-thio modification of the tRNAs in both of the subcellular compartments of yeast cells. To elucidate this question, we asked whether mitochondrial ISC and/or cytosolic CIA components besides Nfs1 were involved in the 2-thio modification of these tRNAs. We demonstrate here that the three CIA components, Cfd1, Nbp35, and Cia1, are required for the 2-thio modification of cy-tRNAs but not of mt-tRNAs. Interestingly, the mitochondrial scaffold proteins Isu1 and Isu2 are required for the 2-thio modification of the cy-tRNAs but not of the mt-tRNAs, while mitochondrial Nfs1 is required for both 2-thio modifications. These results clearly indicate that the 2-thio modification of cy-tRNAs is Fe/S protein dependent and thus requires both CIA and ISC machineries but that of mt-tRNAs is Fe/S cluster independent and does not require key mitochondrial ISC components except for Nfs1.
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49

Halwani, Rabih, Shan Cen, Hassan Javanbakht, Jenan Saadatmand, Sunghoon Kim, Kiyotaka Shiba, and Lawrence Kleiman. "Cellular Distribution of Lysyl-tRNA Synthetase and Its Interaction with Gag during Human Immunodeficiency Virus Type 1 Assembly." Journal of Virology 78, no. 14 (July 15, 2004): 7553–64. http://dx.doi.org/10.1128/jvi.78.14.7553-7564.2004.

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ABSTRACT Lysyl-tRNA synthetase (LysRS) is packaged into human immunodeficiency virus type 1 (HIV-1) via its interaction with Gag, and this enzyme facilitates the selective packaging of tRNA3 Lys, the primer for initiating reverse transcription, into HIV-1. The Gag/LysRS interaction is detected at detergent-resistant membrane but not in membrane-free cell compartments that contain Gag and LysRS. LysRS is found (i) in the nucleus, (ii) in a cytoplasmic high-molecular-weight aminoacyl-tRNA synthetase complex (HMW aaRS complex), (iii) in mitochondria, and (iv) associated with plasma membrane. The cytoplasmic form of LysRS lacking the mitochondrial import signal was previously shown to be efficiently packaged into virions, and in this report we also show that LysRS compartments in nuclei, in the HMW aaRS complex, and at the membrane are also not required as a primary source for viral LysRS. Exogenous mutant LysRS species unable to either enter the nucleus or bind to the cell membrane are still incorporated into virions. Many HMW aaRS components are not packaged into the virion along with LysRS, and the interaction of LysRS with p38, a protein that binds tightly to LysRS in the HMW aaRS complex, is not required for the incorporation of LysRS into virions. These data indicate that newly synthesized LysRS may interact rapidly with Gag before the enzyme has the opportunity to move to the above-mentioned cellular compartments. In confirmation of this idea, we found that newly synthesized LysRS is associated with Gag after a 10-min pulse with [35S]cysteine/methionine. This observation is also supported by previous work indicating that the incorporation of LysRS into HIV-1 is very sensitive to the inhibition of new synthesis of LysRS.
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50

Vargas-Rodriguez, Oscar, and Karin Musier-Forsyth. "Exclusive Use of trans-Editing Domains Prevents Proline Mistranslation." Journal of Biological Chemistry 288, no. 20 (April 5, 2013): 14391–99. http://dx.doi.org/10.1074/jbc.m113.467795.

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Abstract:
Aminoacyl-tRNA synthetases (ARSs) catalyze the attachment of specific amino acids to cognate tRNAs. Although the accuracy of this process is critical for overall translational fidelity, similar sizes of many amino acids provide a challenge to ARSs. For example, prolyl-tRNA synthetases (ProRSs) mischarge alanine and cysteine onto tRNAPro. Many bacterial ProRSs possess an alanine-specific proofreading domain (INS) but lack the capability to edit Cys-tRNAPro. Instead, Cys-tRNAPro is cleared by a single-domain homolog of INS, the trans-editing YbaK protein. A global bioinformatics analysis revealed that there are six types of “INS-like” proteins. In addition to INS and YbaK, four additional single-domain homologs are widely distributed throughout bacteria: ProXp-ala (formerly named PrdX), ProXp-x (annotated as ProX), ProXp-y (annotated as YeaK), and ProXp-z (annotated as PA2301). The last three are domains of unknown function. Whereas many bacteria encode a ProRS containing an INS domain in addition to YbaK, many other combinations of INS-like proteins exist throughout the bacterial kingdom. Here, we focus on Caulobacter crescentus, which encodes a ProRS with a truncated INS domain that lacks catalytic activity, as well as YbaK and ProXp-ala. We show that C. crescentus ProRS can readily form Cys- and Ala-tRNAPro, and deacylation studies confirmed that these species are cleared by C. crescentus YbaK and ProXp-ala, respectively. Substrate specificity of C. crescentus ProXp-ala is determined, in part, by elements in the acceptor stem of tRNAPro and further ensured through collaboration with elongation factor Tu. These results highlight the diversity of approaches used to prevent proline mistranslation and reveal a novel triple-sieve mechanism of editing that relies exclusively on trans-editing factors.
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