Archaeal Tuc1/Ncs6 Homolog Required for Wobble Uridine tRNA Thiolation Is Associated with Ubiquitin-Proteasome, Translation, and RNA Processing System Homologs

Chavarria, Nikita E.; Hwang, Sungmin; Cao, Shiyun; Fu, Xian; Holman, M. M.; Elbanna, Dina; Rodríguez, S.; Arrington, Deanna; Englert, Markus; Uthandi, Sivakumar; Söll, Dieter; Maupin-Furlow, Julie A.

doi:10.1371/journal.pone.0099104

Cited by 35 publications

(37 citation statements)

References 43 publications

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“…C-5 of U34 is located between Phe154 and Asp99, which are 3.6 Å and 3.3 Å from C-5, respectively. (3,(32)(33)(34)(35). However, the biosynthetic pathway involving thiolation of C-2 of U34 of tRNA has not been reported in Grampositive bacteria.…”

Section: Levels Of Expression Of Mnma Affects Abundance Of Smentioning

confidence: 99%

“…Similarly, inactivation of the nonessential 2-thiouridylase gene MTU1, while leaving the organism viable, causes respiratory defects in yeast and humans (38,39). On the other hand, the archaeal 2-thiouridylase gene Ncs6 is essential in Methanococcus maripaludis (33) and necessary for growth at high temperatures in Haloferax volcanii (34). In the model Gram-positive bacterium B. subtilis, we and others failed when attempting to inactivate yrvO or mnmA (24), indicating that both proteins participate in essential cellular processes.…”

Section: Levels Of Expression Of Mnma Affects Abundance Of Smentioning

confidence: 99%

“…Distinct mechanisms of s 2 U in eukaryotic, archaeal, and Gramnegative model species have been reported. The unifying feature in all reported pathways is the participation of a pyrophosphatase enzyme involved in the adenylation of the C-2 position of U34 tRNA, enabling the subsequent thiolation reaction (3,(32)(33)(34)(35). However, the mechanisms of sulfur activation and insertion vary and are not fully understood.…”

Section: Levels Of Expression Of Mnma Affects Abundance Of Smentioning

confidence: 99%

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Abbreviated Pathway for Biosynthesis of 2-Thiouridine in Bacillus subtilis

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Santos

2015

J Bacteriol

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The 2-thiouridine (s 2 U) 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 IMPORTANCEThe 2-thiouridine (s 2 U) 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 s 2 U in Escherichia coli requires seven proteins: the cysteine desulfurase IscS, the thiouridylase MnmA, and five intermediate sulfur-relay enzymes (TusABCDE). Bacillus subtilis and most Gram-positive bacteria lack a complete set of biosynthetic components. Interestingly, the mnmA coding sequence is located adjacent to yrvO, encoding a cysteine desulfurase. In this work, we provide evidence that the B. subtilis YrvO is able to transfer sulfur directly to MnmA. Both proteins are sufficient for s 2 U biosynthesis in a pathway independent of the one used in E. coli. P osttranscriptional RNA modifications are found among all organisms and are essential for their cellular function. More than 100 RNA modifications have been identified thus far which have a variety of physiological functions (1). In particular, posttranscriptional modifications of tRNA are often necessary for translational fidelity and efficiency, especially those found in anticodon bases. The third base in the anticodon is deemed the wobble position, as it is bound more loosely to the ribosome than the first two. Consequently, wobble bases have greater flexibility, allowing them to make noncanonical base pairs, leading to a greater chance of amino acid misincorporation into a growing peptide chain. An explanation of how this phenomenon is overcome is provided by the modified wobble hypothesis, which states that certain base modifications have evolved to adjust the anticodon shape, either to limit or to enable the occurrence of wobble pairing (2).The modification of the wobble (34th position) in glutamate (Glu), glutamine (Gln), and lysine (Lys) tRNA molecules produces 5-methyl-2-thiouridine derivatives (xm 5 s 2 U) (Fig. 1). Thiolation of the wobble uridine places the base in an anti, C-3=-endo, gauche conformation, thus forming a rigid structure, which increases its affinity for pairing with adenosine and thereby yields higher accuracy in the corresponding peptide sequence. Additionally, this modification stabilizes the anticodon structures and confers the tRNA molecule's ability to bind to the ribosome. Tighter ribosomal binding to tRNA subsequently improves reading frame maintenance and deficiencies in the translational process (2-5). Lack of the 2-thiouridine (s 2 U) modification in tRNA causes growth defects in bacteria attributed to accumulation of frameshifting during translation (6). In humans, mutations within the gene coding for the 2-thiouridylase TrmU, responsible for the sulfur insertion step, has been associated with acute in...

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Section: Levels Of Expression Of Mnma Affects Abundance Of Smentioning

confidence: 99%

Section: Levels Of Expression Of Mnma Affects Abundance Of Smentioning

confidence: 99%

Section: Levels Of Expression Of Mnma Affects Abundance Of Smentioning

confidence: 99%

See 1 more Smart Citation

Abbreviated Pathway for Biosynthesis of 2-Thiouridine in Bacillus subtilis

Black

Santos

2015

J Bacteriol

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“…This is based on the observations that (i) the ncs6 gene homologs are widespread in archaeal genomes [8]; (ii) the deletion of the ncs6 homolog ( ncsA ) in Haloferax volcanii resulted in only non-thiolated tRNA Lys UUU [71]; (iii) Ncs6 homologs form complexes with the ubiquitin-like small archaeal modifier protein (SAMP), which has high structural homology to Urm1, in H. volcanii [72] and in M. maripaludis [51]; (iv) the H. volcanii E1-like protein UbaA activates SAMP in formation of a thioester intermediate [73]; (v) the deletion of either samp2 or ubaA in H. volcanii eliminated thiolated tRNA Lys UUU [52]; and (vi) the M. maripaludis Ncs6 homolog has a [3Fe-4S] cluster [46]. These findings suggest that both an Fe–S cluster containing Ncs6 homolog and an activated ubiquitin-like protein are required for s 2 U34 formation in Archaea.…”

Section: Fe–s Cluster-dependent and Independent Trna Thiolation Prmentioning

confidence: 99%

Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways

Čavužić

Liu

2017

Biomolecules

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Post-translational tRNA modifications have very broad diversity and are present in all domains of life. They are important for proper tRNA functions. In this review, we emphasize the recent advances on the biosynthesis of sulfur-containing tRNA nucleosides including the 2-thiouridine (s2U) derivatives, 4-thiouridine (s4U), 2-thiocytidine (s2C), and 2-methylthioadenosine (ms2A). Their biosynthetic pathways have two major types depending on the requirement of iron–sulfur (Fe–S) clusters. In all cases, the first step in bacteria and eukaryotes is to activate the sulfur atom of free l-cysteine by cysteine desulfurases, generating a persulfide (R-S-SH) group. In some archaea, a cysteine desulfurase is missing. The following steps of the bacterial s2U and s4U formation are Fe–S cluster independent, and the activated sulfur is transferred by persulfide-carrier proteins. By contrast, the biosynthesis of bacterial s2C and ms2A require Fe–S cluster dependent enzymes. A recent study shows that the archaeal s4U synthetase (ThiI) and the eukaryotic cytosolic 2-thiouridine synthetase (Ncs6) are Fe–S enzymes; this expands the role of Fe–S enzymes in tRNA thiolation to the Archaea and Eukarya domains. The detailed reaction mechanisms of Fe–S cluster depend s2U and s4U formation await further investigations.

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“…LC-MS/MS analysis was carried out at the Interdisciplinary Center for Biotechnology Research (University of Florida, Gainesville, Florida) using an LTQ Orbitrap XL mass spectrometer (ThermoFisher Scientific, West Palm Beach, Florida). Proteins spots of interest were excised from the gels (nymph and adult) and analyzed by LC-MS/MS as described previously (Salganik et al, 2012;Chavarria et al, 2014). Briefly, the samples were digested enzymatically with trypsin, and the peptides were injected onto a capillary trap (LC Packings PepMap), desalted for 5 min with 0.1% (v/v) acetic acid at a flow rate of 3 μL min −1 prior, then loaded onto an LC Packing ® C18 PepMap nanoflow high-performance liquid chromatography column (ThermoFisher Scientific).…”

Section: Lc-ms/ms and Database Searchesmentioning

confidence: 99%

Comparative proteomic analysis between fifth‐instar nymphs and adults of Asian citrus psyllid Diaphorina citri

et al. 2016

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Asian citrus psyllid Diaphorina citri Kuwayama is extremely problematic worldwide, particularly where Huanglongbing (HLB) disease, the most serious and devastating of citrus diseases, is found. The threat is a result of its ability to transmit the causal agent of HLB, Candidatus Liberibacter asiaticus (CLas) bacterium. Improvements in proteomics, mass spectrometry, bioinformatics tools and gene ontology annotation facilitate the mapping and large‐scale identification and quantification of proteins. To date, only a few comparative proteomic studies report the developmental proteomic changes of hemimetabolous and plant–disease vector insects. Two‐dimensional gel electrophoresis analysis of D. citri total protein is able to detect qualitative and quantitative developmental differences. Liquid chromatography‐tandem mass spectrometry identifies 89 protein spots. Most proteins are metabolism and bioenergetics‐related. Nineteen protein spots are found to be implicated in stress/defence/immunity; 7 in development regulation; 9 in nervous system functions; 4 in the reproductive system; 23 in cytoskeleton and muscle organization; and 4 in movement, flight and other processes. Significant increases in the level of proteins related to structural constitution of the skeleton, stress/defence/immunity, reproduction system, muscles, locomotion and flight are found in adults, consistent with the fact that D. citri is a hemimetabolous insect, whereas proteins involved in developmental regulation are higher in the nymphal stage. The identification of these variably expressed proteins between the nymph and adult stages, linked with the basis of their physiological roles, will lead to a better understanding of the factors influencing development in D. citri and the regulation of some crucial metabolic pathways. It may also help to identify targets for genetic manipulation using RNA interference or other techniques to disrupt Asian citrus psyllid development, lifespan or its ability to transmit CLas.

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Archaeal Tuc1/Ncs6 Homolog Required for Wobble Uridine tRNA Thiolation Is Associated with Ubiquitin-Proteasome, Translation, and RNA Processing System Homologs

Cited by 35 publications

References 43 publications

Abbreviated Pathway for Biosynthesis of 2-Thiouridine in Bacillus subtilis

Abbreviated Pathway for Biosynthesis of 2-Thiouridine in Bacillus subtilis

Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways

Comparative proteomic analysis between fifth‐instar nymphs and adults of Asian citrus psyllid Diaphorina citri

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