The transfer RNA of certain Enterobacteriacae contain 2-methylthiozeatin riboside (ms<sup>2</sup>io<sup>6</sup>A) an isopentenyl adenosine derivative

Janzer, Janice J.; Raney, J. P.; McLennan, B. D.

doi:10.1093/nar/10.18.5663

Cited by 20 publications

(14 citation statements)

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“…The ms 2 i 6 A modification is present in all bacteria except Listeria and P. putida , and is found in eukaryotes in S. scrofa but not in any of the fungal species investigated. According to the literature, the hydroxy derivatives io 6 A and ms 2 io 6 A are predominantly present in γ‐proteobacteria such as Pseudomonas 13. Surprisingly, we detected large quantities of these compounds also in the β‐proteobacteria Burkholderia .…”

Section: Methodssupporting

confidence: 49%

Systems‐Based Analysis of Modified tRNA Bases

et al. 2011

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The genetic system contains several levels of information. Firstly, the sequence of the canonical bases A, C, G, and T/U in DNA and RNA encodes amino acids through specific base triplets. Secondly, the methylation status of the cytosine base in DNA imprints epigenetic information into the genetic system, thereby contributing to the division of genes into active and inactive elements. Both information layers are chemically well investigated. Less is known about a putative third level of information associated with the chemical modification of RNA nucleobases. Although RNA, and in particular tRNA, is known to contain more than 100 different modified nucleosides, [1] the exact type of information added by base modification is largely unknown. A number of common modifications have been shown to improve the maintenance of the reading frame, [2] influence RNA stability, [3] and to be involved in proof-reading by tRNA synthetases. [4] Recently, it was discovered that the collective set of modified tRNA nucleosides is a regulated component of stress response and gives us a first hint that cells may actively adjust the modification pattern in response to external factors. [5] To learn more about the function of modified nucleobases we have investigated relationships between species by quantification of the modification content. By using a parallel systems-type approach we discovered that the collective set of modified bases is highly species-specific and linked to phylogeny. These data then enabled us to calculate a detailed phylogenetic tree that is consistent with those obtained from traditional data such as the homology of rRNA sequences, [6] conserved orthologous genes, [7] sequences of tRNA synthetases, [8] and tRNA-dependent amidotransferases.[9] The result shows that the set of base modifications is not universal, but rather a highly species-specific code under evolutionary selection to appropriately match base triplets with the corresponding cognate amino acids.For the study, we applied our recently developed LC-MSbased method for the quantification of modified nucleosides by using isotopically labeled standards.[10] For the parallel quantification we synthesized 18 tRNA modifications in both their natural and isotopically labeled forms (Scheme 1). A number of these nucleosides are present in the 3'-position to the anticodon in position 37, while others are distributed through the tRNA structure. The modifications studied are involved in a range of biological processes such as structural stabilization, codon binding, and translation initiation. [2a, 3, 10b, 11] With these tRNA nucleosides in hand, we analyzed the tRNA modification pattern of 16 species, so as to cover several branches of the phylogenetic tree. These species include five eukaryotes as well as five Gram-negative proteobacteria and five Gram-positive bacteria of the firmicutes. In addition we studied the bacterium Deinococcus radiodurans, which has a somewhat ambiguous classification. D. radiodurans is typically identified as Gram-positive, but ...

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Section: Methodssupporting

confidence: 49%

Systems‐Based Analysis of Modified tRNA Bases

et al. 2011

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“…In Escherichia coli , ms 2 i 6 A37 is present in tRNAs that read codons that start with uridine, except tRNA Ser(GGA) 1, 6. The 4‐hydroxy derivative of ms 2 i 6 A, N 6 ‐( cis ‐4‐hydroxyisopentenyl)‐2‐thiomethyladenosine (ms 2 io 6 A, also called 2‐methyltio‐ cis ‐ribozeatin) is present in the corresponding tRNAs in Salmonella typhimurium ,7 it was also found in tRNA from several other Gram‐negative bacteria8 and in plants 9. Interestingly, the free base N 6 ‐(Δ 2 ‐isopentenyl) adenine i 6 A and its derivatives function as cytokinins, plant growth factors that promote cell division (for review, see Ref 10…”

Section: Introductionmentioning

confidence: 99%

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms²io⁶A37 in tRNA

et al. 2007

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TRNAs from all organisms contain posttranscriptionally modified nucleosides, which are derived from the four canonical nucleosides. In most tRNAs that read codons beginning with U, adenosine in the position 37 adjacent to the 3' position of the anticodon is modified to N(6)-(Delta(2)-isopentenyl) adenosine (i(6)A). In many bacteria, such as Escherichia coli, this residue is typically hypermodified to N(6)-isopentenyl-2-thiomethyladenosine (ms(2)i(6)A). In a few bacteria, such as Salmonella typhimurium, ms(2)i(6)A can be further hydroxylated to N(6)-(cis-4-hydroxyisopentenyl)-2-thiomethyladenosine (ms(2)io(6)A). Although the enzymes that introduce the respective modifications (prenyltransferase MiaA, methylthiotransferase MiaB, and hydroxylase MiaE) have been identified, their structures remain unknown and sequence-function relationships remain obscure. We carried out sequence analysis and structure prediction of MiaA, MiaB, and MiaE, using the protein fold-recognition approach. Three-dimensional models of all three proteins were then built using a new modeling protocol designed to overcome uncertainties in the alignments and divergence between the templates. For MiaA and MiaB, the catalytic core was built based on the templates from the P-loop NTPase and Radical-SAM superfamilies, respectively. For MiaB, we have also modeled the C-terminal TRAM domain and the newly predicted N-terminal flavodoxin-fold domain. For MiaE, we confidently predict that it shares the three-dimensional fold with the ferritin-like four-helix bundle proteins and that it has a similar active site and mechanism of action to diiron carboxylate enzymes, in particular, methane monooxygenase (E.C.1.14.13.25) that catalyses the biological hydroxylation of alkanes. Our models provide the first structural platform for enzymes involved in the biosynthesis of i(6)A, ms(2)i(6)A, and ms(2)io(6)A, explain the data available from the literature and will help to design further experiments and interpret their results.

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“…1). The last step performed by the tRNA(ms2io6A37)hydroxylase takes place in most strains in the family Enterobacteriacae so far examined but not in E. coli, which has the unhydroxylated derivative ms2i6A in its tRNA (13,39). Knowing this, we cloned the gene for the tRNA(ms io6A37)hydroxylase (miaE) (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Cellular metabolism is also influenced by the tRNA modification level. Mutations in hisT and miaA, which cause deficiencies in pseudouridine (38,39,40) and ms2io6A37, respectively, influence the synthesis (7,8,19,50,66) and degradation (29) of many amino acids through tRNAmediated attenuation. However, several regulatory features of such modification-deficient strains are not easily reconciled with regulation through attenuation (3,6,8,46,52,57,65).…”

Section: Discussionmentioning

confidence: 99%

Isolation of the gene (miaE) encoding the hydroxylase involved in the synthesis of 2-methylthio-cis-ribozeatin in tRNA of Salmonella typhimurium and characterization of mutants

Persson

Björk

1993

J Bacteriol

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The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with U except tRNASer in Escherichia coli. Salmonella typhimurium 2-methylthio-cis-ribozeatin (ms2io6A) is found in tRNA, probably in the corresponding species that have ms2i6A in E. coli. The gene (miaE) for the tRNA(ms2io6A)hydroxylase of S. typhimurium was isolated by complementation in E. coli. The miaE gene was localized close to the argI gene at min 99 of the S. typhimurium chromosomal map. Its DNA sequence and transcription pattern together with complementation studies revealed that the miaE gene is the second gene of a dicistronic operon. Southern blot analysis showed that the miaE gene is absent in E. coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species. Mutants of S. typhimurium which have MudJ inserted in the miaE gene and which, consequently, are blocked in the ms2i6A hydroxylation reaction were isolated. Unexpectedly, such mutants cannot utilize the citric acid cycle intermediates malate, fumarate, and succinate as carbon sources.

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The transfer RNA of certain Enterobacteriacae contain 2-methylthiozeatin riboside (ms²io⁶A) an isopentenyl adenosine derivative

Cited by 20 publications

References 21 publications

Systems‐Based Analysis of Modified tRNA Bases

Systems‐Based Analysis of Modified tRNA Bases

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms²io⁶A37 in tRNA

Isolation of the gene (miaE) encoding the hydroxylase involved in the synthesis of 2-methylthio-cis-ribozeatin in tRNA of Salmonella typhimurium and characterization of mutants

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The transfer RNA of certain Enterobacteriacae contain 2-methylthiozeatin riboside (ms2io6A) an isopentenyl adenosine derivative

Cited by 20 publications

References 21 publications

Systems‐Based Analysis of Modified tRNA Bases

Systems‐Based Analysis of Modified tRNA Bases

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms2io6A37 in tRNA

Isolation of the gene (miaE) encoding the hydroxylase involved in the synthesis of 2-methylthio-cis-ribozeatin in tRNA of Salmonella typhimurium and characterization of mutants

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The transfer RNA of certain Enterobacteriacae contain 2-methylthiozeatin riboside (ms²io⁶A) an isopentenyl adenosine derivative

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms²io⁶A37 in tRNA