NMR analyses on the molecular mechanism of the conformational rigidity of 2‐thioribothymidine, a modified nucleoside in extreme thermophile tRNAs

Yamamoto, Yuriko; Yokoyama, Shigeyuki; Miyazawa, Tatsuo; Watanabe, Kimitsuna; Higuchi, Shigesada

doi:10.1016/0014-5793(83)81123-5

Cited by 59 publications

(33 citation statements)

References 12 publications

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“…A number of these modifications serve to stabi-lize the C-3Ј-endo form of ribose in the polynucleotide chain, effectively stabilizing the A-type helical conformation that is common to RNA (26,27,57). They also promote stability through hydrogen bonding and enhanced base stacking (13), and they provide nuclease protection by ribose methylation (1).…”

Section: Discussionmentioning

confidence: 99%

Posttranscriptional modification of tRNA in psychrophilic bacteria

et al. 1997

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Posttranscriptional modification in tRNA is known to play a multiplicity of functional roles, including maintenance of tertiary structure and cellular adaptation to environmental factors such as temperature. Nucleoside modification has been studied in unfractionated tRNA from three psychrophilic bacteria (ANT-300 and Vibrio sp. strains 5710 and 29-6) and one psychrotrophic bacterium (Lactobacillus bavaricus). Based on analysis of total enzymatic hydrolysates by liquid chromatography-mass spectrometry, unprecedented low amounts of modification were found in the psychrophiles, particularly from the standpoint of structural diversity of modifications observed. Thirteen to 15 different forms of posttranscriptional modification were found in the psychrophiles, and 10 were found in L. bavaricus, compared with approximately 29 known to occur in bacterial mesophiles and 24 to 31 known to occur in the archaeal hyperthermophiles. The four most abundant modified nucleosides in tRNA from each organism were dihydrouridine, pseudouridine, 7-methylguanosine, and 5-methyluridine. The molar abundances of the latter three nucleosides were comparable to those found in tRNA from Escherichia coli. By contrast, the high levels of dihydrouridine observed in all three psychrophiles are unprecedented for any organism in any of the three phylogenetic domains. tRNA from these organisms contains 40 to 70% more dihydrouridine, on average, than that of the mesophile E. coli or the psychrotroph L. bavaricus. This finding supports the concept that a functional role for dihydrouridine is in maintenance of conformational flexibility of RNA, especially important to organisms growing under conditions where the dynamics of thermal motion are severely compromised. This is in contrast to the role of modifications contained in RNA from thermophiles, which is to reduce regional RNA flexibility and provide structural stability to RNA for adaptation to high temperature.The structural diversity (31) and multiplicity of roles played by posttranscriptional modification in RNA, particularly tRNA (3, 4, 59), has been clearly established. Despite the fact that 80 different modified nucleosides are presently known (8) to occur in tRNA from organisms representing all three phylogenetic domains (31), nearly all knowledge of posttranscriptional modification in RNA is derived from studies of mesophiles and thermophiles. Of 521 reported tRNA sequences (46), the only apparent exception is the initiator tRNA from the arthropod Euphausia sperba, which inhabits the Antarctic Sea (52). We are unaware of previous investigations reporting modification in tRNA from any psychrophilic microorganism, despite the fact that greater than 80% of the biosphere is characterized by temperatures below 5ЊC. Nevertheless, interest in these organisms and their biotechnological potential has increased substantially in recent years (25, 32), and they represent a fundamentally important but understudied segment of the biosphere. Psychrophilic microorganisms have an optimum temperature for g...

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Section: Discussionmentioning

confidence: 99%

Posttranscriptional modification of tRNA in psychrophilic bacteria

et al. 1997

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“…We have already found that the C3'-endo form is predominant in 2-thiopyrimidine nucleosides and nucleotides (16,18). The remarkable stability of the C3'-endo form is due to the steric interaction between the bulky 2-thiocarbonyl group and the 2'-hydroxyl group (17). As shown in Table 1, the relative stabilities of the C3'-endo form of 2-thiouridine derivatives (s2U, ps2U, and m5s2U) are higher, by 0.8 kcal/mol, than those of non-thiosubstituted derivatives (uridine, pU, and m5U).…”

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confidence: 99%

Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon.

Yokoyama¹,

Watanabe²,

Murao³

et al. 1985

Proc. Natl. Acad. Sci. U.S.A.

252

234

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Proton NMR analyses have been made to elucidate the conformational characteristics of modified nucleotides as found in the first position of the anticodon of tRNA [derivatives of 5-methyl-2-thiouridine 5'-monophosphate (pxm5s2U) and derivatives of 5-hydroxyuridine 5'-monophosphate (pxo5U)]. In pxm5s2U, the C3'-endo form is extraordinarily more stable than the C2'-endo form for the ribose ring, because of the combined effects of the 2-thiocarbonyl group and the 5-substituent. By contrast, in pxo5U, the C2'-endo form is much more stable than the C3'-endo form, because of the interaction between the 5-substituent and the 5'-phosphate group. The enthalpy differences between the C2'-endo form and the C3'-endo form have been obtained as 1.1, -0.7, and 0.1 kcal/mol (1 cal = 4.184 J) for pxm5s2U, pxo5U, and

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“…It was reported that s 2 U derivatives prefer C3 0 -endo ribose puckering. [28][29][30] This conformational predominance is known to be caused by steric repulsion between the 2-thiocarbonyl group of s 2 U and the 2 0 -hydroxy group. 28 The C3 0 -endo predominance observed could be explained by the same type of steric repulsion.…”

Section: -15mentioning

confidence: 99%

Synthesis of 4-Thiopseudoisocytidine and 4-Thiopseudouridine as Components of Triplex-forming Oligonucleotides

Okamoto¹,

Cao²,

Tanaka³

et al. 2009

Chemistry Letters

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In this paper, we report convenient methods for the synthesis of 4-thiopseudoisocytidine (s 4 iC) and 4-thiopseudouridine (s 4 É). 1 H NMR spectral analysis of these modified nucleosides showed that both s 4 É and s 4 iC prefer C3 0 -endo ribose puckering. These conformational properties are favorable for the stabilization of triplex formation.Using the antigene strategy, a large number of modified nucleosides have been synthesized to enhance the thermal stability of DNA triplexes formed by hybridization of the third DNA strands with DNA duplexes.

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NMR analyses on the molecular mechanism of the conformational rigidity of 2‐thioribothymidine, a modified nucleoside in extreme thermophile tRNAs

Cited by 59 publications

References 12 publications

Posttranscriptional modification of tRNA in psychrophilic bacteria

Posttranscriptional modification of tRNA in psychrophilic bacteria

Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon.

Synthesis of 4-Thiopseudoisocytidine and 4-Thiopseudouridine as Components of Triplex-forming Oligonucleotides

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