Conformation of the tRNA minor constituent dihydrouridine

Suck, Dietrich

doi:10.1016/0014-5793(71)80191-6

Cited by 8 publications

(6 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Due to the saturation of the C5–C6 bond, D is the only described non-aromatic base found in nucleic acids [90]. The base is no longer planar, but puckered, and positions C5 and C6 are displaced on opposite sides of the plane consisting of positions N1, C2, N3 and C4, resulting in a half-chair conformation [145,146]. The saturated non-planar shape of D has two structural consequences.…”

Section: Structural Impact Of Modificationsmentioning

confidence: 99%

tRNA Modifications: Impact on Structure and Thermal Adaptation

2017

View full text Add to dashboard Cite

Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots—the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA. The highly conserved tRNA shape is crucial for the interaction with a variety of proteins and other RNA molecules, but also needs a certain flexibility for a correct interplay. In this context, it was shown that tRNA modifications are important for temperature adaptation in thermophilic as well as psychrophilic organisms, as they modulate rigidity and flexibility of the transcripts, respectively. Here, we give an overview on the impact of modifications on tRNA structure and their importance in thermal adaptation.

show abstract

Section: Structural Impact Of Modificationsmentioning

confidence: 99%

tRNA Modifications: Impact on Structure and Thermal Adaptation

2017

View full text Add to dashboard Cite

show abstract

“…D is produced via the reduction of uridine's C5 = C6 double bond to give a non-aromatic base. This loss of aromaticity, which is a unique feature among nucleic acids, disrupts the base planarity and consequently prevents D from participating in stacking interactions [2]. The physiological role of D is yet to be fully understood, although several convergent observations suggest its importance for structuring RNAs.…”

Section: Introductionmentioning

confidence: 99%

Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes

Faivre

Lombard

Fakroun³

et al. 2021

RNA Biology

View full text Add to dashboard Cite

Dihydrouridine (D) is a tRNA-modified base conserved throughout all kingdoms of life and assuming an important structural role. The conserved dihydrouridine synthases (Dus) carries out D-synthesis. DusA, DusB and DusC are bacterial members, and their substrate specificity has been determined in Escherichia coli. DusA synthesizes D20/D20a while DusB and DusC are responsible for the synthesis of D17 and D16, respectively. Here, we characterize the function of the unique dus gene encoding a DusB detected in Mollicutes, which are bacteria that evolved from a common Firmicute ancestor via massive genome reduction. Using in vitro activity tests as well as in vivo E. coli complementation assays with the enzyme from Mycoplasma capricolum (DusB MCap ), a model organism for the study of these parasitic bacteria, we show that, as expected for a DusB homolog, DusB MCap modifies U17 to D17 but also synthetizes D20/ D20a combining therefore both E. coli DusA and DusB activities. Hence, this is the first case of a Dus enzyme able to modify up to three different sites as well as the first example of a tRNA-modifying enzyme that can modify bases present on the two opposite sides of an RNA-loop structure. Comparative analysis of the distribution of DusB homologs in Firmicutes revealed the existence of three DusB subgroups namely DusB1, DusB2 and DusB3. The first two subgroups were likely present in the Firmicute ancestor, and Mollicutes have retained DusB1 and lost DusB2. Altogether, our results suggest that the multisite specificity of the M. capricolum DusB enzyme could be an ancestral property.

show abstract

“…In addition, molecular models of I and III do not indicate any difficulty in the interconversion of the syn and anti conformations of the nucleosides, a factor to be considered (Kapuler et al, 1970). According to X-ray analysis III exists in the anti conformation (Suck et al, 1971;Sundaralingam et al, 1971) as does dihydrothymidine (Konnert et al, 1970) and the common nucleotides.…”

Section: Discussionmentioning

confidence: 99%

“…), 5-bromo(Michelson et al, 1962),5-iodo (Michelson et al, 1962), 5-ethyl(Swierkowski and Shugar, 1970), and 5sulfonylmethyl(Carpenter and Shaw, 1970), can be polymerized into homopolymers. The puckering of the dihydrouracil ring(Suck et al, 1971;Sundaralingam et al, 1971) in Illb biochemistry, vol. 11, no.…”

mentioning

confidence: 99%

Enzymic synthesis of polynucleotides containing 5.6-methylene- and 5,6-dihydropyrimidines

Torrence¹,

Witkop²

1972

Biochemistry

View full text Add to dashboard Cite

1 -(/3-D-Ribofuranosyl>(a+j3)5,6-methyleneuracil 5 '-diphosphate (lb), a bicyclic isomer of 5-methyluridine, was synthesized and investigated as a substrate for polynucleotide phosphorylase from Micrococcus luteus. In the same way as dihydrouridine 5'-diphosphate (Mb), lb could not be converted directly into a homopolymer by the enzyme. However, both lb and Mb could be copolymerized with ADP, IDP, CDP, or UDP into polymers which contained 5-40 residues of lb or Mb per 100 [of the normal] nucleotide units and were shown to be distributed internally in the polynucleotide chain. The ratios obtained depended on the rel-In electronic and spectral terms the cyclopropane ring may be regarded as an intermediate between a carbon-carbon single and double bond; e.g., the bond length of cyclopropane (Bastiansen et al., 1964) bond angles of vicinal hydrogens (Bastiansen et al., 1964) and CH hybridization (Wiberg, 1964) lie between the corresponding values of ethane and ethylene. Electronically, such an intermediacy is demonstrated by its ability to stabilize a photoexcited state (Yoshida and Ogoski, 1970) or an incipient carbonium ion (Deno et Brown and Cleveland, 1966). In a purely steric sense this comparison fails, since the methylene group adds considerable bulk to the corresponding ethane or ethylene. Thus, investigation of the relative activities of substrates with ethane, ethylene, and cyclopropane unit variations in a dynamic enzymic system might permit an assessment of the relative importance of steric vs. electronic factors.The recent synthesis (Kunieda and Witkop, 1971) of 1 -(0-D-ribofuranosyl>a(or /3)-5,6-methyleneuracil ("cyclo-5-methyluridine," I) permits a test of this approach in the field of nucleic acids, since I can be considered an intermediate between uridine (II), 5-methyluridine, and their dihydro derivatives. The cyclopropane ring contributes to the aromaticity which shows up in the ultraviolet spectrum of I (Xmax 245 nm, shoulder), intermediate between II(Xmax 260 nm)and III (Xmax 206 nm). If electronic factors, i.e., aromaticity, were overriding in determining the ability of I, II, and III to serve as substrates, the order should be II>I>III. If steric factors involving the 5,6 bond of uridine were important, then the order should be II>III>I. Initial results with compound I in biological systems have been discouraging. I does not arrest the growth of HeLa and L5178Y cells nor production of vaccinia virus in HeLa cells when tested at 10-4 m (C. Heidelberger, personal communication), is inactive against Vaccinia, Polio III, Herpes, Coe, Adeno, Rhino (two strains

show abstract

Conformation of the tRNA minor constituent dihydrouridine

Cited by 8 publications

References 10 publications

tRNA Modifications: Impact on Structure and Thermal Adaptation

tRNA Modifications: Impact on Structure and Thermal Adaptation

Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes

Enzymic synthesis of polynucleotides containing 5.6-methylene- and 5,6-dihydropyrimidines

Contact Info

Product

Resources

About