Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling

Babin, Patricia; Dolan, Michael; Wollenzien, Paul; Gutell, Robin R.

doi:10.1017/s1355838299990659

Cited by 7 publications

(3 citation statements)

References 33 publications

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“…For comparison, mismatches in regular base pairs of the TAR stem occur between 0.3% (e.g., A27-U38) and 4.6% (e.g., C18-G44) within this set of sequences. In fact, the mismatch frequency of 6.2% is rather low compared to the relatively high level of uncorrelated base changes associated with base triples in rRNA, tRNA, and group I introns (Gautheret et al 1995;Tanner et al 1997;Babin et al 1999). Thus, this comparative sequence analysis presents strong phylogenetic support for a (22-40)31 base triple in the HIV-1 TAR element.…”

Section: Comparative Sequence Analysis Suggests the Existence Of A Bamentioning

confidence: 69%

Evidence for a base triple in the free HIV-1 TAR RNA

Huthoff

Girard²,

Wijmenga³

et al. 2004

RNA

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We propose the existence of a novel base triple in the HIV-1 TAR hairpin. This triple is supported by covariation of loop residue 31 with residue 22, which is part of an unusual base pair with U40 below the 3-nucleotide bulge. A set of mutants was constructed to test the involvement of bases A22, U31, and U40 in a triple interaction. RNA structure probing, trans-activation assays, and structure modeling are consistent with the existence of this base triple in a bent conformation of the free TAR element. However, disruption of the base triple does not affect binding of a Tat-derived peptide. We therefore compared the structure of free and Tat-bound TAR RNA by footprinting and site-specific cross-linking analyses. These studies indicate that the Tat arginine-rich motif, in addition to its known binding site at the bulge, is in close contact with U31 in the TAR loop. Because binding of Tat to TAR is known to coincide with the formation of a base triple with residues U23, A27, and U38, we hypothesize that Tat binding and the associated straightening of TAR triggers the disruption of the (A22-U40)U31 triple.

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Section: Comparative Sequence Analysis Suggests the Existence Of A Bamentioning

confidence: 69%

Evidence for a base triple in the free HIV-1 TAR RNA

Huthoff

Girard²,

Wijmenga³

et al. 2004

RNA

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“…Considering the stringency of picornavirus packaging, if the recombinant RNA, in three-dimensional structure, is too voluminous to be encased in the rigid capsid, packaging pressure may cause a deletion of the nonessential foreign insert. The three-dimensional conformation of the insert RNA is associated, at least in part, with the number of hydrogen bonds in canonically base-paired regions and sequence-dependent free energy (4,6,15,31). Based on this rationale, we have studied the correlation between genetic stability and the G/C contents of each insert and found that most of the stable inserts showed a high G/C content of over 40% (Table 1 and Fig.…”

Section: Vol 76 2002 Design Architecture For Genetic Stability Of Rmentioning

confidence: 99%

Novel Design Architecture for Genetic Stability of Recombinant Poliovirus: the Manipulation of G/C Contents and Their Distribution Patterns Increases the Genetic Stability of Inserts in a Poliovirus-Based RPS-Vax Vector System

Lee

Kim

Hyun

et al. 2002

J Virol

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Poliovirus has been studied as a live recombinant vaccine vector because of its attractive characteristics. The genetic instability, however, has hampered recombinant polioviruses (PVs) from being developed as an appropriate vaccine. A variety of different foreign inserts were cloned directly into our poliovirus Sabin 1-based RPS-Vax vector system, resulting in the production of recombinant PVs. The genetic stability of each recombinant PV was examined during 12 rounds of consecutive passage. It was found that the genetic stability of the recombinants was not well correlated with their insert size. Instead, elevated stability was frequently observed in recombinants with inserts of high G/C contents. Furthermore, a comparative study using different constructs of the human immunodeficiency virus env gene revealed that the internal deletion of the unstable insert was seemingly caused by the presence of the adjacent A/T-rich region. The instability of these inserts was completely remedied by (i) increasing the G/C contents and (ii) replacing the local A/T-rich region with the G/C-rich codon without a change of the amino acid. This means that stability is closely associated with the G/C content and the G/C distribution pattern. To see whether these findings can be applied to the design of genetically stable recombinant PV, we have reconstructed the heteromultimeric insert based on our design architecture, including the above-mentioned G/C rules and the template/ligation-free PCR protocol. The heteromultimeric insert was very unstable, as expected, but the manipulated insert with the same amino acid sequence showed complete genetic stability, not only in vitro, but also in vivo. Even though this guideline was established with our RPS-Vax vector system, to some extent, it can also be applied to other live viral vaccine vectors.Many attempts have been made to manipulate poliovirus (PV) as a favorable vaccine vector because of its attractive characteristics of safe use, low cost, convenient administration, and long-lasting protective immunity in both mucosal and systemic immune responses, which have been established for decades. Four different strategies have been employed to date in the development of PV-based versatile vaccine vectors. Early efforts were devoted to attaching small epitopes to one of the neutralizing domains in the capsid protein (9, 10, 14, 17, 36). However, widespread application of this hybrid virion strategy was limited by the size of the epitope (smaller than 25 amino acids) that could be inserted. The second strategy was to replace one of the structural viral genes with the protein insert (8,9,12,30,34,35). Using this method, desired foreign antigens could be incorporated without size restriction; however, the recombinant virus is replication defective and requires a helper virus or capsid protein-expressing system for each cycle of propagation (12,30,34,35). The propagation-defective viral vector is attractive for its safety feature, even in the neuronal delivery of cytokine (8), but may also pos...

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“…In A. pleuropneumoniae , C. beijerinckii , H. influenzae , L. lactis ssp. cremoris , and T. auensis , the abnormally high diversity among their 5S rRNA genes with significant alterations of secondary structures suggested diminished ribosomal constraints in some individual rRNA genes, or constraints in higher order structures (Gutell et al ., ; Woese & Gutell, ; Babin et al ., ). Alternatively, the apparent violation of ribosomal constraints in 5S rRNA genes in these species may be explained by physiological requirement of different types of 5S rRNA genes by these prokaryotic organisms, similar to the above‐mentioned eukaryotes.…”

Section: Discussionmentioning

confidence: 97%

Diversity of 5S rRNA genes within individual prokaryotic genomes

Pei

Oberdorf

et al. 2012

FEMS Microbiol Lett

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We examined intragenomic variation of paralogous 5S rRNA genes to evaluate the concept of ribosomal constraints. In a dataset containing 1161 genomes from 779 unique species, 96 species exhibited > 3% diversity. Twenty‐seven species with > 10% diversity contained a total of 421 mismatches between all pairs of the most dissimilar copies of 5S rRNA genes. The large majority (401 of 421) of the diversified positions were conserved at the secondary structure level. The high diversity was associated with partial rRNA operon, split operon, or spacer length–related divergence. In total, these findings indicated that there are tight ribosomal constraints on paralogous 5S rRNA genes in a genome despite of the high degree of diversity at the primary structure level.

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Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling

Cited by 7 publications

References 33 publications

Evidence for a base triple in the free HIV-1 TAR RNA

Evidence for a base triple in the free HIV-1 TAR RNA

Novel Design Architecture for Genetic Stability of Recombinant Poliovirus: the Manipulation of G/C Contents and Their Distribution Patterns Increases the Genetic Stability of Inserts in a Poliovirus-Based RPS-Vax Vector System

Diversity of 5S rRNA genes within individual prokaryotic genomes

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