Common evolutionary trends for SINE RNA structures

Sun, Feng; Fleurdépine, Sophie; Bousquet‐Antonelli, Cécile; Caetano‐Anollés, Gustavo; Deragon, Jean-Marc

doi:10.1016/j.tig.2006.11.005

Cited by 67 publications

(74 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Phylogenetic trees reconstructed using geometrical and statistical characters and derived from several functional RNA molecules were congruent and similarly rooted (78,93,94). Consequently, geometrical considerations in structure appeared intimately linked to molecular order, supporting both the evolutionary model and arguments of character polarization.…”

Section: Evolution Of Rna Structurementioning

confidence: 57%

“…Correlation between RNA folding and the occurrence of structural motifs in natural nucleic acids also supports tendencies towards order (86). Finally, tendencies towards order have been experimentally supported by phylogenetic congruence in the reconstruction of rooted trees generated from sequence, structure, and genomic rearrangements (see below) at different taxonomical levels (78,(87)(88)(89)(90)(91)(92)(93)(94). Note that order is seldom achieved in frustrated systems that are driven by the energetics of conformation and stability, such as RNA or proteins.…”

Section: Universal Tendencies Towards Molecular Ordermentioning

confidence: 94%

See 1 more Smart Citation

Origins and evolution of modern biochemistry: insights from genomes and molecular structure

et al. 2008

View full text Add to dashboard Cite

Section: Evolution Of Rna Structurementioning

confidence: 57%

Section: Universal Tendencies Towards Molecular Ordermentioning

confidence: 94%

Origins and evolution of modern biochemistry: insights from genomes and molecular structure

et al. 2008

View full text Add to dashboard Cite

“…Their copy number ranges from a few hundred to more than a million. Most eukaryotic SINEs are ancestrally derived from tRNA genes (and in rare cases from 7SL or 5S RNAs), although the typical tRNA cloverleaf structure is not apparent anymore for most SINE RNAs (Sun et al 2007). SINEs derived from tRNAs usually have a composite structure made of a 59 tRNArelated portion followed by a tRNA-unrelated portion (Okada and Ohshima 1995;Deragon and Zhang 2006).…”

Section: Resultsmentioning

confidence: 99%

“…With a few exceptions (Matsumoto et al 1986;Lin et al 2001), the majority of SINEs derived from tRNAs do not fold as their ancestral tRNA molecule and it was recently shown that most tRNA-related SINEs have very similar RNA structures (Rozhdestvensky et al 2001;Sun et al 2007). Remarkably, when the intron is spliced, SINEX-3_CR, SINEX-5_CR, and SINEX-6_CR tRNA-related sequences can be folded in the theoretical cloverleaf structure.…”

Section: Resultsmentioning

confidence: 99%

On the Evolution and Expression of Chlamydomonas reinhardtii Nucleus-Encoded Transfer RNA Genes

et al. 2008

Self Cite

View full text Add to dashboard Cite

In Chlamydomonas reinhardtii, 259 tRNA genes were identified and classified into 49 tRNA isoaccepting families. By constructing phylogenetic trees, we determined the evolutionary history for each tRNA gene family. The majority of the tRNA sequences are more closely related to their plant counterparts than to animals ones. Northern experiments also permitted us to show that at least one member of each tRNA isoacceptor family is transcribed and correctly processed in vivo. A short stretch of T residues known to be a signal for termination of polymerase III transcription was found downstream of most tRNA genes. It allowed us to propose that the vast majority of the tRNA genes are expressed and to confirm that numerous tRNA genes separated by short spacers are indeed cotranscribed. Interestingly, in silico analyses and hybridization experiments show that the cellular tRNA abundance is correlated with the number of tRNA genes and is adjusted to the codon usage to optimize translation efficiency. Finally, we studied the origin of SINEs, short interspersed elements related to tRNAs, whose presence in Chlamydomonas is exceptional. Phylogenetic analysis strongly suggests that tRNA Asp -related SINEs originate from a prokaryotic-type tRNA either horizontally transferred from a bacterium or originally present in mitochondria or chloroplasts.

show abstract

“…This assumes the accumulation of changes from the original structure. For instance, transcripts of simple tRNA-derived SINEs cannot form the clover leaf structure, and their nucleotides are not modified as in tRNAs (Rozhdestvensky et al, 2007;Sun et al, 2007). As a result of such changes, SINE transcripts lose the capacity to bind to at least some protein factors of tRNA processing or transport.…”

Section: Reverse Transcriptional Competencementioning

confidence: 99%