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Disrupted tRNA Genes and tRNA Fragments: A Perspective on tRNA Gene Evolution.

Kanai A - Life (Basel) (2015)

Bottom Line: Even tRNA molecules themselves are fragmented post-transcriptionally in many species.These fragmented small RNAs are known as tRNA-derived fragments (tRFs).In this review, I summarize the progress of research into the disrupted tRNA genes and the tRFs, and propose a possible model for the molecular evolution of tRNAs based on the concept of the combination of fragmented tRNA halves.

View Article: PubMed Central - PubMed

Affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan. akio@sfc.keio.ac.jp.

ABSTRACT
Transfer RNAs (tRNAs) are small non-coding RNAs with lengths of approximately 70-100 nt. They are directly involved in protein synthesis by carrying amino acids to the ribosome. In this sense, tRNAs are key molecules that connect the RNA world and the protein world. Thus, study of the evolution of tRNA molecules may reveal the processes that led to the establishment of the central dogma: genetic information flows from DNA to RNA to protein. Thanks to the development of DNA sequencers in this century, we have determined a huge number of nucleotide sequences from complete genomes as well as from transcriptomes in many species. Recent analyses of these large data sets have shown that particular tRNA genes, especially in Archaea, are disrupted in unique ways: some tRNA genes contain multiple introns and some are split genes. Even tRNA molecules themselves are fragmented post-transcriptionally in many species. These fragmented small RNAs are known as tRNA-derived fragments (tRFs). In this review, I summarize the progress of research into the disrupted tRNA genes and the tRFs, and propose a possible model for the molecular evolution of tRNAs based on the concept of the combination of fragmented tRNA halves.

No MeSH data available.


Models for the molecular evolution of tRNA. (A) Model of the origin of the tRNA molecule proposed by Di Giulio [34]. Anti, anticodon; ID, the region defining the identity of the tRNA. (B) Model of the early evolution of tRNA molecules inspired by the analysis of split tRNAs. See text for details.
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life-05-00321-f004: Models for the molecular evolution of tRNA. (A) Model of the origin of the tRNA molecule proposed by Di Giulio [34]. Anti, anticodon; ID, the region defining the identity of the tRNA. (B) Model of the early evolution of tRNA molecules inspired by the analysis of split tRNAs. See text for details.

Mentions: Di Giulio hypothesized that the ancestral tRNA was encoded by two separate minigenes, which later fused to encode the modern tRNAs (Figure 4A) [34]. In fact, there are reports that the complete cloverleaf structure of tRNA is not necessary for tRNA function. For example, (i) a mini-helix RNA was efficiently aminoacylated by Escherichia coli leucyl-tRNA synthetase [35] and (ii) a top-half tRNA mini-helix is a good substrate for the eubacterial CCA-adding enzyme [36]. It was also recently reported that a ribozyme of only 5 nt effectively generated aminoacyl-RNA (self-aminoacylation) [37]. However, it is also true that there are no such short functional tRNAs in the current species.


Disrupted tRNA Genes and tRNA Fragments: A Perspective on tRNA Gene Evolution.

Kanai A - Life (Basel) (2015)

Models for the molecular evolution of tRNA. (A) Model of the origin of the tRNA molecule proposed by Di Giulio [34]. Anti, anticodon; ID, the region defining the identity of the tRNA. (B) Model of the early evolution of tRNA molecules inspired by the analysis of split tRNAs. See text for details.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390854&req=5

life-05-00321-f004: Models for the molecular evolution of tRNA. (A) Model of the origin of the tRNA molecule proposed by Di Giulio [34]. Anti, anticodon; ID, the region defining the identity of the tRNA. (B) Model of the early evolution of tRNA molecules inspired by the analysis of split tRNAs. See text for details.
Mentions: Di Giulio hypothesized that the ancestral tRNA was encoded by two separate minigenes, which later fused to encode the modern tRNAs (Figure 4A) [34]. In fact, there are reports that the complete cloverleaf structure of tRNA is not necessary for tRNA function. For example, (i) a mini-helix RNA was efficiently aminoacylated by Escherichia coli leucyl-tRNA synthetase [35] and (ii) a top-half tRNA mini-helix is a good substrate for the eubacterial CCA-adding enzyme [36]. It was also recently reported that a ribozyme of only 5 nt effectively generated aminoacyl-RNA (self-aminoacylation) [37]. However, it is also true that there are no such short functional tRNAs in the current species.

Bottom Line: Even tRNA molecules themselves are fragmented post-transcriptionally in many species.These fragmented small RNAs are known as tRNA-derived fragments (tRFs).In this review, I summarize the progress of research into the disrupted tRNA genes and the tRFs, and propose a possible model for the molecular evolution of tRNAs based on the concept of the combination of fragmented tRNA halves.

View Article: PubMed Central - PubMed

Affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan. akio@sfc.keio.ac.jp.

ABSTRACT
Transfer RNAs (tRNAs) are small non-coding RNAs with lengths of approximately 70-100 nt. They are directly involved in protein synthesis by carrying amino acids to the ribosome. In this sense, tRNAs are key molecules that connect the RNA world and the protein world. Thus, study of the evolution of tRNA molecules may reveal the processes that led to the establishment of the central dogma: genetic information flows from DNA to RNA to protein. Thanks to the development of DNA sequencers in this century, we have determined a huge number of nucleotide sequences from complete genomes as well as from transcriptomes in many species. Recent analyses of these large data sets have shown that particular tRNA genes, especially in Archaea, are disrupted in unique ways: some tRNA genes contain multiple introns and some are split genes. Even tRNA molecules themselves are fragmented post-transcriptionally in many species. These fragmented small RNAs are known as tRNA-derived fragments (tRFs). In this review, I summarize the progress of research into the disrupted tRNA genes and the tRFs, and propose a possible model for the molecular evolution of tRNAs based on the concept of the combination of fragmented tRNA halves.

No MeSH data available.