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

Kanai A - Life (Basel) (2015)

Bottom Line: In this sense, tRNAs are key molecules that connect the RNA world and the protein world.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.

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.


Related in: MedlinePlus

tRNA-derived fragments (tRFs). (A) Mature tRNA-derived fragments (shown in blue). The arrowheads indicate the possible cleavage sites by endoribonucleases. (B) Pre-tRNA-derived fragments (shown in blue). Enzymes required for pre-tRNA processing are shown with each arrowhead.
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life-05-00321-f003: tRNA-derived fragments (tRFs). (A) Mature tRNA-derived fragments (shown in blue). The arrowheads indicate the possible cleavage sites by endoribonucleases. (B) Pre-tRNA-derived fragments (shown in blue). Enzymes required for pre-tRNA processing are shown with each arrowhead.

Mentions: In the first decade of the 21st century, small non-coding RNAs, such as microRNA (miRNA) and small interfering RNA (siRNA), were recognized as major factors in gene regulation. A recent analysis of transcriptomes in all three domains of life has suggested that tRNA-derived fragments (tRFs) constitute a novel class of small regulatory RNAs. As reviewed by Raina and Ibba [21], there are many examples of tRFs (Figure 3A). In the initial stage of this research, the greatest concern was that these tRFs might simply be the degradation products of mature tRNAs. However, at least some of the tRFs appear to be biologically functional, based on the following observations: (i) in many cases, tRFs do not derive from abundant cellular tRNAs, and the numbers of tRFs do not correlate with the parental tRNA gene copy numbers; (ii) their fragmentation patterns are depended on their anticodons; (iii) the fragmentation patterns can change according to the developmental stage or cell conditions; and (iv) it is reported that some tRFs are bound to Argonaute/Piwi proteins, well-known components of the RNA-induced silencing complex [21,22].


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

Kanai A - Life (Basel) (2015)

tRNA-derived fragments (tRFs). (A) Mature tRNA-derived fragments (shown in blue). The arrowheads indicate the possible cleavage sites by endoribonucleases. (B) Pre-tRNA-derived fragments (shown in blue). Enzymes required for pre-tRNA processing are shown with each arrowhead.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00321-f003: tRNA-derived fragments (tRFs). (A) Mature tRNA-derived fragments (shown in blue). The arrowheads indicate the possible cleavage sites by endoribonucleases. (B) Pre-tRNA-derived fragments (shown in blue). Enzymes required for pre-tRNA processing are shown with each arrowhead.
Mentions: In the first decade of the 21st century, small non-coding RNAs, such as microRNA (miRNA) and small interfering RNA (siRNA), were recognized as major factors in gene regulation. A recent analysis of transcriptomes in all three domains of life has suggested that tRNA-derived fragments (tRFs) constitute a novel class of small regulatory RNAs. As reviewed by Raina and Ibba [21], there are many examples of tRFs (Figure 3A). In the initial stage of this research, the greatest concern was that these tRFs might simply be the degradation products of mature tRNAs. However, at least some of the tRFs appear to be biologically functional, based on the following observations: (i) in many cases, tRFs do not derive from abundant cellular tRNAs, and the numbers of tRFs do not correlate with the parental tRNA gene copy numbers; (ii) their fragmentation patterns are depended on their anticodons; (iii) the fragmentation patterns can change according to the developmental stage or cell conditions; and (iv) it is reported that some tRFs are bound to Argonaute/Piwi proteins, well-known components of the RNA-induced silencing complex [21,22].

Bottom Line: In this sense, tRNAs are key molecules that connect the RNA world and the protein world.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.

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.


Related in: MedlinePlus