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Parallel relaxation of stringent RNA recognition in plant and mammalian L1 retrotransposons.

Ohshima K - Mol. Biol. Evol. (2012)

Bottom Line: L1 elements are mammalian non-long terminal repeat retrotransposons, or long interspersed elements (LINEs), that significantly influence the dynamics and fluidity of the genome.This strongly suggests that plant LINEs require a particular 3'-end sequence during initiation of reverse transcription.As one L1-clade LINE was also found to share the 3'-end sequence with a SINE in a green algal genome, I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized the specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution.

View Article: PubMed Central - PubMed

ABSTRACT
L1 elements are mammalian non-long terminal repeat retrotransposons, or long interspersed elements (LINEs), that significantly influence the dynamics and fluidity of the genome. A series of observations suggest that plant L1-clade LINEs, just as mammalian L1s, mobilize both short interspersed elements (SINEs) and certain messenger RNA by recognizing the 3'-poly(A) tail of RNA. However, one L1 lineage in monocots was shown to possess a conserved 3'-end sequence with a solid RNA structure also observed in maize and sorghum SINEs. This strongly suggests that plant LINEs require a particular 3'-end sequence during initiation of reverse transcription. As one L1-clade LINE was also found to share the 3'-end sequence with a SINE in a green algal genome, I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized the specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution.

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The number of LINE families belonging to each LINE clade according to biological taxa. LINE clades in which the partner LINE of a SINE was identified are shown. Remaining clades are grouped as “Others” (Repbase 16.10). “other vertebrates”: nonmammalian vertebrates; “land plants”: mostly flowering plants.
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mss147-F1: The number of LINE families belonging to each LINE clade according to biological taxa. LINE clades in which the partner LINE of a SINE was identified are shown. Remaining clades are grouped as “Others” (Repbase 16.10). “other vertebrates”: nonmammalian vertebrates; “land plants”: mostly flowering plants.

Mentions: Figure 1 shows the number of LINEs belonging to each LINE clade according to biological taxa (supplementary table S2, Supplementary Material online). The genomes of land plants (mainly flowering plants) exclusively harbor only L1-clade LINEs (RTE-clade LINEs are also found in several species). Moreover, although a significant number of SINEs, more than half of which end in poly(A) repeats, have been identified in the genomes of flowering plants (supplementary table S3, Supplementary Material online), only three SINE/LINE pairs have been discovered: namely, maize ZmSINE2 and ZmSINE3 (LINE1-1_ZM; Baucom et al. 2009) and tobacco TS SINE (RTE-1_STu; this study; supplementary fig. S3, Supplementary Material online). Interestingly, many processed pseudogenes have been reported in flowering plants (Faris et al. 2001; Zhang et al. 2005; Benovoy and Drouin 2006; Nurhayati et al. 2009). As mammalian L1s are thought to recognize the 3′-poly(A) tail of RNA when forming processed pseudogenes (Esnault et al. 2000), it is possible that plant LINE machinery is similar to mammalian L1s (Lenoir et al. 2001). That is, by presumably recognizing the 3′-poly(A) tail of RNA, plant L1-clade LINEs thereby mobilize SINEs with a poly(A) tail and mRNA. In accordance with this hypothesis, almost all L1-clade LINEs in flowering plants were shown to end in poly(A) repeats and all RTE-clade LINEs in (TTG)n or (TTGATG)n (table 1). Poly(T)-ending SINEs: p-SINEs and Au-like SINEs (supplementary table S3, Supplementary Material online) would be mobilized by the LINE machinery that recognize a poly(U) repeat of RNA at the 3′-terminus, although such LINE has never been reported in plants.Fig. 1.


Parallel relaxation of stringent RNA recognition in plant and mammalian L1 retrotransposons.

Ohshima K - Mol. Biol. Evol. (2012)

The number of LINE families belonging to each LINE clade according to biological taxa. LINE clades in which the partner LINE of a SINE was identified are shown. Remaining clades are grouped as “Others” (Repbase 16.10). “other vertebrates”: nonmammalian vertebrates; “land plants”: mostly flowering plants.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472496&req=5

mss147-F1: The number of LINE families belonging to each LINE clade according to biological taxa. LINE clades in which the partner LINE of a SINE was identified are shown. Remaining clades are grouped as “Others” (Repbase 16.10). “other vertebrates”: nonmammalian vertebrates; “land plants”: mostly flowering plants.
Mentions: Figure 1 shows the number of LINEs belonging to each LINE clade according to biological taxa (supplementary table S2, Supplementary Material online). The genomes of land plants (mainly flowering plants) exclusively harbor only L1-clade LINEs (RTE-clade LINEs are also found in several species). Moreover, although a significant number of SINEs, more than half of which end in poly(A) repeats, have been identified in the genomes of flowering plants (supplementary table S3, Supplementary Material online), only three SINE/LINE pairs have been discovered: namely, maize ZmSINE2 and ZmSINE3 (LINE1-1_ZM; Baucom et al. 2009) and tobacco TS SINE (RTE-1_STu; this study; supplementary fig. S3, Supplementary Material online). Interestingly, many processed pseudogenes have been reported in flowering plants (Faris et al. 2001; Zhang et al. 2005; Benovoy and Drouin 2006; Nurhayati et al. 2009). As mammalian L1s are thought to recognize the 3′-poly(A) tail of RNA when forming processed pseudogenes (Esnault et al. 2000), it is possible that plant LINE machinery is similar to mammalian L1s (Lenoir et al. 2001). That is, by presumably recognizing the 3′-poly(A) tail of RNA, plant L1-clade LINEs thereby mobilize SINEs with a poly(A) tail and mRNA. In accordance with this hypothesis, almost all L1-clade LINEs in flowering plants were shown to end in poly(A) repeats and all RTE-clade LINEs in (TTG)n or (TTGATG)n (table 1). Poly(T)-ending SINEs: p-SINEs and Au-like SINEs (supplementary table S3, Supplementary Material online) would be mobilized by the LINE machinery that recognize a poly(U) repeat of RNA at the 3′-terminus, although such LINE has never been reported in plants.Fig. 1.

Bottom Line: L1 elements are mammalian non-long terminal repeat retrotransposons, or long interspersed elements (LINEs), that significantly influence the dynamics and fluidity of the genome.This strongly suggests that plant LINEs require a particular 3'-end sequence during initiation of reverse transcription.As one L1-clade LINE was also found to share the 3'-end sequence with a SINE in a green algal genome, I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized the specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution.

View Article: PubMed Central - PubMed

ABSTRACT
L1 elements are mammalian non-long terminal repeat retrotransposons, or long interspersed elements (LINEs), that significantly influence the dynamics and fluidity of the genome. A series of observations suggest that plant L1-clade LINEs, just as mammalian L1s, mobilize both short interspersed elements (SINEs) and certain messenger RNA by recognizing the 3'-poly(A) tail of RNA. However, one L1 lineage in monocots was shown to possess a conserved 3'-end sequence with a solid RNA structure also observed in maize and sorghum SINEs. This strongly suggests that plant LINEs require a particular 3'-end sequence during initiation of reverse transcription. As one L1-clade LINE was also found to share the 3'-end sequence with a SINE in a green algal genome, I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized the specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution.

Show MeSH
Related in: MedlinePlus