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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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Phylogenetic relationships among the L1-clade LINEs. LINE-clades are shown in bold italics. Several lineages in which a stringent or relaxed L1 was found are indicated by asterisks: (*1) LINE1-1_ZM (stringent), (*2) L1-1_CR (stringent), and (*3) L1HS (relaxed). The phylogenetic relationships among 146 LINEs were inferred using the amino acid sequences of ORF2 proteins from plant L1 entries in the database (Repbase 15.08; Viridiplantae) and from other LINEs (Ohshima and Okada 2005). A total of 404 positions made up the final data set. The linearized NJ consensus tree obtained from bootstrap analysis with 1,000 replications is shown (an ML consensus tree formed with the same data set is available as supplementary fig. S5, Supplementary Material online). The evolutionary distances were computed using the Jones-Taylor-Thornton (JTT) matrix-based method. For clarity, some clades were collapsed with filled triangles, the widths of which were in proportion to the number of LINEs. The full expanded tree is shown in supplementary figure S4, Supplementary Material online. Bootstrap values are only shown for nodes with scores > 45.
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mss147-F2: Phylogenetic relationships among the L1-clade LINEs. LINE-clades are shown in bold italics. Several lineages in which a stringent or relaxed L1 was found are indicated by asterisks: (*1) LINE1-1_ZM (stringent), (*2) L1-1_CR (stringent), and (*3) L1HS (relaxed). The phylogenetic relationships among 146 LINEs were inferred using the amino acid sequences of ORF2 proteins from plant L1 entries in the database (Repbase 15.08; Viridiplantae) and from other LINEs (Ohshima and Okada 2005). A total of 404 positions made up the final data set. The linearized NJ consensus tree obtained from bootstrap analysis with 1,000 replications is shown (an ML consensus tree formed with the same data set is available as supplementary fig. S5, Supplementary Material online). The evolutionary distances were computed using the Jones-Taylor-Thornton (JTT) matrix-based method. For clarity, some clades were collapsed with filled triangles, the widths of which were in proportion to the number of LINEs. The full expanded tree is shown in supplementary figure S4, Supplementary Material online. Bootstrap values are only shown for nodes with scores > 45.

Mentions: Figure 2 shows the results from comprehensive phylogenetic analysis of L1-clade LINEs (supplementary fig. S4 and supplementary table S4, Supplementary Material online). Three important points were revealed. First, L1-clade LINEs from distinct taxa, namely, land plants, green algae, and vertebrates, formed monophyletic groups. Statistical support for the monophyly of land plants and green algae was high, with bootstrap values of 100 and 97, respectively (82 and 83; maximum likelihood [ML] method; supplementary fig. S5, Supplementary Material online). Monophyly of the vertebrate F and M lineages (Ichiyanagi et al. 2007), however, was not supported by the ML method (supplementary fig. S5, Supplementary Material online). Second, the L1 lineages from these three taxa formed a monophyletic group (55/45; neighbor-joining [NJ]/ML methods) among diverged LINE clades such as RTE and CR1. The Tx1 LINE, with target-specific insertion, was also found in this clade, as observed in previous studies (Kojima and Fujiwara 2004; Ichiyanagi et al. 2007). The Tx1 and vertebrate F lineage formed a monophyletic group with high confidence (94/85). Third, comparison with the species phylogeny revealed that plant L1-clade LINEs consist of at least three deeply branching lineages that have descended from the common ancestor of monocots and eudicots (ME1-3; supplementary fig. S6, Supplementary Material online). These three lineages must have arisen more than 130 million years ago, around the approximate divergence of monocots and eudicots (Moore et al. 2007).Fig. 2.


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

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

Phylogenetic relationships among the L1-clade LINEs. LINE-clades are shown in bold italics. Several lineages in which a stringent or relaxed L1 was found are indicated by asterisks: (*1) LINE1-1_ZM (stringent), (*2) L1-1_CR (stringent), and (*3) L1HS (relaxed). The phylogenetic relationships among 146 LINEs were inferred using the amino acid sequences of ORF2 proteins from plant L1 entries in the database (Repbase 15.08; Viridiplantae) and from other LINEs (Ohshima and Okada 2005). A total of 404 positions made up the final data set. The linearized NJ consensus tree obtained from bootstrap analysis with 1,000 replications is shown (an ML consensus tree formed with the same data set is available as supplementary fig. S5, Supplementary Material online). The evolutionary distances were computed using the Jones-Taylor-Thornton (JTT) matrix-based method. For clarity, some clades were collapsed with filled triangles, the widths of which were in proportion to the number of LINEs. The full expanded tree is shown in supplementary figure S4, Supplementary Material online. Bootstrap values are only shown for nodes with scores > 45.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC3472496&req=5

mss147-F2: Phylogenetic relationships among the L1-clade LINEs. LINE-clades are shown in bold italics. Several lineages in which a stringent or relaxed L1 was found are indicated by asterisks: (*1) LINE1-1_ZM (stringent), (*2) L1-1_CR (stringent), and (*3) L1HS (relaxed). The phylogenetic relationships among 146 LINEs were inferred using the amino acid sequences of ORF2 proteins from plant L1 entries in the database (Repbase 15.08; Viridiplantae) and from other LINEs (Ohshima and Okada 2005). A total of 404 positions made up the final data set. The linearized NJ consensus tree obtained from bootstrap analysis with 1,000 replications is shown (an ML consensus tree formed with the same data set is available as supplementary fig. S5, Supplementary Material online). The evolutionary distances were computed using the Jones-Taylor-Thornton (JTT) matrix-based method. For clarity, some clades were collapsed with filled triangles, the widths of which were in proportion to the number of LINEs. The full expanded tree is shown in supplementary figure S4, Supplementary Material online. Bootstrap values are only shown for nodes with scores > 45.
Mentions: Figure 2 shows the results from comprehensive phylogenetic analysis of L1-clade LINEs (supplementary fig. S4 and supplementary table S4, Supplementary Material online). Three important points were revealed. First, L1-clade LINEs from distinct taxa, namely, land plants, green algae, and vertebrates, formed monophyletic groups. Statistical support for the monophyly of land plants and green algae was high, with bootstrap values of 100 and 97, respectively (82 and 83; maximum likelihood [ML] method; supplementary fig. S5, Supplementary Material online). Monophyly of the vertebrate F and M lineages (Ichiyanagi et al. 2007), however, was not supported by the ML method (supplementary fig. S5, Supplementary Material online). Second, the L1 lineages from these three taxa formed a monophyletic group (55/45; neighbor-joining [NJ]/ML methods) among diverged LINE clades such as RTE and CR1. The Tx1 LINE, with target-specific insertion, was also found in this clade, as observed in previous studies (Kojima and Fujiwara 2004; Ichiyanagi et al. 2007). The Tx1 and vertebrate F lineage formed a monophyletic group with high confidence (94/85). Third, comparison with the species phylogeny revealed that plant L1-clade LINEs consist of at least three deeply branching lineages that have descended from the common ancestor of monocots and eudicots (ME1-3; supplementary fig. S6, Supplementary Material online). These three lineages must have arisen more than 130 million years ago, around the approximate divergence of monocots and eudicots (Moore et al. 2007).Fig. 2.

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