Lateral DNA Transfer MECHANISMS AND CONSEQUENCES Frederic Bushman

Transcription

1 Lateral DN ransfer MECHNISMS ND CONSEQUENCES y1 mrn Intron ranscription gag pol Integrated y1 DN Yeast cell Excised intron Reverse RN splicing transcription Integration C Old copy of y1 New copy lacking intron Lateral DN ransfer: Mechanisms and Consequences FIGURE 8.1. he experiment establishing that y1 elements in yeast replicate by retrotransposition. () n integrated y1 DN element acts as a transcriptional template directing production of y1 RN. he artificial y1 element studied contained an engineered artificial intron. () he y1 RN is spliced to remove the engineered intron, then the RN is reverse-transcribed and integrated. (C) fter a cycle of retrotransposition, the newly formed y1 element is identical to the parental copy but lacks the engineered intron. his establishes that replication must have gone through an RN intermediate. (dapted from oeke et al [4]) COLD SPRING HROR LORORY PRESS

2 Lateral DN ransfer MECHNISMS ND CONSEQUENCES y1-copia LR PS GG R-RNaseH PR IN ppt LR DN y3-gypsy LR PS GG R-RNaseH C NC PR IN ppt LR RN DN Lateral DN ransfer: Mechanisms and Consequences RN FIGURE 8.2. Genetic structure of the two main families of LR retrotransposons. Some members of the y3/gypsy class contain in addition an env gene between IN and the PP, and can replicate as retroviruses. (dapted from ennetzen and Kumar 1999.[1]) COLD SPRING HROR LORORY PRESS

3 Lateral DN ransfer MECHNISMS ND CONSEQUENCES +/+ /+ +/+ +/+ / / Lateral DN ransfer: Mechanisms and Consequences FIGURE 8.3. Distribution of the copia transposon in populations of D. willistoni from the Caribbean region. he +/+ designation indicates that copia was found (or not in / ) in each of two different assays. (Redrawn, with permission, from Jordan et al [ National cademy of Sciences].[30]) COLD SPRING HROR LORORY PRESS

4 Lateral DN ransfer MECHNISMS ND CONSEQUENCES LINE element UR Orf1 Orf2 UR EN R-RNaseH () 5 11 Variable length repeat of target Variable length repeat of target typical SINE Pol lll Pol lll () 5 11 Variable length repeat of target Lateral DN ransfer: Mechanisms and Consequences Variable length repeat of target FIGURE 8.4. LINEs and SINEs. LINEs are typically several kilobases long; SINEs comprise only a few hundred base pairs. (dapted from ennetzen and Kumar 1999.[1]) COLD SPRING HROR LORORY PRESS

5 Lateral DN ransfer MECHNISMS ND CONSEQUENCES LINE RN LINE-encoded proteins arget DN arget site cleavage, RN DN hybrid formation LINE cdn Synthesis of first cdn strand LINE RN C Second strand synthesis DN joining and repair D Lateral DN ransfer: Mechanisms and Consequences FIGURE 8.5. arget-primed reverse transcription mediating LINE element replication. () complex containing the LINE element RN (dark green) and LINE proteins (light gray) binds to a chromosomal DN site rich in / base pairs (gray). () he LINE En protein cleaves the target DN site, and LINE RN becomes annealed to the target site DN. (C) he 3 end of the target site DN acts as a primer for reverse transcription of the LINE RN. (D) he second strand of DN is synthesized, LINE RN is removed, and the 5 end of the LINE DN becomes joined to host cell DN (by unknown mechanisms), yielding the integrated LINE copy. (dapted from Luan et al [41]) COLD SPRING HROR LORORY PRESS

6 Lateral DN ransfer MECHNISMS ND CONSEQUENCES Exon Group II intron Exon Pr Z R X Zn Protease domain Conserved R domain of non-lr family Reverse transcriptase RN binding important for maturase? Zn fingerlike domain Intron group II II I I I I I I I II COX 1 gene Lateral DN ransfer: Mechanisms and Consequences FIGURE 8.6. Self-splicing introns in the COX1 gene of S. cerevisiae mitochondria. n intact Group II mobile intron is shown at the top (green), exons are shown with the horizontal hatching. Proteins encoded by the element are indicated. he COX1 gene contains fully 10 introns, three Group II introns and 7 Group I introns. (dapted from Lambowitz et al [38]) COLD SPRING HROR LORORY PRESS

7 Lateral DN ransfer MECHNISMS ND CONSEQUENCES Intron 2'OH Exon Exon 3'OH C + 3'OH Lateral DN ransfer: Mechanisms and Consequences FIGURE 8.7. he self-splicing reaction of Group II introns. () he reaction begins when a 2 hydroxyl of an internal RN nucleotide attacks the 5 intron exon junction, resulting in the formation of a lariat intermediate (). he free exon 3 end then attacks the 3 intron exon boundary. second exchange (transesterification) reaction joins the two exons and frees the lariat RN. (dapted from Lambowitz et al [38]) COLD SPRING HROR LORORY PRESS

8 Lateral DN ransfer MECHNISMS ND CONSEQUENCES Lariat RN Intron-encoded proteins 3' OH + Insertion of lariat RN by reverse splicing Cleavage of target DN arget DN C +10 Revenge transcription, repair/ligation New mobile intron DN D +10 Lateral DN ransfer: Mechanisms and Consequences FIGURE 8.8. Insertion of a mobile Group II intron by reverse splicing. () he excised lariat RN remains bound to element-encoded proteins. () Reversal of the steps in splicing (attack of the RN 3 end on DN, thereby joining the RN to DN) attaches the mobile intron into one DN strand. (C) Cleavage of the other DN strand, followed by polymerization along one DN strand, then removal of the RN and repair DN synthesis, yields the fully integrated DN copy of the mobile intron (D). (dapted from Lambowitz et al ([8]) COLD SPRING HROR LORORY PRESS

9 Lateral DN ransfer MECHNISMS ND CONSEQUENCES Group 1 intron self-splicing Intron RN Exon RN G Exon RN OH G OH G C Lateral DN ransfer: Mechanisms and Consequences FIGURE 8.9. Self-splicing by Group I introns. Splicing begins () by binding of a G residue to an RN site within the intron. he 3 OH of the G residue then attacks the 5 intron exon junction. s result, the G residue becomes attached to the intron 5 end (). he free 3 end of the exon then attacks the 3 intron exon junction (C), joining the two exons and releasing the intron RN. (dapted from Lambowitz et al [38]) COLD SPRING HROR LORORY PRESS

10 Lateral DN ransfer MECHNISMS ND CONSEQUENCES Gene (with mobile intron) 1 Intron RN + arget mrn (gene ) Reverse splice into cellular mrn 1 Gene (lacking mobile intron) 2 Cleavage of Gene by intron-encoded nuclease 3 Reverse transcription DN copy 2 Incorporate into genome by recombination 4 Chromosomal copy of gene Repair using information in intron-containing allele 5 3 oth copies of Gene have intron Lateral DN ransfer: Mechanisms and Consequences FIGURE Pathways for incorporation of mobile introns into cellular DN involving homologous DN recombination. () free mobile intron (1) becomes incorporated into a cellular mrn by an exact reversal of normal self-splicing. his intermediate is either a lariat RN (Group II introns) or the linear intron with the 5 terminal G (Group I) (2). Reverse transcription of this sequence (3) yields a DN copy (shown here as singlestranded, but involvement of double-stranded DN is not ruled out). Recombination of the reverse transcript with the chromosomal gene copy (4) can install a DN copy of the intron sequence into the cellular gene (5). () DN-mediated pathway for movement of Group I mobile introns. his pathway operates in cases where one sister chromosome contains a copy of the intron and the other does not (homing) (1). n intron-encoded nuclease cleaves the copy of gene that lacks the intron (2). Repair of the lesion by homologous recombination using the other allele of gene as template installs the intron in the sister copy of gene (3). (dapted from Lambowitz et al [38]) COLD SPRING HROR LORORY PRESS