FIGURE 1 | Structural plasticity of group II introns and its functional and evolutionary implications. (A) Outline of the secondary structure of a typical mitochondrial subgroup IIB1 intron. Only highly conserved intron nucleotides that are discussed in the manuscript are noted. Tertiary base-pairing interactions between the intron and its fl anking exonsaredesignated as(EBS-IBS) 1,2, 2aand 3pairings (see text).Long-rangeinteractionsinvolving intron sequences aredesignatedbygreekletters. The 5 ′ and3 ′ splicejunctionsareindicatedasblacksquares.ThecurveddoublearrowillustratestogglingofdomainVIoccurringbetweenthetwostepsofsplicing.The RNAtertiaryinteractionsinvolvedinthismovementare: ι - ι ′ ,whichisspeci fi ctothe fi rst(branching)step,and η - η ′ and π - π ′ ,whicharespeci fi ctothesecond(exonligation) step. In addition, the intron-encoded RT also helps position domain VI for the branching reaction. The dashed-line arrows fl anking the middle section of domain VI illustrate the strand shifting mechanism responsible for the alternate branchpoint-bulge conformations discussed in the text (only the 1-nt branchpoint conformation is depicted). The intron segment ( “ spacer ” ) from the branchpoint adenosine (bpA) to the 3 ’ splice site (3 ’ ss), which is 7-nt long in these introns, is highlighted in green. The greendashedlinesmarkedwitha+symbolthatemergefromthisspacerillustratetheconservedinsertionsthatcanbefoundinthisregioninsomeintrons,asdiscussed in the text. The reverse transcriptase ORF is always inserted in domain IV. (B) Diagram of the RNA-DNA interactions between IIB1 or IIB2 introns and their target sites highlightingthecrucialroleofthenovelEBS2a-IBS2abase-pairinunwindingtheDNAtargetduplex.Thecolorsofthestructuralelementsrepresentedareconsistentwith the coloring of the secondary structure in (A) . Formation of EBS2a-IBS2a induces a “ loop ” around the EBS2-IBS2 pairing that should stabilize this small helix thus preventingre-associationofthetwoDNAstrands ofthetarget. (C) Structuralhomology betweenthecatalytic coreofgroupIIintronsand theU2/U5/U6snRNA catalytic ( Continued