Figure 1

HDV-like ribozymes in trypanosomatid mobile elements. The structure of L1Tc/ingi clade mobile elements is shown in (A). The wide white boxes indicate ORFs or degenerated ORFs (mutations are represented as crosses inside white boxes). The narrow white boxes located at the 5'-ends of all elements indicate the common and conserved Pr77-hallmark and the percentage similarity at the nucleotide level. Dotted lines mark out the conserved regions in long and short elements. LINEs (Long Interspersed Nucleotide Elements) such as L1Tc and ingi and the DIRE or L1Tc/ingi degenerated versions, are indicated at the top of panel A. NARTc and RIME are truncated versions of L1Tc and ingi elements and are shown at the bottom of panel A; these elements are also known as SIDE (Short Internally Deleted Elements) and short interspersed degenerate elements bearing one (SIDER1) or two (SIDER2) Pr77-hallmarks, referred as signature I and II, The proposed folding for L1TcRz [25], the HDV-like ribozyme previously described in L1Tc from Trypanosoma cruzi, is shown in (B). The arrow indicates the cleavage point and relevant structural helixes (P1, P2 and P4) and pseudoknots (P1.1 and P3). The switch from L1TcRz to a three-helix structure proposed for after L1Tc downstream region transcription [25] is shown in (C). The white boxes in C, indicate the structural components of the HDV-like ribozyme helixes. The black lines indicate single stranded regions. The grey lines indicate the attenuator downstream region.