Structural and Functional Diversity of Plant Virus 3′-Cap-Independent Translation Enhancers (3′-CITEs)

FIGURE 1. RNA secondary structures of BTEs, which are 3′-CITEs that interact with eIF4F through its eIF4G subunit. Assayed RNA secondary structures of representative BTEs of BYDV, TNV-D, and RCNMV, based on data derived from Wang et al. (2010). The conserved BTE-specific 17 nt are indicted with arrows (start/end). Bases protected by eIF4G, apart from the 17 nt stretch, are encircled (Kraft et al., 2013). Sequences proved or proposed to be involved in 5′–3′ interaction through sequence complementarity are shown for BYDV and TNV-D BTEs.

FIGURE 2. RNA secondary structures of TED, PTE, ISS, and YSS, which are 3′-CITEs shown or proposed to interact with eIF4F through its eIF4E subunit. (A) Assayed (PLPV) and predicted (STNV) TED structures, based on data derived from Blanco-Pérez et al. (2016). (B) Assayed PTE structures of SCV, based on data derived from Chattopadhyay et al. (2011) and of PEMV and predicted PTE structure for PMV, based on data derived from Wang et al. (2009). The pseudoknot (ψ) between C- and G-domain is indicated with a dashed line. (C) Assayed (MNSV and MNeSV) and predicted (MWLMV and MNSV-264) ISS (Nicholson et al., 2010; Miras et al., 2017b). (D) Predicted YSS of TBSV, as proposed by Fabian and White (2006) and CIRV, as proposed by Nicholson et al. (2013). (E) Assayed structures of eIF4E sensitivity elements (4E-SE) of Histone H4, based on data derived from Martin et al. (2011) and Cyclin D mRNAs, based on data derived from Culjkovic et al. (2006). Dashes point to conserved residues shown or predicted to be involved in eIF4E binding. The sequences proposed or shown to be involved in 5′–3′- interaction through sequence complementarity are shown. In the case of MNeSV the 5′–3′-interaction was proved with…

FIGURE 3. RNA secondary structures of T-shaped 3′-CITEs and CXTE. (A) Assayed two- (McCormack et al., 2008) and three-dimensional structure Zuo et al. (2010) of the TCV TSS, based on data derived from McCormack and Zuo and collegues, respectively. Pseudoknots (ψ2 and ψ3) are indicated with a dashed line. Hairpins are H4a/b and H5. Additional nucleotides present in the extended TSS model appear in red (Le et al., 2017). (B) Assayed RNA secondary structures of the two PEMV2 TSS, kl-TSS (Gao et al., 2012, 2013) and TSS (Gao et al., 2014), based on data derived from Gao and colleagues. 5′-end sequence interacting by sequence complementarity with the kl-TSS and with kl-H is shown. (C) Assayed RNA secondary structure of CXTE, the newest 3′-CITE, based on our data derived from Miras et al. (2014).

FIGURE 4. Conservation of unpaired 3′-CITE residues suggested to be involved in eIF4E binding. (A) Residues of the first bulge present downstream of the final stem-loop of ISS, PTE, TED, and YSS CITEs and of the histone H4 and cyclin D1 4E-sensitivity elements. (B) Residues of the second bulge present upstream of the final stem-loop of these 3′-CITEs. Conserved adenosine [in (A), similar to A32 of MNSV ISS] and guanosine residues [similar in (A) to G47 of MNeSV ISS and in (B) to G13 of MNeSV ISS and the highly reactive G17 residue from the G-domain of PTE] are framed. (C) 3D structural alignment [Rclick server (Nguyen et al., 2017)] of the left arm of the YSS of CIRV and TBSV (colored in yellow and green, respectively) with the ISS of MNeSV (red colored), based on the predicted tertiary structures [RNAComposer server (Popenda et al., 2012)]. YSS of CIRV and TBSV and ISS of MNeSV are based on data derived from Nicholson et al. (2010, 2013), respectively. Below, alignment of sequence stretch of both structures aligning in the 3D prediction (Rclick server). Identity of residues is emphasized in bold. Adenosine and guanosine residues predicted to be important for eIF4E binding are shown in…

FIGURE 5. New 3′-CITEs acquired by MNSV isolates through recombination. (A) Sequence alignment of the 5′-end of the 3′-UTR of MNSV isolates. GenBank accession numbers of MNSV sequences included in the alignment are Ma5-AY122286, HM-GU480022.1, Chiba-AB250684, Yamaguchi-AB250687, Nagasaki-AB250686, Al-DQ339157, Dutch-NC001504, ISR (Israel)-DQ922807, Kochi-AB250685, Kouchi-AB189943, Ma24-EU589616, Ma71-EU589619, Pa58-EU589620, Pa57-EU589621, 17A/01A-M29671, ABCA13-01-KR094068, USA-2016-KY124137, N- KF060715, GX-KY264755. The inserted sequence is marked in gray. Asterisks mark conserved nucleotides of all sequences or in gray of the insertions. (B) Proposed recombination event generated by the RDP4 software, a computer program for characterizing recombination events in sequence alignments using several different recombination analysis methods and tests for recombination hot-spots. The sequences included in this analysis are the 3′-UTRs of MNSV [see part (A) of this figure] and CABYV isolates [GenBank accession numbers are CABYV-Xinjiang: EU636992; CABYV-Beijing: EU000535; CABYV esp (JF939814), CABYV-N (NC_003688), CABYV-K1 (LC082306), CABYV-FJ: GQ221223; CABYV-JAN: GQ221224; CABYV-R_TW82:…