Tertiary architecture of the<i>Oceanobacillus iheyensis</i>group II intron

Toor, Navtej; Keating, Kevin S.; Fedorova, Olga; Rajashankar, Kanagalaghatta R.; Wang, Jimin; Pyle, Anna Marie

doi:10.1261/rna.1844010

Cited by 74 publications

(94 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An evolutionary relationship between group II and spliceosomal introns is suggested by the similarities in their splicing 4 mechanisms, by structural and functional similarities between group II intron RNA domains and snRNAs, and by the ability of group II introns to be fragmented into functionally reassociating segments, suggesting an evolutionary origin for snRNAs (Sharp 1985(Sharp , 1991Cech 1986;Madhani and Guthrie 1992;Shukla and Padgett 2002;Toor et al 2010). …”

Section: Introductionmentioning

confidence: 99%

Genetic identification of potential RNA-binding regions in a group II intron-encoded reverse transcriptase

Gu¹,

Cui²,

Mou³

et al. 2010

RNA

View full text Add to dashboard Cite

Mobile group II introns encode a reverse transcriptase that binds the intron RNA to promote RNA splicing and intron mobility, the latter via reverse splicing of the excised intron into DNA sites, followed by reverse transcription. Previous work showed that the Lactococcus lactis Ll.LtrB intron reverse transcriptase, denoted LtrA protein, binds with high affinity to DIVa, a stem-loop structure at the beginning of the LtrA open reading frame and makes additional contacts with intron core regions that stabilize the active RNA structure for forward and reverse splicing. LtrA's binding to DIVa down-regulates its translation and is critical for initiation of reverse transcription. Here, by using high-throughput unigenic evolution analysis with a genetic assay in which LtrA binding to DIVa down-regulates translation of GFP, we identified regions at LtrA's N terminus that are required for DIVa binding. Then, by similar analysis with a reciprocal genetic assay, we confirmed that residual splicing of a mutant intron lacking DIVa does not require these N-terminal regions, but does require other reverse transcriptase (RT) and X/thumb domain regions that bind the intron core. We also show that N-terminal fragments of LtrA by themselves bind specifically to DIVa in vivo and in vitro. Our results suggest a model in which the N terminus of nascent LtrA binds DIVa of the intron RNA that encoded it and nucleates further interactions with core regions that promote RNP assembly for RNA splicing and intron mobility. Features of this model may be relevant to evolutionarily related non-long-terminal-repeat (non-LTR)-retrotransposon RTs.

show abstract

Section: Introductionmentioning

confidence: 99%

Genetic identification of potential RNA-binding regions in a group II intron-encoded reverse transcriptase

Gu¹,

Cui²,

Mou³

et al. 2010

RNA

View full text Add to dashboard Cite

show abstract

“…This motif contains a T-loop (D1A), a sharp backbone kink of 57°at position U 26 (D1(ii)-D1A junction), a ribose zipper, and a type-I A-minor motif (D1 (ii)-D1C interface) (Toor et al 2010). The five-way junction region contains five M-sites (M11, M15, M20, M26, and M33) and two K-sites (K9 and K12).…”

Section: The Five-way Junction and The T-loop Motifmentioning

confidence: 99%

“…4) lies just beneath A 245 (D1d1), which is the base that intercalates into the T-loop (Toor et al 2010). Binding of monovalent ions to this site of the T-loop may …”

Section: The Five-way Junction and The T-loop Motifmentioning

confidence: 99%

“…However, a systematic structural characterization of intron-bound ions has been missing due to the limited resolution of available crystal structures. In addition, the small number of structures solved in the presence of anomalous scattering ions did not allow for an unambiguous identification of all metal sites (Toor et al 2008a(Toor et al , 2010. However, we recently succeeded in obtaining high-resolution structures of the Oceanobacillus iheyensis group II intron (OiGIIi) ) (Marcia and Pyle 2012;Marcia et al 2013b).…”

Section: Introductionmentioning

confidence: 99%

“…Finally, the ribose zipper that joins the base of D1C (U 66 and A 67 ) with the base of D1(ii) (U 24 ) (Toor et al 2010) contains two divalent ion sites, M15 and M20 (Supplemental Fig. S3).…”

Section: Site-bound Ions In Group II Intronsmentioning

confidence: 99%

See 2 more Smart Citations

Principles of ion recognition in RNA: insights from the group II intron structures

Marcia

Pyle

2014

RNA

Self Cite

View full text Add to dashboard Cite

Metal ions promote both RNA folding and catalysis, thus being essential in stabilizing the structure and determining the function of large RNA molecules, including group II introns. The latter are self-splicing metalloribozymes, containing a heteronuclear fourmetal-ion center within the active site. In addition to these catalytic ions, group II introns bind many other structural ions, including delocalized ions that bind the RNA diffusively and well-ordered ions that bind the RNA tightly with high occupancy. The latter ions, which can be studied by biophysical methods, have not yet been analyzed systematically. Here, we compare crystal structures of the group IIC intron from Oceanobacillus iheyensis and classify numerous site-bound ions, which are primarily localized in the intron core and near long-range tertiary contacts. Certain ion-binding sites resemble motifs observed in known RNA structures, while others are idiosyncratic to the group II intron. Particularly interesting are (1) ions proximal to the active site, which may participate in splicing together with the catalytic four-metal-ion center, (2) organic ions that bind regions predicted to interact with intron-encoded proteins, and (3) unusual monovalent ions bound to GU wobble pairs, GA mismatches, the S-turn, the tetraloop-receptor, and the T-loop. Our analysis extends the general principles by which ions participate in RNA structural organization and it will aid in the determination and interpretation of future RNA structures.

show abstract