Group I introns and RNA folding

2002 ◽  
Vol 30 (6) ◽  
pp. 1149-1152 ◽  
Author(s):  
E. Westhof
Keyword(s):  
Catalytic Activity ◽  
Self Assembly ◽  
Rna Folding ◽  
Catalytic Rna ◽  
Group I Introns ◽  
Rna Motifs ◽  
X Ray ◽  
Rna Molecules ◽  
Group I ◽  
Self Splicing

Before the discovery of catalytic RNA, tRNA molecules were the most studied RNA molecules for understanding RNA folding. Afterwards, group I introns, because of their stability and the fact that structural folding could be monitored by following their catalytic activity, became the molecule of choice for studying RNA architecture and folding. A major advantage of group I introns for studying the catalytic activity of RNA molecules is that catalytic activity is triggered by the addition of external guanosine co-factors. The self-splicing activity can therefore be precisely controlled. Using group I introns, several RNA motifs central to RNA-RNA self-assembly and folding were discovered. The analysis of the recent X-ray structures of the rRNA subunits indicates that several motifs present in the ribosome occur also in various group I introns.

Folding mechanisms of group I ribozymes: role of stability and contact order

2002 ◽  
Vol 30 (6) ◽  
pp. 1166-1169 ◽  
Author(s):  
S. A. Woodson
Keyword(s):  
Catalytic Activity ◽  
Rna Folding ◽  
Three Dimensional ◽  
Model System ◽  
Folding Pathway ◽  
Primary Sequence ◽  
Rna Molecules ◽  
Contact Order ◽  
Group I

The mechanism by which RNA molecules assemble into unique three-dimensional conformations is important for understanding their function, regulation and interactions with substrates. The Tetrahymena group I ribozyme is an excellent model system for understanding RNA folding mechanisms, because the catalytic activity of the native RNA is easily measured. Folding of the Tetrahymena ribozyme is dominated by intermediates in which the stable P4-P6 domain is correctly formed, but the P3-P9 domain is partially misfolded. The propensity of the RNA to misfold depends on the relative stability of native and non-native interactions. Circular permutation of the Tetrahymena ribozyme shows that the distance in the primary sequence between native interactions also influences the folding pathway.

scholarly journals Mobile Self-Splicing Group I Introns from thepsbA Gene of Chlamydomonas reinhardtii: Highly Efficient Homing of an Exogenous Intron Containing Its Own Promoter

2001 ◽  
Vol 21 (10) ◽  
pp. 3472-3481 ◽  
Author(s):  
Obed W. Odom ◽  
Stephen P. Holloway ◽  
Nita N. Deshpande ◽  
Jaesung Lee ◽  
David L. Herrin
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Open Reading Frames ◽  
Group I Introns ◽  
Resistance Marker ◽  
Free Standing ◽  
Spectinomycin Resistance ◽  
Highly Efficient ◽  
Group I ◽  
Short Exon ◽  
Self Splicing

ABSTRACT Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 andCr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing. Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in both orientations and then cotransformed into IL along with a spectinomycin resistance marker (16Srrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both orientations produced highly efficient cointegration of the intron. Efficient cointegration of Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron, consistent with homing. TheCr.psbA4 constructs also contained a 3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary selection for this marker gave >100-fold more transformants (>10,000/μg of DNA) than did the spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay was used to identify an intronic region between bp −88 and −194 (relative to the ORF) that stimulated homing and contained a possible bacterial (−10, −35)-type promoter. Primer extension analysis detected a transcript that could originate from this promoter. Thus, this mobile, self-splicing intron also contains its own promoter for ORF expression. The implications of these results for horizontal intron transfer and organelle transformation are discussed.

scholarly journals A Unique Group I Intron in Coxiella burnetii Is a Natural Splice Mutant

2009 ◽  
Vol 191 (12) ◽  
pp. 4044-4046 ◽  
Author(s):  
Rahul Raghavan ◽  
Linda D. Hicks ◽  
Michael F. Minnick
Keyword(s):  
Coxiella Burnetii ◽  
Group I Intron ◽  
23S Rrna ◽  
Rrna Gene ◽  
Group I Introns ◽  
Group I ◽  
23S Rrna Gene ◽  
Self Splicing

ABSTRACT Cbu.L1917, a group I intron present in the 23S rRNA gene of Coxiella burnetii, possesses a unique 3′-terminal adenine in place of a conserved guanine. Here, we show that, unlike all other group I introns, Cbu.L1917 utilizes a different cofactor for each splicing step and has a decreased self-splicing rate in vitro.

Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria

Science ◽  
1990 ◽  
Vol 250 (4987) ◽  
pp. 1566-1570 ◽  
Author(s):  
M. Xu ◽  
S. Kathe ◽  
H. Goodrich-Blair ◽  
S. Nierzwicki-Bauer ◽  
D. Shub
Keyword(s):  
Group I Introns ◽  
Bacterial Origin ◽  
Group I ◽  
Self Splicing

scholarly journals A Self-Splicing Group I Intron in DNA Polymerase Genes of T7-Like Bacteriophages

2004 ◽  
Vol 186 (23) ◽  
pp. 8153-8155 ◽  
Author(s):  
Richard P. Bonocora ◽  
David A. Shub
Keyword(s):  
Dna Polymerase ◽  
Group I Intron ◽  
Group I Introns ◽  
Homing Endonucleases ◽  
Structural Element ◽  
Group I ◽  
Close Relatives ◽  
Self Splicing

ABSTRACT Group I introns are inserted into genes of a wide variety of bacteriophages of gram-positive bacteria. However, among the phages of enteric and other gram-negative proteobacteria, introns have been encountered only in phage T4 and several of its close relatives. Here we report the insertion of a self-splicing group I intron in the coding sequence of the DNA polymerase genes of ΦI and W31, phages that are closely related to T7. The introns belong to subgroup IA2 and both contain an open reading frame, inserted into structural element P6a, encoding a protein belonging to the HNH family of homing endonucleases. The introns splice efficiently in vivo and self-splice in vitro under mild conditions of ionic strength and temperature. We conclude that there is no barrier for maintenance of group I introns in phages of proteobacteria.

Hoechst 33258 Selectively Inhibits Group I Intron Self-Splicing by Affecting RNA Folding

ChemBioChem ◽  
2004 ◽  
Vol 5 (12) ◽  
pp. 1647-1652 ◽  
Author(s):  
Matthew D. Disney ◽  
Jessica L. Childs ◽  
Douglas H. Turner
Keyword(s):  
Rna Folding ◽  
Group I Intron ◽  
Hoechst 33258 ◽  
Group I ◽  
Self Splicing

Base pairing between the 3' exon and an internal guide sequence increases 3' splice site specificity in the Tetrahymena self-splicing rRNA intron

1990 ◽  
Vol 10 (6) ◽  
pp. 2960-2965
Author(s):  
E R Suh ◽  
R B Waring
Keyword(s):  
Splice Site ◽  
Site Specificity ◽  
Group I Introns ◽  
Base Pairing ◽  
Group I ◽  
Guide Sequence ◽  
Compensatory Mutations ◽  
Self Splicing ◽  
Splice Site Usage ◽  
Selection Of

It has been proposed that recognition of the 3' splice site in many group I introns involves base pairing between the start of the 3' exon and a region of the intron known as the internal guide sequence (R. W. Davies, R. B. Waring, J. Ray, T. A. Brown, and C. Scazzocchio, Nature [London] 300:719-724, 1982). We have examined this hypothesis, using the self-splicing rRNA intron from Tetrahymena thermophila. Mutations in the 3' exon that weaken this proposed pairing increased use of a downstream cryptic 3' splice site. Compensatory mutations in the guide sequence that restore this pairing resulted in even stronger selection of the normal 3' splice site. These changes in 3' splice site usage were more pronounced in the background of a mutation (414A) which resulted in an adenine instead of a guanine being the last base of the intron. These results show that the proposed pairing (P10) plays an important role in ensuring that cryptic 3' splice sites are selected against. Surprisingly, the 414A mutation alone did not result in activation of the cryptic 3' splice site.

Sign in / Sign up

Export Citation Format

Share Document