GISSD: Group I Intron Sequence and Structure Database

Zhou, Yu; Chen, Lu; Wu, Qinghua; Wang, Yu; Sun, Zhihua; Deng, Jia-Cong; Zhang, Yi

doi:10.1093/nar/gkm766

Cited by 80 publications

(88 citation statements)

References 20 publications

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“…The general conservation of the catalytic cores of group I introns has been emphasized and contrasted with the very different peripheral architectures present in different group I intron subclasses (Burke 1988;Cech 1988Cech , 1990Zhou et al 2008), and there has been some exploration of the influence of tertiary architecture on the conserved functions of the catalytic core (e.g., Ikawa et al 2000aIkawa et al ,b, 2003Dolan and Muller 2014). Strong interpretation of such results requires certainty about the processes and reaction steps being compared.…”

Section: Discussionmentioning

confidence: 99%

“…Different classes of group I introns have distinct interactions and domains that surround the catalytic core (Michel and Westhof 1990;Zhou et al 2008). For example, the catalytic core of the Tetrahymena intron is encircled by peripheral domains that connect to one another via five long-range tertiary contacts, while the smaller Azoarcus intron has a simpler tertiary architecture with fewer peripheral domains and only two longrange contacts (Fig.…”

Section: Introductionmentioning

confidence: 99%

“…For example, the catalytic core of the Tetrahymena intron is encircled by peripheral domains that connect to one another via five long-range tertiary contacts, while the smaller Azoarcus intron has a simpler tertiary architecture with fewer peripheral domains and only two longrange contacts (Fig. 1;Tanner and Cech 1996;Adams et al 2004a,b;Zhou et al 2008). Prior work revealed similar binding thermodynamics of the guanosine nucleophile by ribozymes derived from these group I introns, as well as significant differences in the binding of oligonucleotide substrate mimics of their respective 5 ′ -splice sites (Kuo et al 1999;Kuo and Piccirilli 2001).…”

Section: Introductionmentioning

confidence: 99%

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A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction

Gleitsman

Herschlag

2014

RNA

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Determination of quantitative thermodynamic and kinetic frameworks for ribozymes derived from the Azoarcus group I intron and comparisons to their well-studied analogs from the Tetrahymena group I intron reveal similarities and differences between these RNAs. The guanosine (G) substrate binds to the Azoarcus and Tetrahymena ribozymes with similar equilibrium binding constants and similar very slow association rate constants. These and additional literature observations support a model in which the free ribozyme is not conformationally competent to bind G and in which the probability of assuming the bindingcompetent state is determined by tertiary interactions of peripheral elements. As proposed previously, the slow binding of guanosine may play a role in the specificity of group I intron self-splicing, and slow binding may be used analogously in other biological processes. The internal equilibrium between ribozyme-bound substrates and products is similar for these ribozymes, but the Azoarcus ribozyme does not display the coupling in the binding of substrates that is observed with the Tetrahymena ribozyme, suggesting that local preorganization of the active site and rearrangements within the active site upon substrate binding are different for these ribozymes. Our results also confirm the much greater tertiary binding energy of the 5 ′ -splice site analog with the Azoarcus ribozyme, binding energy that presumably compensates for the fewer base-pairing interactions to allow the 5 ′ -exon intermediate in self splicing to remain bound subsequent to 5 ′ -exon cleavage and prior to exon ligation. Most generally, these frameworks provide a foundation for design and interpretation of experiments investigating fundamental properties of these and other structured RNAs.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction

Gleitsman

Herschlag

2014

RNA

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“…The region between p46 and p44 (682 bp; nt 33575 to 34256, including the p46 stop codon TAA) was a self-splicing group I intron (subgroup IA2; http://www.rna.whu.edu.cn/gissd /gIRfam.html), which contained p45 (Fig. 4A) (57). Removal of the predicted intron between p46 and p44 would give rise to a fusion protein with a molecular mass of 92.5 kDa, similar in size and amino acid sequence to DNA polymerase I from X. oryzae pv.…”

Section: Resultsmentioning

confidence: 99%

Genomic Characterization of the Intron-Containing T7-Like Phage phiL7 ofXanthomonas campestris

Lee

Lin

Weng

et al. 2009

Appl Environ Microbiol

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The lytic phage phiL7, which morphologically belongs to the Siphoviridae family, infects Xanthomonas campestris pv. campestris. Nucleotide sequence analysis has revealed that phiL7 contains a linear doublestranded DNA genome (44,080 bp, 56% G؉C) with a 3-protruding cos site (5-TTACCGGAC-3) and 59 possible genes. Among the deduced proteins, 32 have homologs with known functions and 18 show no database similarities; moreover, the genes encoding these 18 proteins mostly have varying G؉C contents and form clusters dispersed along the genome. Only 39 genes have sequences related (27% to 78%) to those of sequenced genes of X. oryzae pv. oryzae phages, although the genome size and architecture of these Xanthomonas phages are similar. These findings suggest that phiL7 acquired genes by horizontal transfer, followed by evolution via various types of mutations. Major differences were found between phiL7 and the X. oryzae pv. oryzae phages: (i) phiL7 has a group I intron inserted in the DNA polymerase gene, the first such intron observed in Xanthomonas phages; (ii) although infection of phiL7 exerted inhibition to the host RNA polymerase, similar to the situations in X. oryzae pv. oryzae phages Xp10 and Xop411, sequence analysis did not identify a homologue of the Xp10 p7 that controls the shift from host RNA polymerase (RNAP) to viral RNAP during transcription; and (iii) phiL7 lacks the tail fiber protein gene that exhibits domain duplications thought to be important for host range determination in OP1, and sequence analysis suggested that p20 (tail protein III) instead has the potential to play this role.The genus Xanthomonas in the gamma subdivision of the Proteobacteria is a diverse and economically important group of bacterial plant pathogens consisting of 27 species (35), causing tremendous loss in agriculture worldwide. Individual species of this genus comprise multiple pathogenic variants (pathovars) and collectively cause diseases on at least 124 monocot species and 268 dicot species: for example, Xanthomonas campestris pv. campestris causes black rot in crucifers, X. campestris pv. vesicatoria causes spot disease in peppers and tomatoes, X. axonopodis pv. citri causes citrus canker, and X. oryzae pv. oryzae causes bacterial leaf blight on rice plants (17). In addition, members of the genus Xanthomonas commonly produce great amounts of an exopolysaccharide (xanthan gum) and X. campestris pv. campestris has been the organism of choice in industry for production of xanthan, which is useful in food, agriculture, industry and cosmetics (55).For controlling bacterial plant diseases, chemical control with antibiotics and copper compounds has been the standard (31, 46). However, many agrochemicals are toxic and may pose significant environmental and health risks (14). Therefore, there has been a resurgence of interest recently in using bacteriophages to replace the currently prevalent chemical measures, in which phages can be used effectively as part of integrated disease management strategies (12,15,16,32). Although pha...

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“…To date, only four different group I introns have been tested for their trans-splicing potential replacing the substrate 3 ′ portion (Sullenger and Cech 1994;Lundblad et al 2004;Fiskaa et al 2006), compared to the more than 16,000 known group I introns (Zhou et al 2008). Of these four, the Tetrahymena ribozyme achieved the highest trans-splicing efficiencies in vitro, is understood at the most detailed biochemical level, and remains the only group I intron tested for mRNA repair / replacement trans-splicing in vivo (Michel and Westhof 1990;Lehnert et al 1996;Kuo and Piccirilli 2001;Koduvayur and Woodson 2004;Shi et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Trans-splicing with the group I intron ribozyme from Azoarcus

Dolan

Müller

2013

RNA

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Group I introns are ribozymes (catalytic RNAs) that excise themselves from RNA primary transcripts by catalyzing two successive transesterification reactions. These cis-splicing ribozymes can be converted into trans-splicing ribozymes, which can modify the sequence of a separate substrate RNA, both in vitro and in vivo. Previous work on trans-splicing ribozymes has mostly focused on the 16S rRNA group I intron ribozyme from Tetrahymena thermophila. Here, we test the trans-splicing potential of the tRNA Ile group I intron ribozyme from the bacterium Azoarcus. This ribozyme is only half the size of the Tetrahymena ribozyme and folds faster into its active conformation in vitro. Our results showed that in vitro, the Azoarcus and Tetrahymena ribozymes favored the same set of splice sites on a substrate RNA. Both ribozymes showed the same trans-splicing efficiency when containing their individually optimized 5 ′ terminus. In contrast to the previously optimized 5 ′ -terminal design of the Tetrahymena ribozyme, the Azoarcus ribozyme was most efficient with a trans-splicing design that resembled the secondary structure context of the natural cis-splicing Azoarcus ribozyme, which includes base-pairing between the substrate 5 ′ portion and the ribozyme 3 ′ exon. These results suggested preferred trans-splicing interactions for the Azoarcus ribozyme under near-physiological in vitro conditions. Despite the high activity in vitro, however, the splicing efficiency of the Azoarcus ribozyme in Escherichia coli cells was significantly below that of the Tetrahymena ribozyme.

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GISSD: Group I Intron Sequence and Structure Database

Cited by 80 publications

References 20 publications

A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction

A kinetic and thermodynamic framework for the Azoarcus group I ribozyme reaction

Genomic Characterization of the Intron-Containing T7-Like Phage phiL7 ofXanthomonas campestris

Trans-splicing with the group I intron ribozyme from Azoarcus

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