Structural and functional evolution of group II intron ribozymes: Insights from unusual elements carrying a 3′ extension

Tourasse, Nicolas J.; Stabell, Fredrik B.; Kolstø, Anne‐Brit

doi:10.1016/j.nbt.2010.02.014

Cited by 6 publications

(12 citation statements)

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“…Sequence similarity searches of public sequence databases using BLASTN conducted in the present study revealed six additional group II introns carrying a 3' extension similar to those previously identified in refs [19,17], and [18] (Table 1). Interestingly, while all introns with a 3' extension known to date were found in closely related bacteria forming the B. cereus group, two of the newly discovered elements are encoded by strains of unrelated species, namely Bacillus pseudofirmus OF4 (previously classified as B. firmus OF4; [25]) and the uncharacterized Bacillus sp .…”

Section: Resultssupporting

confidence: 82%

“…With respect to the phylogeny of the introns themselves, many of the introns with a 3' extension belong to the β subgroup within the bacterial B class [17,18], and in particular eight are highly similar to the B.th .I6 intron from B. thuringiensis kurstaki BGSC 4D1/HD1 (Table 1). The B.th .I6-like introns ( B.th .I6 and B.c .I16) are all inserted in the same homing site within the pXO1-42 plasmid gene, and the two intron copies ( B.th .I6a and b) found in B. thuringiensis kurstaki BGSC 4D1/HD1 were suggested to be the result of intron mobility [17,18].…”

Section: Resultsmentioning

confidence: 99%

“…The B.th .I6-like introns ( B.th .I6 and B.c .I16) are all inserted in the same homing site within the pXO1-42 plasmid gene, and the two intron copies ( B.th .I6a and b) found in B. thuringiensis kurstaki BGSC 4D1/HD1 were suggested to be the result of intron mobility [17,18]. Here, by combining all the available sequence data, supplemented by a PCR screen for pXO1-42, and by using the high sequence similarity between the introns and between the host genes, together with reconstructions of the phylogenetic relationships of the host genes and host strains, we attempted to detect further signs of intron mobility and to identify the events that have driven the dispersal of the unusual introns.…”

Section: Resultsmentioning

confidence: 99%

“…These bacterial species are genetically closely related and are known to harbor a range of mobile elements such as plasmids and introns [13,20-23]. Functional analysis demonstrated that the extra segment is part of the intron RNA molecule and affects the self-splicing reaction in vitro, and thus could be considered as a domain VII [17,18,24]. Phylogenetic analysis revealed that the unusual introns belong to two subgroups α and β within the bacterial B class [17,18].…”

Section: Introductionmentioning

confidence: 99%

“…Functional analysis demonstrated that the extra segment is part of the intron RNA molecule and affects the self-splicing reaction in vitro, and thus could be considered as a domain VII [17,18,24]. Phylogenetic analysis revealed that the unusual introns belong to two subgroups α and β within the bacterial B class [17,18]. In the present study we report the identification of the first introns with a 3' extension in bacterial species from outside the B. cereus group.…”

Section: Introductionmentioning

confidence: 99%

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Diversity, mobility, and structural and functional evolution of group II introns carrying an unusual 3' extension

2011

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BackgroundGroup II introns are widespread genetic elements endowed with a dual functionality. They are catalytic RNAs (ribozymes) that are able of self-splicing and they are also mobile retroelements that can invade genomic DNA. The group II intron RNA secondary structure is typically made up of six domains. However, a number of unusual group II introns carrying a unique extension of 53-56 nucleotides at the 3' end have been identified previously in bacteria of the Bacillus cereus group.MethodsIn the present study, we conducted combined sequence comparisons and phylogenetic analyses of introns, host gene, plasmid and chromosome of host strains in order to gain insights into mobility, dispersal, and evolution of the unusual introns and their extension. We also performed in vitro mutational and kinetic experiments to investigate possible functional features related to the extension.ResultsWe report the identification of novel copies of group II introns carrying a 3' extension including the first two copies in bacteria not belonging to the B. cereus group, Bacillus pseudofirmus OF4 and Bacillus sp. 2_A_57_CT2, an uncharacterized species phylogenetically close to B. firmus. Interestingly, the B. pseudofirmus intron has a longer extension of 70 bases. From sequence comparisons and phylogenetic analyses, several possible separate events of mobility involving the atypical introns could be identified, including both retrohoming and retrotransposition events. In addition, identical extensions were found in introns that otherwise exhibit little sequence conservation in the rest of their structures, with the exception of the conserved and catalytically critical domains V and VI, suggesting either separate acquisition of the extra segment by different group II introns or a strong selection pressure acting on the extension. Furthermore, we show by in vitro splicing experiments that the 3' extension affects the splicing properties differently in introns belonging to separate evolutionary branches.ConclusionsAltogether this study provides additional insights into the structural and functional evolution of unusual introns harboring a 3' extension and lends further evidence that these introns are mobile with their extension.

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Section: Resultssupporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Diversity, mobility, and structural and functional evolution of group II introns carrying an unusual 3' extension

2011

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Mitochondrial Genome Evolution

Bernt

Machné²,

Sahyoun

et al. 2013

Encyclopedia of Life Sciences

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Mitochondria are membrane‐enclosed organelles present in most eukaryotic cells that generate most of the cell's adenosine triphosphate (ATP) supply. Derived from a proteobacterial ancestor, mitochondria harbour their own, drastically reduced genome. Starting from a prokaryote‐like ancestral state encoding a complete ribosomal ribonucleic acid (rRNA) operon, a complete set of transfer RNAs (tRNAs) required for translation, and key enzymes of the respiratory chain as well as some ribosomal proteins, the mitogenome has been dramatically restructured and further reduced in many of the eukaryotic lineages. The loss and transfer to the nucleus of mitochondrial genes is a common trend in most phyla, in particular in Metazoa and Alveolata. In extreme, phylogenetically dispersed cases, often associated with parasitic or anaerobic life styles, mitochondria have been transformed to the so‐called mitosomes or hydrogenosomes devoid of their own genetic material. Ancestrally a single circular deoxyribonucleic acid (DNA) , mitogenomes have evolved to complex, fragmented architectures in particular in Euglenozoa. Key Concepts: Mitochondria have an endosymbiotic origin deriving from a proteobacterial ancestor. Various evolutionary mechanisms operate on mitochondrial genomes. Mitochondrial genomes have developed very diverse properties during eukaryote evolution. Mitogenomic gene content declines in most eukaryotic lineages by horizontal transfer to the nuclear genome. Complex idiosyncratic genome organisations have independently evolved in several eukaryotic phyla.

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Natural circularly permuted group II introns in bacteria produce RNA circles

et al. 2021

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Summary Group II self-splicing introns are large structured RNAs that remove themselves from transcripts while simultaneously sealing the resulting gaps. Some representatives can subsequently reverse splice into DNA, accounting for their pervasive distribution in bacteria. The catalytically active tertiary structure of each group II intron is assembled from six domains that are arranged in a conserved order. Here, we report structural isomers of group II introns, called CP group II ribozymes, wherein the characteristic order of domains has been altered. Domains five and six, which normally reside at the 3′ end of group II introns, instead occupy the 5′ end to form circularly permuted variants. These unusual group II intron derivatives are catalytically active and generate large linear branched and small circular RNAs, reaction products that are markedly different from those generated by canonical group II introns. The biological role of CP group II ribozymes is currently unknown.

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Structural and functional evolution of group II intron ribozymes: Insights from unusual elements carrying a 3′ extension

Cited by 6 publications

References 62 publications

Diversity, mobility, and structural and functional evolution of group II introns carrying an unusual 3' extension

Diversity, mobility, and structural and functional evolution of group II introns carrying an unusual 3' extension

Mitochondrial Genome Evolution

Natural circularly permuted group II introns in bacteria produce RNA circles

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