Dataset Information

Diversity and strength of internal outward-oriented promoters in group IIC-attC introns.

ABSTRACT: Integrons are genetic elements that incorporate mobile gene cassettes by site-specific recombination and express them as an operon from a promoter (Pc) located upstream of the cassette insertion site. Most gene cassettes found in integrons contain only one gene followed by an attC recombination site. We have recently shown that a specific lineage of group IIC introns, named group IIC-attC introns, inserts into the bottom strand sequence of attC sites. Here, we show that S.ma.I2, a group IIC-attC intron inserted in an integron cassette array of Serratia marcescens, impedes transcription from Pc while allowing expression of the following antibiotic resistance cassette using an internal outward-oriented promoter (P(out)). Bioinformatic analyses indicate that one or two putative P(out), which have sequence similarities with the Escherichia coli consensus promoters, are conserved in most group IIC-attC intron sequences. We show that P(out) with different versions of the -35 and -10 sequences are functionally active in expressing a promoterless chloramphenicol acetyltransferase (cat) reporter gene in E. coli. P(out) in group IIC-attC introns may therefore play a role in the expression of one or more gene cassettes whose transcription from Pc would otherwise be impeded by insertion of the intron.

SUBMITTER: Leon G

PROVIDER: S-EPMC3001079 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature

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Diversity and strength of internal outward-oriented promoters in group IIC-attC introns.

Léon Grégory G Quiroga Cecilia C Centrón Daniela D Roy Paul H PH

Nucleic acids research 20100816 22

Integrons are genetic elements that incorporate mobile gene cassettes by site-specific recombination and express them as an operon from a promoter (Pc) located upstream of the cassette insertion site. Most gene cassettes found in integrons contain only one gene followed by an attC recombination site. We have recently shown that a specific lineage of group IIC introns, named group IIC-attC introns, inserts into the bottom strand sequence of attC sites. Here, we show that S.ma.I2, a group IIC-attC ...[more]

PMID: 20716518

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Project description:The eight iron meteorites currently classified as belonging to the IIC group were characterized with respect to the compositions of 21 siderophile elements. Several of these meteorites were also characterized for mass independent isotopic compositions of Mo, Ru and W. Chemical and isotopic data for one, Wiley, indicate that it is not a IIC iron meteorite and should be reclassified as ungrouped. The remaining seven IIC iron meteorites exhibit broadly similar bulk chemical and isotopic characteristics, consistent with an origin from a common parent body. Variations in highly siderophile element (HSE) abundances among the members of the group can be well accounted for by a fractional crystallization model with all the meteorites crystallizing between ~10 and ~26% of the original melt, assuming initial S and P concentrations of 8 wt.% and 2 wt.%, respectively. Abundances of HSE estimated for the parental melt suggest a composition with chondritic relative abundances of HSE ~6 times higher than in bulk carbonaceous chondrites, consistent with the IIC irons sampling a parent body core comprising ~17% of the mass of the body. Radiogenic 182W abundances of two group IIC irons, corrected for a nucleosynthetic component, indicate a metal-silicate segregation age of 3.2 ± 0.5 Myr subsequent to the formation of Calcium-Aluminum-rich Inclusions (CAI). When this age is coupled with thermal modeling, and assumptions about the Hf/W of precursor materials, a parent body accretion age of 1.4 ± 0.5 Myr (post-CAI) is obtained. The IIC irons and Wiley have 100Ru mass independent "genetic" isotopic compositions that are identical to other irons with so-called carbonaceous chondrite (CC) type genetic affinities, but enrichments in 94,95,97Mo and 183W that indicate greater s-process deficits relative to most known CC iron meteorites. If the IIC irons and Wiley are of the CC type, this indicates variable s-process deficits within the CC reservoir, similar to the s-process variability within the NC reservoir observed for iron meteorites. Nucleosynthetic models indicate that Mo and 183W s-process variability should correlate with Ru isotopic variability, which is not observed. This may indicate the IIC irons and Wiley experienced selective thermal processing of nucleosynthetic carriers, or are genetically distinct from the CC and NC precursor materials.

Project description:BACKGROUND:Group 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. METHODS:In 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. RESULTS:We 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. CONCLUSIONS:Altogether 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.

Dataset Information

Diversity and strength of internal outward-oriented promoters in group IIC-attC introns.

Publications

Diversity and strength of internal outward-oriented promoters in group IIC-attC introns.

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