Interaction between conjugative and retrotransposable elements in horizontal gene transfer.

Mobile genetic elements either encode their own mobilization machineries or hijack them from other mobile elements. Multiple classes of mobile elements often coexist within genomes and it is unclear whether they have the capacity to functionally interact and even collaborate. We investigate the possibility that molecular machineries of disparate mobile elements may functionally interact, using the example of a retrotransposon, in the form of a mobile group II intron, found on a conjugative plasmid pRS01 in Lactococcus lactis.

Identification and characterization of small RNAs in Yersinia pestis.

Yersinia pestis, the etiologic agent of plague, is closely related to Yersinia pseudotuberculosis evolutionarily but has a very different mode of infection. The RNA-binding regulatory protein, Hfq, mediates regulation by small RNAs (sRNAs) and is required for virulence of both Y. pestis and Y.

Structural effects of linkage disequilibrium on the transcriptome.

A majority of SNPs (single nucleotide polymorphisms) map to noncoding and intergenic regions of the genome. Noncoding SNPs are often identified in genome-wide association studies (GWAS) as strongly associated with human disease. Two such disease-associated SNPs in the 5' UTR of the human FTL (Ferritin Light Chain) gene are predicted to alter the ensemble of structures adopted by the mRNA.

Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions.

The take and give between retrotransposable elements and their hosts.

Retrotransposons mobilize via RNA intermediates and usually carry with them the agent of their mobility, reverse transcriptase. Retrotransposons are streamlined, and therefore rely on host factors to proliferate. However, retrotransposons are exposed to cellular forces that block their paths.

Bipolar localization of the group II intron Ll.LtrB is maintained in Escherichia coli deficient in nucleoid condensation, chromosome partitioning and DNA replication.

Group II introns are mobile genetic elements that invade their cognate intron-minus alleles via an RNA intermediate, in a process known as retrohoming. They can also retrotranspose to ectopic sites at low frequency. In Escherichia coli, retrotransposition of the lactococcal group II intron, Ll.

Retrotransposition strategies of the Lactococcus lactis Ll.LtrB group II intron are dictated by host identity and cellular environment.

Group II introns are mobile retroelements that invade their cognate intron-minus gene in a process known as retrohoming. They can also retrotranspose to ectopic sites at low frequency. Previous studies of the Lactococcus lactis intron Ll.

A bacterial group II intron favors retrotransposition into plasmid targets.

Group II introns, widely believed to be the ancestors of nuclear pre-mRNA introns, are catalytic RNAs found in bacteria, archaea, and eukaryotes. They are mobile genetic elements that move via an RNA intermediate. They retrohome to intronless alleles and retrotranspose to ectopic sites, aided by an intron-encoded protein with reverse transcriptase, maturase, and endonuclease activities.

Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets.

Catalytic group II introns are mobile retroelements that invade cognate intronless genes via retrohoming, where the introns reverse splice into double-stranded DNA (dsDNA) targets. They can also retrotranspose to ectopic sites at low frequencies. Whereas our previous studies with a bacterial intron, Ll.