Dataset Information

Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations.

ABSTRACT: The availability of multiple genome-wide human polymorphism datasets has led to an increase in efforts to scan the genome for signals of positive selection. As a result, the number of loci in the human genome predicted to be adaptively evolving increases monthly. Yet, these numerous genome-wide scans have identified minimally overlapping sets of candidate loci, potentially due to biases in genotype versus sequence data or power of statistical tests to detect selection in different time frames. Because of these issues, a critical step is to confirm the evidence for positive selection through direct sequencing. In this study, we describe the resequencing and analysis of two loci, RAGE and POLL, that were identified by a recent genome-wide scan of the Perlegen data to be under selection in the Han Chinese population. By resequencing these loci in additional populations, we have found that the evolutionary history of these regions is more complex than observed in the initial genome-wide scan and that the sweep patterns are shared across several populations. The resequencing data provide evidence for selection on RAGE in the non-African populations and on POLL in the Asian and Sub-Saharan African populations. In addition to confirming the signatures of selection from the genome-wide scan, direct resequencing reveals more extensive patterns of selection than the genotype data.

SUBMITTER: Kelley JL

PROVIDER: S-EPMC2638832 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

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Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations.

Kelley Joanna L JL Turkheimer Kayley K Haney Margo M Swanson Willie J WJ

Human molecular genetics 20081205 4

The availability of multiple genome-wide human polymorphism datasets has led to an increase in efforts to scan the genome for signals of positive selection. As a result, the number of loci in the human genome predicted to be adaptively evolving increases monthly. Yet, these numerous genome-wide scans have identified minimally overlapping sets of candidate loci, potentially due to biases in genotype versus sequence data or power of statistical tests to detect selection in different time frames. B ...[more]

PMID: 19060005

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Project description:Efficient horizontal gene transfer of the conjugative plasmid pCF10 from Enterococcus faecalis depends on the expression of its type 4 secretion system (T4SS) genes, controlled by the PQ promoter. Transcription from the PQ promoter is tightly regulated, partially to limit cell toxicity caused by overproduction of PrgB, a T4SS adhesin. PrgU plays an important role in regulating this toxicity by decreasing PrgB levels. PrgU has an RNA-binding fold, prompting us to test whether PrgU exerts its regulatory control through binding of prgQ transcripts. We used a combination of in vivo methods to quantify PrgU effects on prgQ transcripts at both single-cell and population levels. PrgU function requires a specific RNA sequence within an intergenic region (IGR) about 400 bp downstream of PQ. PrgU interaction with the IGR reduces levels of downstream transcripts. Single-cell expression analysis showed that cells expressing prgU decreased transcript levels more rapidly than isogenic prgU-minus cells. PrgU bound RNA in vitro without sequence specificity, suggesting that PrgU requires a specific RNA structure or one or more host factors for selective binding in vivo. PrgU binding to its IGR target might recruit RNase(s) for targeted degradation of downstream transcripts or reduce elongation of nascent transcripts beyond the IGR. IMPORTANCE Bacteria utilize type 4 secretion systems (T4SS) to efficiently transfer DNA between donor and recipient cells, thereby spreading genes encoding antibiotic resistance as well as various virulence factors. Regulation of expression of the T4SS proteins and surface adhesins in Gram-positive bacteria is crucial, as some of these are highly toxic to the cell. The significance of our research lies in identifying the novel mechanism by which PrgU performs its delicate fine-tuning of the expression levels. As prgU orthologs are present in various conjugative plasmids and transposons, our results are likely relevant to understanding of diverse clinically important transfer systems.

Dataset Information

Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations.

Publications

Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations.

Similar Datasets

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