Journal article
Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells
Nucleic acids research, v 40(17), pp 8536-8549
01 Sep 2012
PMID: 22753031
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Some naturally competent bacteria exhibit both a strong preference for DNA fragments containing specific 'uptake sequences' and dramatic overrepresentation of these sequences in their genomes. Uptake sequences are often assumed to directly reflect the specificity of the DNA uptake machinery, but the actual specificity has not been well characterized for any bacterium. We produced a detailed analysis of Haemophilus influenzae's uptake specificity, using Illumina sequencing of degenerate uptake sequences in fragments recovered from competent cells. This identified an uptake motif with the same consensus as the motif overrepresented in the genome, with a 9 bp core (AAGTGCGGT) and two short flanking T-rich tracts. Only four core bases (GCGG) were critical for uptake, suggesting that these make strong specific contacts with the uptake machinery. Other core bases had weaker roles when considered individually, as did the T-tracts, but interaction effects between these were also determinants of uptake. The properties of genomic uptake sequences are also constrained by mutational biases and selective forces acting on USSs with coding and termination functions. Our findings define constraints on gene transfer by natural transformation and suggest how the DNA uptake machinery overcomes the physical constraints imposed by stiff highly charged DNA molecules.
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Details
- Title
- Defining the DNA uptake specificity of naturally competent Haemophilus influenzae cells
- Creators
- Joshua Chang Mell - University of VirginiaIra M. Hall - University of VirginiaRosemary J. Redfield - University of Virginia
- Publication Details
- Nucleic acids research, v 40(17), pp 8536-8549
- Publisher
- Oxford Univ Press
- Number of pages
- 14
- Grant note
- 5F32AI084427; DP2OD006493 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA Canadian Institute for Health Research; Canadian Institutes of Health Research (CIHR) MOP-53263 / Canadian Institute for Health Research; Canadian Institutes of Health Research (CIHR)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology
- Web of Science ID
- WOS:000309464300039
- Scopus ID
- 2-s2.0-84866932869
- Other Identifier
- 991020830155104721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology