Physical Mapping and Fingerprinting of Bacterial Genomes using Rare Cutting Restriction Enzymes

McClelland, Michael; Wong, Kim; Sanderson, K E

doi:10.1007/978-1-4615-6369-3_24

Cited by 5 publications

(2 citation statements)

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“…Computational search for candidate binding sites in upstream gene regions [400 nucleotides (nt) upstream and 50 nt downstream relative to the annotated translational gene start] was performed using the built PWMs and the GenomeExplorer program package (Mironov et al, 2000). Score thresholds for the identification of sites were selected so that candidate sites upstream of functionally relevant genes were accepted, while the fraction of genes preceded by candidate sites did not exceed 5% in studied genomes.…”

Section: Reconstruction and Analysis Of Regulons And Regulogsmentioning

confidence: 99%

Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content

Suvorova

Gelfand

2021

Front. Microbiol.

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The IclR-family is a large group of transcription factors (TFs) regulating various biological processes in diverse bacteria. Using comparative genomics techniques, we have identified binding motifs of IclR-family TFs, reconstructed regulons and analyzed their content, finding co-occurrences between the regulated COGs (clusters of orthologous genes), useful for future functional characterizations of TFs and their regulated genes. We describe two main types of IclR-family motifs, similar in sequence but different in the arrangement of the half-sites (boxes), with GKTYCRYW3–4RYGRAMC and TGRAACAN1–2TGTTYCA consensuses, and also predict that TFs in 32 orthologous groups have binding sites comprised of three boxes with alternating direction, which implies two possible alternative modes of dimerization of TFs. We identified trends in site positioning relative to the translational gene start, and show that TFs in 94 orthologous groups bind tandem sites with 18–22 nucleotides between their centers. We predict protein–DNA contacts via the correlation analysis of nucleotides in binding sites and amino acids of the DNA-binding domain of TFs, and show that the majority of interacting positions and predicted contacts are similar for both types of motifs and conform well both to available experimental data and to general protein–DNA interaction trends.

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Section: Reconstruction and Analysis Of Regulons And Regulogsmentioning

confidence: 99%

Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content

Suvorova

Gelfand

2021

Front. Microbiol.

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“…In practice, it seems that appropriate restriction enzymes have to be selected for PFGE analysis of each bacterial species and that a combination of different enzymes is necessary for optimal strain discrimination within the species. An overview of rare cutting enzymes useful for PFGE analysis of several bacteria is given by McClelland et al (1998). The standard protocol for PFGE is time-consuming (up to 6 days), but more rapid procedures for specific organisms (e.g.…”

Section: Typing Techniques Based On Chromosomal Restriction Fragment mentioning

confidence: 99%

Applied Microbiology

2002

Focus on Biotechnology

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Molecular Detection and Typing of Foodborne Bacterial Pathogens: A Review

Heyndrickx¹,

Rijpens²,

Herman³

2001

Applied Microbiology

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Physical Mapping and Fingerprinting of Bacterial Genomes using Rare Cutting Restriction Enzymes

Cited by 5 publications

References 358 publications

Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content

Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content

Applied Microbiology

Molecular Detection and Typing of Foodborne Bacterial Pathogens: A Review

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