Information analysis of Fis binding sites

Abstract

Originally discovered in the bacteriophage Mu DNA inversion system gin, Fis (Factor for Inversion Stimulation) regulates many genetic systems. To determine the base frequency conservation required for Fis to locate its binding sites, we collected a set of 60 experimentally defined wild-type Fis DNA binding sequences. The sequence logo for Fis binding sites showed the significance and likely kinds of base contacts, and these are consistent with available experimental data. Scanning with an information theory based weight matrix within fis, nrd, tgt/sec and gin revealed Fis sites not previously identified, but for which there are published footprinting and biochemical data. DNA mobility shift experiments showed that a site predicted to be 11 bases from the proximal Salmonella typhimurium hin site and a site predicted to be 7 bases from the proximal P1 cin site are bound by Fis in vitro. Two predicted sites separated by 11 bp found within the nrd promoter region, and one in the tgt/sec promoter, were also confirmed by gel shift analysis. A sequence in aldB previously reported to be a Fis site, for which information theory predicts no site, did not shift. These results demonstrate that information analysis is useful for predicting Fis DNA binding.

Differential expression of two bc 1 complexes in the strict acidophilic chemolithoautotrophic bacterium Acidithiobacillus ferrooxidans suggests a model for their respective roles in iron or sulfur oxidation

“…Although no explanation for this low amount of transient expression has been experimentally validated, it has been speculated that, in the case of the rus operon, it could be a response to an increase in particular nutrients to allow quick adaptation to the environment, perhaps mediated by a Fis-like protein (Yarzábal et al, 2004). However, no obvious Fis-binding DNA motif, which is particularly degenerate (Hengen et al, 1997), was detected in the proposed regulatory region of petII.…”

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

“…The Fis-DNA crystals provide a second form where the entire b-hairpin arm region (residues 1-27 from subunit A, 10-26 from subunit B) can be traced. Alignment of the Fis-DNA structure (Finkel and Johnson 1992;Hengen et al 1997;Ussery et al 2001;Cho et al 2008;Shao et al 2008b). Bases denoted below the numbers are inhibitory for binding.…”

“…Highly degenerate 15-bp consensus sequences for Fis binding have been derived by aligning many high-affinity binding sites with respect to their nuclease and chemical reactivity in footprinting experiments (Hubner and Arber 1989;Finkel and Johnson 1992;Hengen et al 1997;Ussery et al 2001), and more recently from SELEX (Shao et al 2008b) and whole-genome chromatin immunoprecipitation (ChIP)-chip analyses ( Fig. 1B; Cho et al 2008).…”

A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium

“…Fis is also required for oriC-directed DNA replication and influences the topological state of DNA in the cell by repressing DNA gyrase and activating topoisomerase I gene expression (Gonzalez-Gil et al, 1996;Ross et al, 1990; Schneider et al, 1999;Weinstein-Fischer et al, 2000). A degenerate consensus sequence has been identified for Fis where it introduces a bend of between 40 u and 90 u upon binding (Hengen et al, 1997). The E. coli Fis protein has a preference for binding sites located within regions of DNA curvature and is known to bind as a dimer (Wagner, 2000).…”