%0 Journal Article
%T Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes
%A Ivaylo Kostadinov
%A Renzo Kottmann
%A Alban Ramette
%A Jost Waldmann
%A Pier Luigi Buttigieg
%A Frank Gl£¿ckner
%J Microbial Informatics and Experimentation
%D 2011
%I BioMed Central
%R 10.1186/2042-5783-1-9
%X We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool.Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to in situ measurements and were essential for quantifying the effect of the environment on the TF content. It is demonstrated that comprehensive and well-structured contextual data will strongly enhance our ability to interpret the functional potential of microbes from metagenomic data.Microorganisms constantly adapt to their environment to survive. An efficient response mechanism is the regulation of transcription, the first step in gene expression, according to environmental demands. Transcription factors (TFs) are the primary agents that perform transcriptional regulation [1]. They consist of a DNA-binding domain (DBD) that typically targets regulatory elements upstream of a gene and an effector domain [2]. The majority of TFs operate by influencing the downstream transcription process and can be classified into 10 super-families according to their DNA-binding mechanisms [3]. Based on the number of genes they regulate, TFs can be divided into 'global regulators' and 'fine tuners' [4]. Both types exert targeted control over gene expression. Global regulators affect a larger number of genes from diverse metabolic pathways and respond to a wider set of stimuli [4,5]. Conve
%K transcription factors
%K ecological metagenomics
%K interpolated environmental data
%K multivariate statistics
%U http://www.microbialinformaticsj.com/content/1/1/9