COMPARATIVE MECHANISMS FOR TRANSCRIPTION AND REGULATORY SIGNALS IN ARCHAEA AND BACTERIA

<p>A review and comparisosn of genetic regulatory mechanisms in archaea and bacteria.</p

Structural and functional map of a bacterial nucleoid

<p>Genome-wide mapping of transcription factor-DNA interactions in bacterial chromosomes in vivo has begun to reveal global zones occupied by these factors that serve two purposes: compacting the bacterial DNA and influencing global programs of gene transcription.</p

Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli

<p>Individual cells need to discern and synchronize transcriptional responses according to variations in external and internal conditions. Metabolites and chemical compounds are sensed by transcription factors (TFs), which direct the corresponding specific transcriptional responses. We propose a classification of the currently known TFs of Escherichia coli based on whether they respond to metabolites incorporated from the exterior, to internally produced compounds, or to both. When analyzing the mutual interactions of TFs, the dominant role of internal signal sensing becomes apparent, greatly due to the role of global regulators of transcription. This work encompasses metabolite–TF interactions, bridging the gap between the metabolic and regulatory networks, thus advancing towards an integrated network model for the understanding of cellular behavior.</p

Frequency Matrices for the −10 and −35 Motifs of σ⁷⁰ Promoters in E. coli

<p>This matrix pair (Matrix_18_15_13_2_1.5) was selected for searching across bacterial genomes from a collection of optimized matrices defined for E. coli in [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020185#pgen-0020185-b001" target="_blank">1</a>]. Note that in order to compare these matrices with the canonical patterns (TTGACA and TATAAT), the spacers of 13 bp to 19 bp between the two boxes correspond to the 15 bp to 21 bp reported in the literature, as the TGT triplet is considered as part of the −10 box. Before searching for promoter-like signals, these matrices were calibrated using the noncoding base composition of each target genome.</p

Internal Versus External Effector and Transcription Factor Gene Pairs Differ in Their Relative Chromosomal Position in Escherichia coli

<p>Here, we analyze the genome organization of the genetic components of these sensing systems, using the classification described earlier. We report the chromosomal proximity of transcription factors and their effector genes to sense periplasmic signals or transported metabolites (i.e. transcriptional sensing systems from the external class) in contrast to the components for sensing internally synthesized metabolites, which tend to be distant on the chromosome. We strengthen our finding that external sensing genetic machinery behaves like chromosomal modules of regulation to respond rapidly to variations in external conditions through co-expression of their genetic components, which is corroborated with microarray data for E. coli. Furthermore, we show several lines of evidence supporting the need for the coordinated activity of external sensing systems in contrast to that of internal sensing machinery, which can explain their close chromosomal organization. The observed functional correlation between the chromosomal organization and the genetic machinery for environmental sensing should contribute to our understanding of the logical functioning and evolution of the transcriptional regulatory networks in bacteria.</p

Schematic Representation of the Main Interactions of RNAP with Promoter DNA and Alignment of the σ⁷⁰ Motifs for Recognition and Binding of −10 (2.4 Region) and −35 Promoter Sequences (4.2 Region) for Representative Eubacteria

<p>Sequence alignments of several σ⁷⁰ factors from different bacteria reveal four conserved regions that can be further divided into subregions [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020185#pgen-0020185-b039" target="_blank">39</a>]. Only regions 2 and 4 are well conserved in all members of the σ⁷⁰ family [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020185#pgen-0020185-b040" target="_blank">40</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020185#pgen-0020185-b043" target="_blank">43</a>] and include subregions involved in binding to the core RNAP complex, promoter melting, and recognition of the −10 and −35 promoter sequences (regions 2.4 and 4.2, respectively) [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020185#pgen-0020185-b010" target="_blank">10</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020185#pgen-0020185-b040" target="_blank">40</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020185#pgen-0020185-b044" target="_blank">44</a>]. CLUSTALW was used to generate the alignment with default parameters (<a href="http://www.ebi.ac.uk/clustalw" target="_blank">http://www.ebi.ac.uk/clustalw</a>) [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020185#pgen-0020185-b045" target="_blank">45</a>].</p