## 4 Topological Arrangements of QS Genes in Bacterial Genomes
\begin{table}
\begin{tabular}{l l l l l l l l} \hline \hline \multirow{2}{*}{**ID**} & \multirow{2}{*}{**Pattern**} & \multirow{2}{*}{**Gene topology**} & \multicolumn{6}{c}{**Occurrence in complete Proteobacteriaial genomes**} \\ \cline{5-8}  & & & **Total** & **alpha** & **beta** & **gamma** & **delta** \\ \hline \multicolumn{8}{c}{**Short, conserved topological patterns**} \\ \hline
**R1** & \(\vec{R}\vec{I}\) & \(\vec{R}\vec{I}\) & 96 & 71 & 14 & 11 & 0 \\
**R2** & \(\vec{R}\vec{I}\) & \(\vec{R}\vec{I}\) & 53 & 2 & 2 & 46 & 3 \\
**R3** & \(\vec{R}\vec{I}\) & \(\vec{R}\vec{I}\) & 11 & 1 & 3 & 7 & 0 \\
**R4** & \(\vec{I}\vec{R}\) & \(\vec{I}\vec{R}\) & 2 & 2 & 0 & 0 & 0 \\
**L1** & \(\vec{R}\vec{L}\vec{I}\) & \(\vec{R}\vec{L}\vec{I}\) & 15 & 0 & 7 & 8 & 0 \\
**M1** & \(\vec{R}\vec{M}\vec{I}\) & \(\vec{R}\vec{I}\) & 30 & 0 & 20 & 10 & 0 \\
**M2** & \(\vec{R}\vec{M}\vec{I}\) & \(\vec{R}\vec{I}\) & 1 & 0 & 1 & 0 & 0 \\
**X1** & \(\vec{R}\vec{X}\vec{I}\) & \(\vec{R}\vec{I}\) & \(\vec{R}\vec{I}\) & 1 & 0 & 0 & 1 & 0 \\
**X2** & \(\vec{R}\vec{X}\vec{I}\) & \(\vec{R}\vec{I}\) & \(\vec{R}\vec{I}\) & 2 & 2 & 0 & 0 & 0 \\
**X3** & \(\vec{R}\vec{X}\vec{I}\) & \(\vec{R}\vec{I}\) & \(\vec{R}\vec{I}\) & 4 & 0 & 2 & 2 & 0 \\
**X4** & \(\vec{R}\vec{X}\vec{I}\) & \(\vec{R}\vec{I}\) & \(\vec{x}\vec{I}\) & 1 & 1 & 0 & 0 & 0 \\
**X5** & \(\vec{R}\vec{X}\vec{I}\) & \(\vec{R}\vec{I}\) & \(\vec{x}\vec{I}\) & 2 & 1 & 1 & 0 & 0 \\ \hline \multicolumn{8}{c}{**Longer, unusual topological patterns**} \\ \hline
**M3** & \(\vec{R}X(2\)–\(11)\vec{M}\vec{I}\) & \(\vec{R}\vec{I}\) & \(\vec{R}\vec{I}\) & 6 & 0 & 6 & 0 & 0 \\
**M’** & \(\vec{M}\vec{I}\) & \(\vec{M}\vec{I}\) & 2 & 0 & 2 & 0 & 0 \\
**X6** & \(\vec{R}\vec{X}(7)\vec{I}\) & \(\vec{R}\vec{I}\) & \(\vec{R}\vec{I}\) & 1 & 1 & 0 & 0 & 0 \\
**X7** & \(\vec{I}X(>7)\vec{R}\) & \(\vec{I}\vec{I}\) & \(\vec{R}\vec{I}\) & \(\vec{R}\vec{I}\) & 5 & 5 & 0 & 0 & 0 \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Typical topological patterns found in complete bacterial genomes. a single intervening gene between the _luxR_ and _luxI_ genes. These intervening genes show interesting commonalities in terms of function (Table 2). Out of 48 such single intervening genes 11 code RsaL and 29 code RsaM proteins that are both known to negatively regulate quorum sensing. In both cases of these proteins, typical topologies were observed: \(\vec{RLI}\) and \(\vec{RMI}\), respectively. RsaL (\(L\) in our notation), is a member of the tetra helical superclass of H-T-H proteins [46] which are recognized as widespread QS repressors in bacteria, binding to DNA as dimers. For example, RsaL (which is predominant in pseudomonad genomes [47]) in _P. aeruginosa_ prevents expression of the \(R\) gene by binding to DNA next to the _lux_-box [21]. In our analysis we also found that homologues of RsaL frequently occur outside QS circuits in various bacterial genomes (data not shown). The significance of this is not clear at this stage. In contrast, we found that RsaM (\(M\) in our notation), a protein of unknown structure that negatively regulates QS in _P. fuscovaginae_[21], seems to only occur in the context of QS circuits (see also [48]). Even though RsaM seems to occur mainly in the \(\vec{RMI}\) arrangement, it also appears in a number of other topologies (M1, M2 and M3; Table 1). Of the rest of the X genes found in RXI topology, _mupX_ of _P. fluorescein_ NCIMB10586 is an amidase-hydrolase, which is able to digest/degrade the AHL signal of the same species [49]. MupX can therefore also be considered as a negative QS regulator. From the rest of the X genes, two are involved in DNA-mobilization (an integrase and a transposase), and the rest are hypothetical proteins of unknown function. Conserved gene overlaps are another commonality observed in short, conserved topologies. In our analysis, two topologies were found to contain this feature, namely \(\vec{RLI}\) (L1) and the \(\vec{RI}\) (R2), which occurred in 15 and 53 proteobacterial genomes respectively.