## 3 Distribution and Frequency of QS Genes in Whole Bacterial Genomes  
It was noted very early that _luxR_ and _luxI_ genes of the same QS circuit were most often located vicinal or very near to each other in the genomes. Other instances of _luxR_ genes have also been identified in locations that are detached from QS circuits lacking a cognate N-AHL synthase. Such _luxR_ genes are termed solos [9] or orphans [39] and are thought to allow bacteria to sense, among others, environmental stimuli and/or AHLs produced by neighboring bacteria. [PERSON] _et al_. analyzed the presence and absence of _luxR_ and _luxI_ genes in 512 genomes [17] in 2007 and found that such genes were exclusively present in proteobacterial genomes. [PERSON] meanwhile, provided an excellent overview of the regulatory design principles of QS, distinguishing two chromosomal arrangements-one tandem _luxR/luxI_ arrangement called type A, and one convergent arrangement called type B [40, 41].  
We recently started to survey the topological arrangements of N-AHL-based QS genes in pseudomonads [20]. In the present review we extend upon this work and survey the main categories of topological arrangements of QS genes in currently available bacterial genome sequences. We analyzed 1,403 complete genomes using standard bioinformatics methods (see Supplementary Materials for detailed methodology). This analysis was based on the reading frames annotated by the depositing authors and showed that 169 complete genomes contained QS genes that were close to other QS genes (_i.e._, according to a distance threshold of 3,000 bp). All these were proteobacterial genomes. As the proteins encoded by _luxR_ and _luxI_ genes have spurious sequence similarities to a number of other protein families, we manually checked the length, sequence coverage and residue conservation of each similarity. We adopted this cautious approach in order to find a more reliable set of examples. For the same reason, draft genomes, solo _luxR_ genes and other orphan occurrences of QS genes were excluded from the detailed analysis. Unannotated genes were included only if they made part of a known topological arrangement. Of the 4.8 million genes we analyzed, 674 were _luxR_ genes (unannotated: 33), 294 were _luxI_ genes (unannotated: 13), 44 were rsa_L_ genes (unannotated: 16) and 37 were rsa_M_ (all were unannotated). The results of our search have been deposited to an open online repository from where the arrangements and the individual sequences can be retrieved ([[http://bacteria.itk.ppke.hu/QStopologies/](http://bacteria.itk.ppke.hu/QStopologies/)]([http://bacteria.itk.ppke.hu/QStopologies/](http://bacteria.itk.ppke.hu/QStopologies/))).  
It is a reasonable question to ask if the found occurrences reflect the frequency of QS genes in nature. We feel that this is not the case. First, we limited our analysis to cases where _luxR_ and _luxI_ genes are located near each other. Second, our analysis was based on similarity to known LuxR and LuxI proteins. Consequently, we left out lonely occurrences of luxR genes (solos), luxR genes that may control a different type of signal synthases, or signal synthases under the control of a different regulator protein. There were a few potential similarities outside the proteobacterial genomes, including the cyanobacterium _Glooeothece_ PCC6909 which was suggested to have a QS system [42]. Nevertheless, we decided to limit our analysis to proteobacterial genomes where most of the well-established examples are found. Third, the analysis was limited to complete genomes, and this is a highly biased dataset. With these limitations we found QS genes in about 12% of complete proteobacterial genomes and it would be tempting to argue that this is in agreement with the expected frequency of AHL positive strains in proteobacteria (6-12%) [17]. At the moment we think however that this apparent agreement has to be confirmed with more rigorous sampling methods.