Editing Operon (section)

== Predicting the number and organization of operons ==

The number and organization of operons has been studied most critically in ''[[Escherichia coli|E. coli]]''. As a result, predictions can be made based on an organism's genomic sequence.

One prediction method uses the intergenic distance between reading frames as a primary predictor of the number of operons in the genome. The separation merely changes the frame and guarantees that the read through is efficient. Longer stretches exist where operons start and stop, often up to 40–50 bases.<ref>{{cite journal | vauthors = Salgado H, Moreno-Hagelsieb G, Smith TF, Collado-Vides J | title = Operons in Escherichia coli: genomic analyses and predictions | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 97 | issue = 12 | pages = 6652–7 | date = June 2000 | pmid = 10823905 | pmc = 18690 | doi = 10.1073/pnas.110147297 | bibcode = 2000PNAS...97.6652S | doi-access = free }}</ref>

An alternative method to predict operons is based on finding gene clusters where gene order and orientation is conserved in two or more genomes.<ref>{{cite journal | vauthors = Ermolaeva MD, White O, Salzberg SL | title = Prediction of operons in microbial genomes | journal = Nucleic Acids Research | volume = 29 | issue = 5 | pages = 1216–21 | date = March 2001 | pmid = 11222772 | pmc = 29727 | doi = 10.1093/nar/29.5.1216 }}</ref>

Operon prediction is even more accurate if the functional class of the molecules is considered. Bacteria have clustered their reading frames into units, sequestered by co-involvement in protein complexes, common pathways, or shared substrates and transporters. Thus, accurate prediction would involve all of these data, a difficult task indeed.

[[Pascale Cossart]]'s laboratory was the first to experimentally identify all operons of a microorganism, ''[[Listeria monocytogenes]]''.  The 517 polycistronic operons are listed in a 2009 study describing the global changes in transcription that occur in ''L. monocytogenes'' under different conditions.<ref>{{cite journal | vauthors = Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy M, Vergassola M, Nahori MA, Soubigou G, Régnault B, Coppée JY, Lecuit M, Johansson J, Cossart P | title = The Listeria transcriptional landscape from saprophytism to virulence | journal = Nature | volume = 459 | issue = 7249 | pages = 950–6 | date = June 2009 | pmid = 19448609 | doi = 10.1038/nature08080 | bibcode = 2009Natur.459..950T | s2cid = 4341657 }}</ref>