23Cystic fibrosis (CF) is a genetic disorder that leads to a buildup of mucus in the 24 lungs ideal for bacterial colonization. When Pseudomonas aeruginosa enters the 25 CF lung, it undergoes a conversion from nonmucoid to mucoid; colonization by a 26 mucoid strain of P. aeruginosa greatly increases mortality.The mucoid 27 phenotype is due to the production of alginate. 44. CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/319004 doi: bioRxiv preprint first posted online May. 10, 2018; 3 phenotype was restored in 28 of the 41 sap mutants when complemented with 45 plasmids harboring algT/U. Four of the sap mutants are complemented 46 by algO. Sequence analyses of the algT/U mutants have found no mutations in 47 the coding region or promoter leading to the hypothesis that there is another, as 48 yet unidentified mechanism of alginate regulation in this clinical strain. 49. CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/319004 doi: bioRxiv preprint first posted online May. 10, 2018; 4 INTRODUCTION 50Cystic fibrosis (CF) is the most common cause of death due to genetic disorder 51(1). CF is an autosomal recessive disorder caused by a mutation in the cystic 52 fibrosis transmembrane conductance regulator (cftr) gene (2-4). The most 53 common CF mutation (~90%) is the ΔF508 which is the deletion of three 54 nucleotides leading to the loss of a phenylalanine in the 508 position, and thus, a 55 defective protein (3). A wide range of other mutations are possible that lead to 56 either impaired function or total loss of activity (5). 57Ordinarily, CFTR functions as anion transporter (6). When mutated, normal anion 58 flow is restricted (7) and mucus accumulates in the CF lung; resulting pulmonary 59 failure is the foremost killer of CF patients (8, 9) The mucus buildup provides a 60 breeding ground for many pathogenic bacterial species especially S. aureus, H. The pathogen that rises to prominence over the life of a CF patient and is the 64 leading cause of mortality is P. aeruginosa (11, 12). 65P. aeruginosa expresses a multitude of virulence factors (13). The major 66 contributor to P. aeruginosa virulence in patients with CF is its ability to change 67 from the standard, non-mucoid form to the mucoid form (14, 15 80Alginate biosynthesis comes at a high metabolic cost, and thus is tightly regulated algT/U, codes for a sigma factor able to bind to RNA polymerase (RNAP), guiding 85 it to transcribe the genes necessary for alginate production (31, 32). 86Under normal circumstances, P. aeruginosa is non-mucoid, as is the case with the 87 prototypic reference strain, PAO1 (33). Upon colonizing...

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