title: Modification of the RpoS network with a synthetic small RNA.
abstract: Translation of the sigma factor RpoS is activated by DsrA, RprA and ArcA, three small non-coding sRNAs (sRNA) that expose the ribosome-binding site (RBS) by opening up an inhibitory loop. In the RpoS network, no sRNAs have been found to pair with the RBS, a most common sRNA target site in bacteria. Here, we generate Ribo-0, an artificial sRNA, which represses rpoS translation by pairing with the RBS. Ribo-0 bypasses the RNA chaperon Hfq but requires the RBS to be loosely blocked. Ribo-0 interacts with DsrA and reshapes the RpoS network. Specifically, in the intact RpoS network, DsrA activates rpoS translation by freeing up the RBS. In the modified RpoS network where Ribo-0 is introduced, the DsrA-caused RBS exposure facilitates Ribo-0 binding, thereby strengthening Ribo-0 inhibition. In other words, Ribo-0 changes DsrA from an activator to an accomplice for repressing rpoS translation. This work presents an artificial mechanism of rpoS regulation, reveals mutual effects of native and synthetic players and demonstrates genetic context-dependency of their functions.
authors.affiliation: Department of Biochemistry, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pok Fu Lam, Hong Kong SAR, People's Republic of China, GIAT-HKU joint Center for Synthetic Biology Engineering Research, Guangzhou Institute of Advanced Technology, Chinese Academy of Sciences, Haibin Road 1121, Nansha district, Guangzhou, Guangdong province, People's Republic of China, Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, China and Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong 518035, China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Jin
authors.forename: Jianting
authors.initials: J
authors.lastname: Wu
authors.forename: Yannan
authors.initials: Y
authors.lastname: Li
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Cai
authors.forename: Jian-Dong
authors.initials: JD
authors.lastname: Huang
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D005786:Gene Expression Regulation; D015723:Gene Library; D053263:Gene Regulatory Networks; D035001:Host Factor 1 Protein / Q000378:metabolism; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000378:metabolism*; D012808:Sigma Factor / Q000235:genetics* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D035001:Host Factor 1 Protein; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria