title: Secondary structure of antisense RNAβ, an internal transcriptional terminator of the plasmid-encoded iron transport-biosynthesis operon of Vibrio anguillarum.
abstract: RNAβ affects the transcription process of the iron transport-biosynthesis operon encoded in the pJM1 plasmid of Vibrio anguillarum at a stem-loop structure located in the intergenic region between the fatA and angR genes. The net result is a higher level of the fatD, fatC, fatB, and fatA moiety as compared with the longer transcript encoding those genes as well as the angR and angT genes. In this work we report the secondary structure of RNAβ determined by treatment with single and double strand specific ribonucleases as well as lead acetate followed by sequencing. The generated in vitro structural data indicated that three of the four previously described loops are in agreement with the original model, however, the alteration of loop IV as well as several other structural differences in the overall shape of the molecule led to the necessity of creating a new in silico model. Using the sites of mutations in the various loops we modeled the change in the RNAβ secondary structure induced by those mutations. Mutations of loops III and IV to their complementary bases alter the overall structure of the RNAβ significantly and increase its function while mutations in loops I and II have the opposite effect, the structure is unchanged but the activity of RNAβ decreases. This indicates that loops I and II are necessary for interaction with the target mRNA. It is possible that the structural rearrangement introduced by mutations in loops III and IV promote activity and binding in loops I and II through reducing steric hindrance or increased binding to the target. This result also indicates that the exact relative positions of the critical loops are unimportant for activity.
authors.affiliation: Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: McIntosh-Tolle
authors.forename: Michiel
authors.initials: M
authors.lastname: Stork
authors.forename: Alejandro
authors.initials: A
authors.lastname: Alice
authors.forename: Jorge H
authors.initials: JH
authors.lastname: Crosa
mesh_terms: D001692:Biological Transport; D007501:Iron / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D009876:Operon / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D016372:RNA, Antisense / Q000737:chemistry* / Q000235:genetics*; D014733:Vibrio / Q000235:genetics* / Q000378:metabolism*
chemical_list: D016372:RNA, Antisense; D007501:Iron