title: RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family.
abstract: In the Gac/Rsm signal transduction pathway of Pseudomonas fluorescens CHA0, the dimeric RNA-binding proteins RsmA and RsmE, which belong to the vast bacterial RsmA/CsrA family, effectively repress translation of target mRNAs containing a typical recognition sequence near the translation start site. Three small RNAs (RsmX, RsmY, RsmZ) with clustered recognition sequences can sequester RsmA and RsmE and thereby relieve translational repression. According to a previously established structural model, the RsmE protein makes optimal contacts with an RNA sequence 5'- (A)/(U)CANGGANG(U)/(A)-3', in which the central ribonucleotides form a hexaloop. Here, we questioned the relevance of the hexaloop structure in target RNAs. We found that two predicted pentaloop structures, AGGGA (in pltA mRNA encoding a pyoluteorin biosynthetic enzyme) and AAGGA (in mutated pltA mRNA), allowed effective interaction with the RsmE protein in vivo. By contrast, ACGGA and AUGGA were poor targets. Isothermal titration calorimetry measurements confirmed the strong binding of RsmE to the AGGGA pentaloop structure in an RNA oligomer. Modeling studies highlighted the crucial role of the second ribonucleotide in the loop structure. In conclusion, a refined structural model of RsmE-RNA interaction accommodates certain pentaloop RNAs among the preferred hexaloop RNAs.
authors: Département de Microbiologie Fondamentale, Université de Lausanne, Bâtiment Biophore, Lausanne, Switzerland. karine.lapouge@unil.ch
authors: Karine
authors: K
authors: Lapouge
authors: Remo
authors: R
authors: Perozzo
authors: Justyna
authors: J
authors: Iwaszkiewicz
authors: Claire
authors: C
authors: Bertelli
authors: Vincent
authors: V
authors: Zoete
authors: Olivier
authors: O
authors: Michielin
authors: Leonardo
authors: L
authors: Scapozza
authors: Dieter
authors: D
authors: Haas
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D009690:Nucleic Acid Conformation; D011551:Pseudomonas fluorescens / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction
chemical_list: D001426:Bacterial Proteins; C091100:GacA protein, Bacteria; D012329:RNA, Bacterial; D012333:RNA, Messenger; D016601:RNA-Binding Proteins
keywords: CsrA/RsmA; Gac/Rsm pathway; RNA-binding protein; Shine-Dalgarno structure; translational regulation
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