Structural Basis of RNA Binding Discrimination between Bacteriophages Qβ and MS2

Horn, W.T.; Tars, K.; Grahn, E.; Helgstrand, Charlotte; Baron, Andrew J.; Lago, H.; Adams, Chris J.; Peabody, David S.; Phillips, Simon E. V.; Stonehouse, Nicola J.; Liljas, Lars; Stockley, Peter G.

doi:10.1016/j.str.2005.12.006

Cited by 33 publications

(36 citation statements)

References 36 publications

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“…The complex has provided a wealth of structural data on the basis of the sequence-specific recognition events. 7,9,11 The TR sequence encompasses the start codon of the viral replicase, and CP dimer binding leads to translational repression of this cistron. Complex formation also results in an allosteric conformational change within the protein, taking it from a largely symmetric structure to an asymmetric one.…”

Section: Introductionmentioning

confidence: 99%

Single-Molecule Fluorescence Resonance Energy Transfer Assays Reveal Heterogeneous Folding Ensembles in a Simple RNA Stem–Loop

Gell

Sabir

Westwood

et al. 2008

Journal of Molecular Biology

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Section: Introductionmentioning

confidence: 99%

Single-Molecule Fluorescence Resonance Energy Transfer Assays Reveal Heterogeneous Folding Ensembles in a Simple RNA Stem–Loop

Gell

Sabir

Westwood

et al. 2008

Journal of Molecular Biology

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“…Biochemical experiments have shown that both coat proteins bind their own RNA hairpins with high affinity (K d ~ 1 nM) and are able to discriminately bind in favor of their own RNA by ~1,000-fold 3,4 . In contrast to the PP7 coat protein, the Qβ coat protein also shares low sequence identity (21%) with the MS2 coat protein, yet it uses an RNAbinding mode similar to that of the MS2 coat protein [5][6][7] Fig. 1 and Supplementary Methods online).…”

mentioning

confidence: 99%

Structural basis for the coevolution of a viral RNA–protein complex

Chao

Patskovsky

Almo

et al. 2007

Nat Struct Mol Biol

228

213

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The cocrystal structure of the PP7 bacteriophage coat protein in complex with its translational operator identifies a distinct mode of sequence-specific RNA recognition when compared to the well-characterized MS2 coat protein-RNA complex. The structure reveals the molecular basis of the PP7 coat protein's ability to selectively bind its cognate RNA, and it demonstrates that the conserved β-sheet surface is a flexible architecture that can evolve to recognize diverse RNA hairpins.The inherent sequence diversity generated by RNA replication, which allows RNA viruses to evolve, must be tempered by the need for conservation of functional elements within the viral genome. The coat proteins of single-stranded (ss) RNA bacteriophages have both structural and regulatory roles in the viral life cycle, as they assemble into the mature capsid and regulate translation of the phage replicase through binding and sequestration of an RNA hairpin that contains the initiation site 1 . The coat protein and translational operator form a pair that must coevolve, so that mutation in one must be accompanied by compensatory mutations in the other. The Pseudomonas aeruginosa bacteriophage PP7 is a model system for exploring coevolution because of the extensive sequence divergence of both the PP7 coat protein and translational operator from other ssRNA bacteriophages 2 . The PP7 and MS2 coat proteins share only 15% sequence identity, and their cognate RNA hairpins differ in the position of the bulged adenosine as well as in the size and nucleotide composition of the loop (Fig. 1a). Biochemical experiments have shown that both coat proteins bind their own RNA hairpins with high affinity (K d ~ 1 nM) and are able to discriminately bind in favor of their own RNA by ~1,000-fold 3,4 . In contrast to the PP7 coat protein, the Qβ coat protein also shares low sequence identity (21%) with the MS2 coat protein, yet it uses an RNAbinding mode similar to that of the MS2 coat protein [5][6][7] Fig. 1 and Supplementary Methods online). PP7ΔFG was generated by removing residues 67-75 and, notably, this truncation binds its translational operator with affinity similar to that of the fulllength protein ( Supplementary Fig. 2 online). The PP7ΔFG monomer adopts the topology characteristic of ssRNA bacteriophage coat proteins, with an N-terminal β hairpin, a fivestranded antiparallel β sheet and two C-terminal α helices ( Supplementary Fig. 3a online) [8][9][10][11] . Antiparallel association of protomers in the dimer positions the last β strands adjacent to one another, resulting in a ten-stranded β sheet that comprises the RNA-binding surface. The interwoven packing of the α helices between each other and the N-terminal β hairpins further stabilizes the dimer, combining with the β sheet interface to bury ~3,000 Å 2 of solvent-accessible surface area. The PP7ΔFG dimer has almost identical free and bound structures (r.m.s. deviation < 0.9 Å for all Cα atoms) and is similar to that of the MS2 coat protein (r.m.s. deviation of < 2.3 Å for all Cα atoms...

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“…3) strongly resembled each other. The ␤-sheets E, F, and G (RNA binding region) (10,13) and the interacting C-terminal helixes especially were conserved. The greatest differences were in the flexible loop regions.…”

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confidence: 99%

Complete Genome Sequence of the Broad Host Range Single-Stranded RNA Phage PRR1 Places It in the Levivirus Genus with Characteristics Shared with Alloleviviruses

Ruokoranta

Grahn

Ravantti

et al. 2006

J Virol

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Single-stranded RNA (ssRNA) bacteriophages of the family Leviviridae infect gram-negative bacteria. They are restricted to a single host genus. Phage PRR1 is an exception, having a broad host range due to the promiscuity of the receptor encoded by the IncP plasmid. Here we report the complete genome sequence of PRR1. Three proteins homologous with those of other ssRNA phages, i.e., maturation, coat, and replicase proteins, were identified. A fourth protein has a lysis function. Comparison of PRR1 with other members of the Leviviridae family places PRR1 in the genus Levivirus with some characteristics more similar to those of members of the genus Allolevivirus.

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Structural Basis of RNA Binding Discrimination between Bacteriophages Qβ and MS2

Cited by 33 publications

References 36 publications

Single-Molecule Fluorescence Resonance Energy Transfer Assays Reveal Heterogeneous Folding Ensembles in a Simple RNA Stem–Loop

Single-Molecule Fluorescence Resonance Energy Transfer Assays Reveal Heterogeneous Folding Ensembles in a Simple RNA Stem–Loop

Structural basis for the coevolution of a viral RNA–protein complex

Complete Genome Sequence of the Broad Host Range Single-Stranded RNA Phage PRR1 Places It in the Levivirus Genus with Characteristics Shared with Alloleviviruses

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