The First Structure of Polarity Suppression Protein, Psu from Enterobacteria Phage P4, Reveals a Novel Fold and a Knotted Dimer

Banerjee, Rita; Nath, Seema; Ranjan, Amitabh; Khamrui, Susmita; Pani, Bibhusita; Sen, Ranjan; Sen, U.

doi:10.1074/jbc.m112.423202

Cited by 19 publications

(35 citation statements)

References 24 publications

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“…On activation of OH-radical generation, we observed that only Fe-BABE conjugated to the 181 position of Psu produced two cleavage products near/at 153 and 205 amino acids positions of Rho (Figure 3B). This cleavage product arose due to the vicinity of this C-terminal helix 7 [marked in red, Figure 3A (12)] of Psu to Rho, and it is consistent with the functional importance of this helix in the anti-termination process (11). The cleavage site on Rho, the amino acid 153, is located close to the position of N151D suppressor.…”

Section: Resultssupporting

confidence: 66%

“…(i) The distance between the two C-terminal tail located diametrically opposite direction from the ‘V’-shaped structure of Psu dimer [(12) Supplementary Figure S7A)]. (ii) The electron microgram of a Psu dimer covering the central hole of the hexameric capsid protein, Sid [(7) Supplementary Figure S7B)].…”

Section: Resultsmentioning

confidence: 99%

“…(iii) Interacting regions defined by the genetic and biochemical data described in Figures 1–5. (iv) The Rho-interacting regions of Psu [Figure 3A; (11,12)]. (v) Inhibition of ATP binding as well as ATPase activity of Rho by Psu (10).…”

Section: Resultsmentioning

confidence: 99%

“…Mutational analyses showed that Psu C-terminal is important for its function, and its N-terminal is required to maintain the structural integrity (11). Recent crystal structure of Psu revealed that it is an α-helical, V-shaped knotted dimer (12) that directly binds to Rho through its C-terminal helix 7 (11). …”

Section: Introductionmentioning

confidence: 99%

“…In this report, using both in vivo and in vitro techniques, we described a conserved looped out structure, encompassing 139–153 amino acids of Rho, as the primary docking site for Psu, and a neighbouring helical structure, spanning the 347–354 amino acids of Rho, plays a supportive role. Based on the conformation of Psu on the capsid structure of the P4 phage (7), its crystal structure (12), and the experimentally determined interacting regions of Rho and Psu, we have built a structural model of a Rho (hexamer): Psu (dimer) complex. In this model, a dimer of Psu forms a ‘lid’ on the central channel of the hexameric Rho.…”

Section: Introductionmentioning

confidence: 99%

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Structural and mechanistic basis of anti-termination of Rho-dependent transcription termination by bacteriophage P4 capsid protein Psu

Ranjan¹,

Sharma²,

Banerjee³

et al. 2013

Nucleic Acids Research

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The conserved bacterial transcription terminator, Rho, is a potent target for bactericidal agents. Psu, a bacteriophage P4 capsid protein, is capable of inducing anti-termination to the Rho-dependent transcription termination. Knowledge of structural and mechanistic basis of this anti-termination is required to design peptide-inhibitor(s) of Rho from Psu. Using suppressor genetics, cross-linking, protein foot-printing and FRET analyses, we describe a conserved disordered structure, encompassing 139–153 amino acids of Rho, as the primary docking site for Psu. Also a neighbouring helical structure, comprising 347–354 amino acids, lining its central channel, plays a supportive role in the Rho–Psu complex formation. Based on the crystal structure of Psu, its conformation in the capsid of the P4 phage, and its interacting regions on Rho, we build an energy-minimized structural model of the Rho:Psu complex. In this model, a V-shaped dimer of Psu interacts with the two diagonally opposite subunits of a hexameric Rho, enabling Psu to form a ‘lid’ on the central channel of the latter. We show that this configuration of Psu makes the central channel of Rho inaccessible, and it causes a mechanical impediment to its translocase activity.

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Section: Resultssupporting

confidence: 66%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Structural and mechanistic basis of anti-termination of Rho-dependent transcription termination by bacteriophage P4 capsid protein Psu

Ranjan¹,

Sharma²,

Banerjee³

et al. 2013

Nucleic Acids Research

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Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

Ghosh

Sharma

Kumar

et al. 2021

Journal of Biological Chemistry

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The transcription terminator Rho regulates many physiological processes in bacteria, such as antibiotic sensitivity, DNA repair, RNA remodeling, and so forth, and hence, is a potential antimicrobial target, which is unexplored. The bacteriophage P4 capsid protein, Psu, moonlights as a natural Rho antagonist. Here, we report the design of novel peptides based on the C-terminal region of Psu using phenotypic screening methods. The resultant 38-mer peptides, in addition to containing mutagenized Psu sequences, also contained plasmid sequences, fused to their C termini. Expression of these peptides inhibited the growth of Escherichia coli and specifically inhibited Rhodependent termination in vivo. Peptides 16 and 33 exhibited the best Rho-inhibitory properties in vivo. Direct high-affinity binding of these two peptides to Rho also inhibited the latter's RNA-dependent ATPase and transcription termination functions in vitro. These two peptides remained functional even if eight to ten amino acids were deleted from their C termini. In silico modeling and genetic and biochemical evidence revealed that these two peptides bind to the primary RNA-binding site of the Rho hexamer near its subunit interfaces. In addition, the gene expression profiles of these peptides and Psu overlapped significantly. These peptides also inhibited the growth of Mycobacteria and inhibited the activities of Rho proteins from Mycobacterium tuberculosis, Xanthomonas, Vibrio cholerae, and Salmonella enterica. Our results showed that these novel anti-Rho peptides mimic the Rho-inhibition function of the 42-kDa dimeric bacteriophage P4 capsid protein, Psu. We conclude that these peptides and their C-terminal deletion derivatives could provide a basis on which to design novel antimicrobial peptides.

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Peptides designed from a bacteriophage capsid protein function as synthetic transcription repressors

Sharma,

Jain,

Sen

2023

Journal of Biological Chemistry

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The First Structure of Polarity Suppression Protein, Psu from Enterobacteria Phage P4, Reveals a Novel Fold and a Knotted Dimer

Cited by 19 publications

References 24 publications

Structural and mechanistic basis of anti-termination of Rho-dependent transcription termination by bacteriophage P4 capsid protein Psu

Structural and mechanistic basis of anti-termination of Rho-dependent transcription termination by bacteriophage P4 capsid protein Psu

Design of novel peptide inhibitors against the conserved bacterial transcription terminator, Rho

Peptides designed from a bacteriophage capsid protein function as synthetic transcription repressors

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