Structural Insight of the Full-Length Ros Protein: A Prototype of the Prokaryotic Zinc-Finger Family

Gianluca D’Abrosca,Luigi Russo,Gaetano Malgieri,Marica Sassano,Roberto Fattorusso,Carla Isernia,Rinaldo Grazioso,Antonella Paladino,Emilia Maria Pedone,Ilaria Baglivo,Luciano Pirone,Rosa Iacovino,Paolo Vincenzo Pedone

doi:10.1038/s41598-020-66204-5

Gianluca D’Abrosca, Luigi Russo + Show 11 more

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https://doi.org/10.1038/s41598-020-66204-5

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Abstract

Ros/MucR is a widespread family of bacterial zinc-finger (ZF) containing proteins that integrate multiple functions such as virulence, symbiosis and/or cell cycle transcription. NMR solution structure of Ros DNA-binding domain (region 56–142, i.e. Ros87) has been solved by our group and shows that the prokaryotic ZF domain shows interesting structural and functional features that differentiate it from its eukaryotic counterpart as it folds in a significantly larger zinc-binding globular domain. We have recently proposed a novel functional model for this family of proteins suggesting that they may act as H-NS-‘like’ gene silencers. Indeed, the N-terminal region of this family of proteins appears to be responsible for the formation of functional oligomers. No structural characterization of the Ros N-terminal domain (region 1–55) is available to date, mainly because of serious solubility problems of the full-length protein. Here we report the first structural characterization of the N-terminal domain of the prokaryotic ZF family examining by means of MD and NMR the structural preferences of the full-length Ros protein from Agrobacterium tumefaciens.

Highlights

Ros/MucR is a widespread family of bacterial zinc-finger (ZF) containing proteins that integrate multiple functions such as virulence, symbiosis and/or cell cycle transcription
We have recently proposed a novel functional model for the prokaryotic zinc-finger (ZF) proteins belonging to the Ros/MucR family:[23,24,25] they act as Histone-like Nucleoid-Structuring (H-NS)-‘like’ gene silencers[26,27] by binding low consensus AT rich regions in DNA rather than functioning like their eukaryotic counterparts that mainly act as DNA sequence-specific transcriptional regulators
Structural and functional similarities and differences between the prokaryotic and the eukaryotic ZF have been largely documented[3,29,30,31,32,33,34,35,36,37]: the two domains are similar in the tetrahedral coordination of a structural zinc ion[38] and in the existence of a ββα topology surrounding it while they differ in the fact that the prokaryotic ZF shows a second α-helix and a larger hydrophobic core

Summary

Introduction

Ros/MucR is a widespread family of bacterial zinc-finger (ZF) containing proteins that integrate multiple functions such as virulence, symbiosis and/or cell cycle transcription. We have recently proposed a novel functional model for the prokaryotic zinc-finger (ZF) proteins belonging to the Ros/MucR family:[23,24,25] they act as H-NS-‘like’ gene silencers[26,27] by binding low consensus AT rich regions in DNA rather than functioning like their eukaryotic counterparts that mainly act as DNA sequence-specific transcriptional regulators. Structural and functional similarities and differences between the prokaryotic and the eukaryotic ZF have been largely documented[3,29,30,31,32,33,34,35,36,37]: the two domains are similar in the tetrahedral coordination of a structural zinc ion[38] and in the existence of a ββα topology surrounding it while they differ in the fact that the prokaryotic ZF shows a second α-helix and a larger hydrophobic core. We report the first structural characterization of the N-terminal oligomerization domain of the prokaryotic ZF family investigating the structural preferences of the full-length Ros protein from Agrobacterium tumefaciens by means of Molecular Dynamics studies and Nuclear Magnetic Resonance experiments

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