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Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics and organization

ABSTRACT: Dps is the most abundant nucleoid-associated protein in starved Escherichia coli with ∼180000 copies per cell. Dps binds DNA and oxidizes iron, facilitating survival in harsh environments. Dps–DNA complexes can form crystalline structures, leading to the proposed model that Dps reorganizes the starved E. coli nucleoid into a compact liquid crystal, slowing chromosome dynamics, and limiting access of other proteins to DNA. In this work, we directly tested this model using live-cell super-resolution microscopy and Hi-C analysis. We found that after 96 h of starvation, Dps compacts the nucleoid, and increases short-range DNA–DNA interactions but does not affect chromosome accessibility to large protein nanocages or small restriction enzymes. We also report that chromosome dynamics and organization are primarily impacted by the bacterial growth phase; the effect of Dps is relatively minor. Our work clarifies the role of Dps in modulating nucleoid properties, and we propose an updated model for Dps–DNA interactions in which Dps binds, protects, and compacts DNA largely without influencing chromosome access, dynamics, and organization. Additionally, this work provides a general framework for assessing the impact of nucleoid-associated proteins on key aspects of chromosome function in live cells.

ORGANISM(S): Escherichia coli str. K-12 substr. W3110

PROVIDER: GSE293552 | GEO | 2026/01/06

REPOSITORIES: GEO

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Project description:Plastids contain multiple copies of the plastid chromosome, folded together with proteins and RNA into nucleoids. The degree to which components of the plastid gene expression and protein biogenesis machineries are nucleoid associated, and the factors involved in plastid DNA organization, repair, and replication, are poorly understood. To provide a conceptual framework for nucleoid function, we characterized the proteomes of highly enriched nucleoid fractions of proplastids and mature chloroplasts isolated from the maize (Zea mays) leaf base and tip, respectively, using mass spectrometry. Quantitative comparisons with proteomes of unfractionated proplastids and chloroplasts facilitated the determination of nucleoid-enriched proteins. This nucleoid-enriched proteome included proteins involved in DNA replication, organization, and repair as well as transcription, mRNA processing, splicing, and editing. Many proteins of unknown function, including pentatricopeptide repeat (PPR), tetratricopeptide repeat (TPR), DnaJ, and mitochondrial transcription factor (mTERF) domain proteins, were identified. Strikingly, 70S ribosome and ribosome assembly factors were strongly overrepresented in nucleoid fractions, but protein chaperones were not. Our analysis strongly suggests that mRNA processing, splicing, and editing, as well as ribosome assembly, take place in association with the nucleoid, suggesting that these processes occur cotranscriptionally. The plastid developmental state did not dramatically change the nucleoid-enriched proteome but did quantitatively shift the predominating function from RNA metabolism in undeveloped plastids to translation and homeostasis in chloroplasts. This study extends the known maize plastid proteome by hundreds of proteins, including more than 40 PPR and mTERF domain proteins, and provides a resource for targeted studies on plastid gene expression. Details of protein identification and annotation are provided in the Plant Proteome Database.

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Dps binds and protects DNA in starved Escherichia coli with minimal effect on chromosome accessibility, dynamics and organization

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