The bacterial nucleoid-associated proteins, HU and Dps, condense DNA into context-dependent biphasic or multiphasic complex coacervates

Gupta, Archit; Joshi, Anjali; Arora, Kanika; Mukhopadhyay, Samrat; Guptasarma, Purnananda

doi:10.1016/j.jbc.2023.104637

Cited by 24 publications

(24 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Biomolecular condensates have emerged as a key structural feature of both eukaryotic and, more recently, bacterial chromatin 25,[65][66][67][68][69][70][71][72][73] . Diverse partners can drive chromatin condensate formation, but the role of polyphosphate, a universal and ancient inorganic polymer, has been largely overlooked in chromatin biology.…”

Section: Discussionmentioning

confidence: 99%

Reentrant DNA shells tune polyphosphate condensate size

Chawla,

Tom,

Boyd

et al. 2023

Preprint

View full text Add to dashboard Cite

The ancient, inorganic biopolymer polyphosphate (polyP) occurs in all three domains of life and affects myriad cellular processes. An intriguing feature of polyP is its frequent proximity to chromatin, and in the case of many bacteria, its occurrence in the form of magnesium-enriched condensates embedded in the nucleoid, particularly in response to stress. The physical basis of the interaction between polyP and DNA, two fundamental anionic biopolymers, and the resulting effects on the organization of both the nucleoid and polyP condensates remain poorly understood. Given the essential role of magnesium ions in the coordination of polymeric phosphate species, we hypothesized that a minimal system of polyP, magnesium ions, and DNA (polyP-Mg2+-DNA) would capture key features of the interplay between the condensates and bacterial chromatin. We find that DNA can profoundly affect polyP-Mg2+coacervation even at concentrations several orders of magnitude lower than found in the cell. The DNA forms shells around polyP-Mg2+condensates and these shells show reentrant behavior, primarily forming in the concentration range close to polyP-Mg2+charge neutralization. This surface association tunes both condensate size and DNA morphology in a manner dependent on DNA properties, including length and concentration. Our work identifies three components that could form the basis of a central and tunable interaction hub that interfaces with cellular interactors. These studies will inform future efforts to understand the basis of polyP granule composition and consolidation, as well as the potential capacity of these mesoscale assemblies to remodel chromatin in response to diverse stressors at different length and time scales.

show abstract

Section: Discussionmentioning

confidence: 99%

Reentrant DNA shells tune polyphosphate condensate size

Chawla,

Tom,

Boyd

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…In support to this model, cells with mutant SSB unable to efficiently phase separate but still able to bind ssDNA are viable in stress-free conditions but more sensitive to UV light damage than wildtype cells. 424 Biomolecular condensation of the DNA protection protein Dps shields DNA under stress conditions by its compaction into a dense complex, also acting as a global regulator of transcription 226,425 (Figure 25). Dps condensates do not prevent binding of RNAP, which has access to buried genes, but exclude some other DNA-binding proteins like restriction enzymes, the activity of which decreases with increasing Dps.…”

Section: Connections Between Phase Separation and Bacterial Fitnessmentioning

confidence: 99%

“… Two isoforms, HU-A and HU-B, contain intrinsically disordered regions and domains for homo- and heterodimerization. In vitro , these proteins form coacervates with DNA, causing phase separation, favored by PEG as crowding agent . Using fluorescently labeled HU, multiple dynamic submicron-sized condensates have been observed in E. coli cells that rearrange, probably through separation and fusion, over a time scale of a few tens of seconds.…”

Section: The Bacterial Nucleoidmentioning

confidence: 99%

“…Biomolecular condensation of the DNA protection protein Dps shields DNA under stress conditions by its compaction into a dense complex, also acting as a global regulator of transcription , (Figure ). Dps condensates do not prevent binding of RNAP, which has access to buried genes, but exclude some other DNA-binding proteins like restriction enzymes, the activity of which decreases with increasing Dps.…”

Section: Connections Between Phase Separation and Bacterial Fitnessmentioning

confidence: 99%

“…In vitro, these proteins form coacervates with DNA, causing phase separation, favored by PEG as crowding agent. 226 Using fluorescently labeled HU, multiple dynamic submicron-sized condensates have been observed in E. coli cells that rearrange, probably through separation and fusion, over a time scale of a few tens of seconds. DNA and protein concentration, increasing temperature, and lower pH and salt concentrations are among the factors that enhance the condensation of HU-B.…”

Section: The Bacterial Nucleoidmentioning

confidence: 99%

See 2 more Smart Citations

Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions

Monterroso,

Margolin,

Boersma

et al. 2024

Chem. Rev.

View full text Add to dashboard Cite

Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress. CONTENTS 1910 2.2.5. Fluidization of the Cytoplasm 1911 3. The Bacterial Nucleoid 1911 4. Crowding and Phase Separation in Membrane Environments 4.1. Remodeling of the Membrane by Crowding and Phase Separation 4.

show abstract

Oligomerization‐mediated phase separation in the nucleoid‐associated sensory protein H‐NS is controlled by ambient cues

Lukose,

Goyal,

Naganathan

2024

Protein Science

View full text Add to dashboard Cite

H‐NS, a nucleoid‐associated protein (NAP) from enterobacteria, regulates gene expression by dynamically transducing environmental cues to conformational assembly and DNA binding. In this work, we show that H‐NS from Escherichia coli, which can assemble into octameric and tetrameric oligomerization states, forms spontaneous micron‐sized liquid‐like condensates with DNA at sub‐physiological concentrations in vitro. The heterotypic condensates are metastable at 298 K, partially solubilizing with time, while still retaining their liquid‐like properties. The condensates display UCST‐like phase behavior solubilizing at higher temperatures, but with a large decrease in droplet‐assembly propensities at 310 K and at higher ionic strength. Condensate formation can be tuned in a cyclic manner between 298 and 310 K with the extent of reversibility determined by the incubation time, highlighting strong hysteresis. An engineered phospho‐mimetic variant of H‐NS (Y61E), which is dimeric and only weakly binds DNA, is unable to form condensates. The Y61E mutant solubilizes pre‐formed H‐NS condensates with DNA in a few minutes with nearly an order of magnitude speed‐up in droplet dissolution at 310 K relative to 298 K, demonstrating rapid molecular transport between dilute and condensed phases. Our results establish that the oligomerization of H‐NS is intrinsically tied not only to DNA binding but also its phase‐separation tendencies, while showcasing the regulatable and programmable nature of heterotypic condensates formed by an archetypal NAP via multiple cues and their lifetimes.

show abstract

The bacterial nucleoid-associated proteins, HU and Dps, condense DNA into context-dependent biphasic or multiphasic complex coacervates

Cited by 24 publications

References 80 publications

Reentrant DNA shells tune polyphosphate condensate size

Reentrant DNA shells tune polyphosphate condensate size

Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions

Oligomerization‐mediated phase separation in the nucleoid‐associated sensory protein H‐NS is controlled by ambient cues

Contact Info

Product

Resources

About