The Histone H1-Like Protein AlgP Facilitates Even Spacing of Polyphosphate Granules in Pseudomonas aeruginosa

Chawla, Ravi; Klupt, Steven; Patsalo, Vadim; Williamson, James R.; Racki, Lisa R.

doi:10.1128/mbio.02463-21

Cited by 11 publications

(6 citation statements)

References 70 publications

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“…NAPs may also modulate the partition of DNA between the surface and the interior, change the properties of the condensates, and provide additional interactions that substitute for and compete with interactions with cations. For example, the histone H1-like protein AlgP in P. aeruginosa , which has a +55 charge at neutral pH, localizes to the granules and alters their consolidation dynamics 26 . Furthermore, our results indicate that other polyvalent cationic species, including other divalent cations, whose concentrations can vary in response to both extracellular and intracellular cues, can likely mediate and tune polyP granule formation, as well as their interactions with DNA and materials properties, and will be an exciting avenue for future investigation.…”

Section: Discussionmentioning

confidence: 99%

“…Recent work also demonstrates that polyphosphate drives heterochromatin formation in E. coli by modulating the DNA-binding affinity of nucleoid associated proteins (NAPs) like Hfq 25 . We previously found that polyP granules in P. aeruginosa are enriched in specific DNA binding proteins, including the histone H1-like protein AlgP 26 . Together, these observations implicate polyP condensates as an important feature of bacterial chromatin.…”

Section: Introductionmentioning

confidence: 99%

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Reentrant DNA shells tune polyphosphate condensate size

Chawla,

Tom,

Boyd

et al. 2023

Preprint

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Reentrant DNA shells tune polyphosphate condensate size

Chawla,

Tom,

Boyd

et al. 2023

Preprint

Self Cite

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“…Little is known about the ultrastructure of the granules where poly-P is accumulated and where the machinery for making poly-P should be associated. Distinct proteome and biochemical analysis have identified several proteins bound to the poly-P granules, such as the histone-like protein AlgP from P. aeruginosa (50) or proteins carrying the positively-charged C onserved H istidine α -helical D omain (CHAD) in Ralstonia eutropha , Magnetospirillum gryphiswaldense and P. putida (51). Diverse Ppk enzymes are also associated with poly-P granules in R. eutropha (52), Caulobacter crescentus (53) or P. aeruginosa (50), but Ppx has not been yet identified in these kind of analyses (50).…”

Section: Discussionmentioning

confidence: 99%

Ppx1 putative exopolyphosphatase is essential for polyphosphate accumulation inLacticaseibacillus paracasei

Corrales,

Alcántara,

Zúñiga

et al. 2023

Preprint

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The linear polymer polyphosphate (poly-P) is present across all three domains of life and serves diverse physiological functions. The enzyme polyphosphate kinase (Ppk) is responsible for poly-P synthesis, whereas poly-P degradation is carried out by the enzyme exopolyphosphatase (Ppx). In manyLactobacillaceae, the Ppk-encoding gene (ppk) is found clustered together with two genes encoding putative exopolyphosphatases (ppx1andppx2) each having different domain compositions, with the gene orderppx1-ppk-ppx2. However, the specific function of theseppxgenes remains unexplored. An in-frame deletion ofppx1inLacticaseibacillus paracaseiBL23 resulted in bacteria unable to accumulate poly-P, whereas disruption ofppx2had no effect on poly-P synthesis. Expression ofppkwas not altered in the Δppx1strain, and poly-P synthesis in this strain was only restored by expressingppx1intrans. Moreover, no poly-P synthesis was observed whenppkwas expressed from a plasmid in the Δppx1strain. Purified Ppx2 exhibitedin vitroexopolyphosphatase activity, whereas noin vitroenzymatic activity could be demonstrated for Ppx1. This observation corresponds with the absence in Ppx1 of conserved motifs essential for catalysis found in characterized exopolyphosphatases. Furthermore, assays with purified Ppk and Ppx1 evidenced that Ppx1 enhanced Ppk activity. These results demonstrate that Ppx1 is essential for poly-P synthesis inLc. paracaseiand have unveiled, for the first time, an unexpected role of Ppx1 exopolyphosphatase in poly-P synthesis.ImportancePoly-P is a pivotal molecular player in bacteria, participating in a diverse array of processes ranging from stress resilience to pathogenesis, while also serving as a functional component in probiotic bacteria. The synthesis of poly-P is tightly regulated, but the underlying mechanisms remain incompletely elucidated. Our study sheds light on the distinctive role played by the two exopolyphosphatases (Ppx) found in theLactobacillaceaebacterial group, of relevance in food and health. This particular group is noteworthy for possessing two Ppx enzymes, supposedly involved in poly-P degradation. Remarkably, our investigation uncovers an unprecedented function of Ppx1 inLacticaseibacillus paracasei, where its absence leads to the total cessation of poly-P synthesis, paralleling the impact observed upon eliminating the poly-P forming enzyme, poly-P kinase. Unlike the anticipated role as a conventional exopolyphosphatase, Ppx1 demonstrates an unexpected function. Our results added a layer of complexity to our understanding of poly-P dynamics in bacteria.

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“…Therefore, Sc10g003170 ( MetRS ) might modulate N accumulation through modulation of extensive protein synthesis, and the direct targets and underlying mechanism need to be further revealed in the future. The transcriptional regulatory protein AlgP is a DNA‐binding protein, that is widely involved in gene expression regulation (Chawla et al., 2022). In the present study, we found that Sc18g015190 ( AlgP ) might modulate P concentration via transcriptional and post‐transcriptional reprogramming in cassava, and the underlying transcriptional modules need to be further investigated.…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide association studies reveal genetic basis of ionomic variation in cassava

Yin

Yan

et al. 2022

The Plant Journal

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SUMMARY As one of the most important food crops, cassava (Manihot esculenta) is the main dietary source of micronutrients for about 1 billion people. However, the ionomic variation in cassava and the underlying genetic mechanisms remain unclear so far. Herein, genome‐wide association studies were performed to reveal the specific single nucleotide polymorphisms (SNPs) that affect the ionomic variation in cassava. We identified 164 SNPs with P‐values lower than the threshold located in 88 loci associated with divergent ionomic variations. Among them, 13 SNPs are related to both calcium (Ca) and magnesium (Mg), and many loci for different ionomic traits seem to be clustered on specific chromosome regions. Moreover, we identified the peak SNPs in the promoter regions of Sc10g003170 (encoding methionyl‐tRNA synthetase [MetRS]) and Sc18g015190 (encoding the transcriptional regulatory protein AlgP) for nitrogen (N) and phosphorus (P) accumulation, respectively. Notably, these two SNPs (chr10_32807962 and chr18_31343738) were directly correlated with the transcript levels of Sc10g003170 (MetRS) and Sc18g015190 (AlgP), which positively modulated N accumulation and P concentration in cassava, respectively. Taken together, this study provides important insight into the genetic basis of cassava natural ionomic variation, which will promote genetic breeding to improve nutrient use and accumulation of elements in cassava.

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The Histone H1-Like Protein AlgP Facilitates Even Spacing of Polyphosphate Granules in Pseudomonas aeruginosa

Abstract: The mechanisms underpinning polyP’s pleiotropic effects on bacterial starvation physiology remain elusive. This simple polyanion’s lack of protein binding specificity has impeded validation of bona fide polyP-binding proteins.

Cited by 11 publications

References 70 publications

Reentrant DNA shells tune polyphosphate condensate size

Reentrant DNA shells tune polyphosphate condensate size

Ppx1 putative exopolyphosphatase is essential for polyphosphate accumulation inLacticaseibacillus paracasei

Genome‐wide association studies reveal genetic basis of ionomic variation in cassava

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