An Overview of Dps: Dual Acting Nanovehicles in Prokaryotes with DNA Binding and Ferroxidation Properties

Williams, Sunanda Margrett; Chatterji, Dipankar

doi:10.1007/978-3-030-58971-4_3

Cited by 10 publications

(11 citation statements)

References 93 publications

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“…The interaction between DNA and the outer surface of protein cages is relatively well characterized in Dps proteins and, in most cases, is mediated by positively charged amino acid residues, lysine, and arginine present in the protruding N- or C- terminal flexible extensions [ 15 , 20 , 29 , 30 ]. However, in encapsulin proteins, the N-terminal regions of each monomer are positioned towards the cavity, interacting with the cargo protein, while the C-termini are part of the pore architecture and thus inaccessible for interaction.…”

Section: Discussionmentioning

confidence: 99%

Condensation and Protection of DNA by the Myxococcus xanthus Encapsulin: A Novel Function

Almeida

Carvalho

Calmeiro

et al. 2022

IJMS

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Encapsulins are protein nanocages capable of harboring smaller proteins (cargo proteins) within their cavity. The function of the encapsulin systems is related to the encapsulated cargo proteins. The Myxococcus xanthus encapsulin (EncA) naturally encapsulates ferritin-like proteins EncB and EncC as cargo, resulting in a large iron storage nanocompartment, able to accommodate up to 30,000 iron atoms per shell. In the present manuscript we describe the binding and protection of circular double stranded DNA (pUC19) by EncA using electrophoretic mobility shift assays (EMSA), atomic force microscopy (AFM), and DNase protection assays. EncA binds pUC19 with an apparent dissociation constant of 0.3 ± 0.1 µM and a Hill coefficient of 1.4 ± 0.1, while EncC alone showed no interaction with DNA. Accordingly, the EncAC complex displayed a similar DNA binding capacity as the EncA protein. The data suggest that initially, EncA converts the plasmid DNA from a supercoiled to a more relaxed form with a beads-on-a-string morphology. At higher concentrations, EncA self-aggregates, condensing the DNA. This process physically protects DNA from enzymatic digestion by DNase I. The secondary structure and thermal stability of EncA and the EncA−pUC19 complex were evaluated using synchrotron radiation circular dichroism (SRCD) spectroscopy. The overall secondary structure of EncA is maintained upon interaction with pUC19 while the melting temperature of the protein (Tm) slightly increased from 76 ± 1 °C to 79 ± 1 °C. Our work reports, for the first time, the in vitro capacity of an encapsulin shell to interact and protect plasmid DNA similarly to other protein nanocages that may be relevant in vivo.

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Section: Discussionmentioning

confidence: 99%

Condensation and Protection of DNA by the Myxococcus xanthus Encapsulin: A Novel Function

Almeida

Carvalho

Calmeiro

et al. 2022

IJMS

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“…They are composed of identical or similar alpha helical bundles, either 24 (ferritins and bacterioferritins) or 12 (Dps) in number, that assemble to form a roughly spherical protein shell surrounding a central cavity which acts as an iron storage reservoir (Figure 1). 27 The larger ferritins and bacterioferritins can accommodate around 4500 iron atoms per 24-mer, whereas the smaller Dps have a lower storage capacity of around 500 iron atoms per 12mer. 28 These proteins contain catalytic centers where the soluble Fe(II) form is oxidized to Fe(III) and deposited in the cavity as a ferric mineral.…”

Section: Oxidative Stress and Iron Homeostasismentioning

confidence: 99%

“…45 Dps homologues have a multifaceted role in bacteria, while retaining some of the classical properties of DNA binding and ferroxidation. 27 The well-studied Dps from E. coli additionally protect the cells from UV and gamma radiations, copper toxicity, thermal stress, and acid/base shock. 46 S. mutans 47 and S. pyogenes 48 do not produce a catalase enzyme responsible for H 2 O 2 elimination, but the Dps homologue present in these bacteria, namely, Dpr (Dps-like peroxide resistance), confers peroxide resistance.…”

Section: Elaborating the Role Of Dps In Iron Homeostasismentioning

confidence: 99%

Dps Functions as a Key Player in Bacterial Iron Homeostasis

Williams,

Chatterji

2023

ACS Omega

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Iron plays a vital role in the maintenance of life, being central to various cellular processes, from respiration to gene regulation. It is essential for iron to be stored in a nontoxic and readily available form. D NA b inding p roteins under s tarvation (Dps) belong to the ferritin family of iron storage proteins and are adept at storing iron in their hollow protein shells. Existing solely in prokaryotes, these proteins have the additional functions of DNA binding and protection from oxidative stress. Iron storage proteins play a functional role in storage, release, and transfer of iron and therefore are central to the optimal functioning of iron homeostasis. Here we review the multifarious properties of Dps through relevant biochemical and structural studies with a focus on iron storage and ferroxidation. We also examine the role of Dps as a possible candidate as an iron donor to iron–sulfur (Fe–S) clusters, which are ubiquitous to many biological processes.

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“…Linking derivatives of C 60 to PNCs generated water-soluble complexes. In particular, the fullerene derivative [6,6]phenyl-C 61 -butyric acid (PCBA) was activated by carbodiimide-N-hydroxysuccinimide chemistry and linked to CPMV VLPs via the solvent-exposed Lys38 residues [52]. This complex holds potential in biomedicine and exemplifies a route to the watersolubilization of hydrophobic drugs.…”

Section: Coupling With Primary Amine Groups Of Lysinementioning

confidence: 99%

“…With typical diameters in the range of 10-200 nm, PNCs can be divided into two categories by the structural component (Fig. 1): virus-like particles (VLPs) formed by viral capsid proteins [2−5] and non-viral PNCs [6,7]. PNCs usually have an inner cavity, an outer surface, and interfaces between subunits.…”

Section: Introductionmentioning

confidence: 99%

Quantitative functionalization of biosynthetic caged protein materials

et al. 2023

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Background: As one of the representative protein materials, protein nanocages (PNCs) are self-assembled supramolecular structures with multiple advantages, such as good monodispersity, biocompatibility, structural addressability, and facile production. Precise quantitative functionalization is essential to the construction of PNCs with designed purposes. Results: With three modifiable interfaces, the interior surface, outer surface, and interfaces between building blocks, PNCs can serve as an ideal platform for precise multi-functionalization studies and applications. This review summarizes the currently available methods for precise quantitative functionalization of PNCs and highlights the significance of precise quantitative control in fabricating PNC-based materials or devices. These methods can be categorized into three groups, genetic, chemical, and combined modification. Conclusion: This review would be constructive for those who work with biosynthetic PNCs in diverse fields.

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An Overview of Dps: Dual Acting Nanovehicles in Prokaryotes with DNA Binding and Ferroxidation Properties

Cited by 10 publications

References 93 publications

Condensation and Protection of DNA by the Myxococcus xanthus Encapsulin: A Novel Function

Condensation and Protection of DNA by the Myxococcus xanthus Encapsulin: A Novel Function

Dps Functions as a Key Player in Bacterial Iron Homeostasis

Quantitative functionalization of biosynthetic caged protein materials

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