SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions

Santos, Sandra P.; Cuypers, M.G.; Round, Adam; Finet, Stéphanie; Narayanan, Theyencheri; Mitchell, Edward P.; Romão, Célia V.

doi:10.1016/j.jmb.2017.01.008

Cited by 15 publications

(15 citation statements)

References 50 publications

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“…Dps1 has a longer N-terminal extension (54 amino acids) before the ferritin fold compared to other Dps, which is essential for stabilising the protein–DNA complex (Santos et al. 2017). The N-terminal extension region is observed in all of the Dps1 homologues (Fig.…”

Section: Oxidative Stress Defence In Deinococcusmentioning

confidence: 99%

“…Although there is some variation of sequences and amino acid composition, the N-terminal extension is rich in positively charged residues, in particular lysine and has been proposed to be involved in the association with DNA (Santos et al. 2017). Similar N-terminal lysine-rich extensions are present in nucleoid-associated HU proteins of Deinococcus (Bouthier de la Tour et al.…”

Section: Oxidative Stress Defence In Deinococcusmentioning

confidence: 99%

See 1 more Smart Citation

Conservation and diversity of radiation and oxidative stress resistance mechanisms inDeinococcusspecies

Lim

Jung

Blanchard

et al. 2018

FEMS Microbiology Reviews

163

140

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Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.

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Section: Oxidative Stress Defence In Deinococcusmentioning

confidence: 99%

Section: Oxidative Stress Defence In Deinococcusmentioning

confidence: 99%

Conservation and diversity of radiation and oxidative stress resistance mechanisms inDeinococcusspecies

Lim

Jung

Blanchard

et al. 2018

FEMS Microbiology Reviews

163

140

View full text Add to dashboard Cite

show abstract

“…Adding to this, its non-cytoplasmic localization and the fact that iron localizes in the septum region, suggests that Dps2 can be involved in Fe-sequestering 4,20 . Recently we showed that D. radiodurans has two dodecameric forms of Dps2, one associated with the membrane (Dps2 M ) and another present in the cytoplasm (Dps2 C ) 22 , suggesting that Dps2 may be involved in Fe-trafficking.…”

Section: Introductionmentioning

confidence: 99%

The interplay between Mn and Fe in Deinococcus radiodurans triggers cellular protection during paraquat-induced oxidative stress

Santos

Yang

Rosa

et al. 2019

Sci Rep

Self Cite

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The bacterium Deinococcus radiodurans is highly resistant to several stress conditions, such as radiation. According to several reports, manganese plays a crucial role in stress protection, and a high Mn/Fe ratio is essential in this process. However, mobilization of manganese and iron, and the role of DNA-binding-proteins-under-starved-conditions during oxidative-stress remained open questions. We used synchrotron-based X-ray fluorescence imaging at nano-resolution to follow element-relocalization upon stress, and its dependency on the presence of Dps proteins, using dps knockout mutants. We show that manganese, calcium, and phosphorus are mobilized from rich-element regions that resemble electron-dense granules towards the cytosol and the cellular membrane, in a Dps-dependent way. Moreover, iron delocalizes from the septum region to the cytoplasm affecting cell division, specifically in the septum formation. These mechanisms are orchestrated by Dps1 and Dps2, which play a crucial role in metal homeostasis, and are associated with the D. radiodurans tolerance against reactive oxygen species.

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“…Interactions with negatively charged phosphodiester backbones of DNA occur through positively charged lysine (Lys5, Lys8, and Lys10) and arginine (Arg18) residues located in the N-terminal fragments of Dps from E. coli [ 9 , 24 ]. Presence of additional positive charges in solution provided by the MgCl 2 salt can change the structure of both the N-terminal fragments of the protein and the structure of the whole macromolecule, disrupting its ability to bind DNA.…”

Section: Resultsmentioning

confidence: 99%

Structural Rearrangement of Dps-DNA Complex Caused by Divalent Mg and Fe Cations

Dadinova

Kamyshinsky

Chesnokov

et al. 2021

IJMS

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Two independent, complementary methods of structural analysis were used to elucidate the effect of divalent magnesium and iron cations on the structure of the protective Dps-DNA complex. Small-angle X-ray scattering (SAXS) and cryo-electron microscopy (cryo-EM) demonstrate that Mg2+ ions block the N-terminals of the Dps protein preventing its interaction with DNA. Non-interacting macromolecules of Dps and DNA remain in the solution in this case. The subsequent addition of the chelating agent (EDTA) leads to a complete restoration of the structure of the complex. Different effect was observed when Fe cations were added to the Dps-DNA complex; the presence of Fe2+ in solution leads to the total complex destruction and aggregation without possibility of the complex restoration with the chelating agent. Here, we discuss these different responses of the Dps-DNA complex on the presence of additional free metal cations, investigating the structure of the Dps protein with and without cations using SAXS and cryo-EM. Additionally, the single particle analysis of Dps with accumulated iron performed by cryo-EM shows localization of iron nanoparticles inside the Dps cavity next to the acidic (hydrophobic) pore, near three glutamate residues.

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SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions

Cited by 15 publications

References 50 publications

Conservation and diversity of radiation and oxidative stress resistance mechanisms inDeinococcusspecies

Conservation and diversity of radiation and oxidative stress resistance mechanisms inDeinococcusspecies

The interplay between Mn and Fe in Deinococcus radiodurans triggers cellular protection during paraquat-induced oxidative stress

Structural Rearrangement of Dps-DNA Complex Caused by Divalent Mg and Fe Cations

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