Dps from Deinococcus radiodurans: oligomeric forms of Dps1 with distinct cellular functions and Dps2 involved in metal storage

Abstract

The DNA binding proteins from starved cells from Deinococcus radiodurans, Dps1-DR2263 and Dps2-DRB0092, have a common overall structure of hollow spherical dodecamers. Their involvement in the homeostasis of intracellular metal and DNA protection was addressed. Our results show that DrDps proteins are able to oxidize ferrous to ferric iron by oxygen or hydrogen peroxide. The iron stored inside the hollow sphere cavity is fully released. Furthermore, these proteins are able to store and release manganese, suggesting they can play a role in manganese homeostasis as well. The interaction of DrDps with DNA was also addressed. Even though DrDps1 binds both linear and coiled DNA, DrDps2 preferentially binds to coiled DNA, forming different protein-DNA complexes, as clearly shown by atomic force microscopy. DrDps1 (dimer and dodecamer) and DrDps2 can protect DNA against reactive oxygen species, although the protection occurs at different Fe to protein ratios. The difference between DrDps could be the result of the DrDps1 higher iron oxidation rate in the presence of hydrogen peroxide and its higher affinity to bind DNA than in DrDps2. Using cellular extracts obtained from D. radiodurans cultures, we showed that DrDps1 oligomers observed in in vitro conditions are also present in vivo. This indicates that DrDps1 has a structural dynamic plasticity that allows its oligomeric state to change between dimer, trimer and dodecamer. This in turn suggests the existence of a regulation mechanism that modulates the oligomer equilibrium and is dependent on growth stages and environmental conditions.

Below-Background Ionizing Radiation as an Environmental Cue for Bacteria

“…Additionally, the upregulation of a putative metal efflux pump (SOA0154) in S. oneidensis, proposed to be involved in the detoxification of UVA-irradiated cells (Qiu et al, 2005) supports the hypothesis that 79 times below normal dose rates of radiation is perceived as a stress. Interestingly, D. radiodurans cultures exhibited the down regulation of dps, known to contribute to DNA protection from ROS through the maintenance of metal homeostasis (Santos et al, 2015), in agreement with previous findings on the reduced transcription of this gene in the presence of H 2 O 2 (Chen et al, 2008); and of gapdH, an essential component of glucose metabolism during glycolysis. After first documenting growth inhibition and the lack of stress-gene response in D. radiodurans to the absence of normal levels of radiation (Castillo et al, 2015), in the data reported here, we added qPCR assays for various previously reported stress-related genes, including homologs to those responsive in S. oneidensis, of which two were regulated, suggesting that D. radiodurans' response to this unusual environmental cue might be derived from different gene regulation events.…”

Biosynthesis of Au, Ag and Au&ndash;Ag bimetallic nanoparticles using protein extracts of <em>Deinococcus radiodurans</em> and evaluation of their cytotoxicity

“…However, the Dps2 could biosynthesize AgNPs rather than AuNPs ( Figures 8C and D and S4B). The different roles of the Dps2 in reducing Au(III) and Ag(I) might be due to the following: first, the Dps2, which functions as a sequester of intracellular Fe 2+ ion and stores iron ions in the form of Fe 3+ , 53 could not adsorb or interact with the trivalent Au ions; however, it did reduce the monovalent Ag ions; second, Dps2 only contains three tryptophan and six tyrosine molecules that have the ability of donating electrons from their NH or OH groups (Table S2) 54,55 and thus could not have enough potential to synthesize the AuNPs, considering the relative higher reduction potential of gold (E =0.799 V). 56,57 Thus, the metal NP's biosynthetic ability with different proteins might be determined by their composition or reducing capability.…”

The Dps4 fromNostoc punctiformeATCC 29133 is a member of His-type FOC containing Dps protein class that can be broadly found among cyanobacteria

“…Our earlier results on the NpDps1-3 showed that none of these three proteins could catalyze the O 2 -mediated oxidation reaction, while H 2 O 2 acted as a good oxidant. To investigate whether NpDps4 exhibits similar oxidant preferences as the canonical NpDps we used kinetic absorption spectroscopy to monitor the oxidation of Fe 2+ to Fe 3+ from which an increase in the absorbance at 310 nm arises [4,34] (Fig 5).…”

“…Kinetic absorption spectroscopy following the wavelength at 310 nm to monitor the formation of Fe 3+ species [4,34]. A.…”