DNA-binding and oligomerization properties of a functionally distinct Dps homolog, Dps-1 from Deinococcus radiodurans

Dps (DNA protection during starvation) proteins play an important role in the protection of prokaryotic macromolecules from damage by reactive oxygen species. The Dps homolog, Dps-1, from the radiation-resistant bacterium Deinococcus radiodurans has an extended N-terminal tail. In the crystal structure of Dps-1, the first ~30 N-terminal residues are invisible and the remaining 25 residues form a loop that harbors a novel metal binding site. The data presented here show that retention of this N-terminal metal site is necessary for formation of the dodecameric protein assembly. Previous studies have suggested that the lysine-rich N-terminus of Dps proteins participates in DNA binding. Accordingly, deletion of the N-terminal tail of Dps-1 obliterates DNA/Dps-1 interaction. Electrophoretic mobility shift assays using DNA modified with specific major/minor groove reagents show that Dps-1 interacts through the DNA major groove. Dodecameric Dps-1 can bind ≥ 22bp DNA duplexes with very high affinity (Kd ~0.4 nM); considering interactions in the DNA major grooves, the requirement for two complete helical turns implies optimal interactions involving two consecutive major grooves. The data further suggests that high-affinity DNA binding depends on occupancy of the N-terminal metal site. Stoichiometric titration of dodecameric Dps-1 with 22 bp DNA revealed the presence of 6 DNA binding sites in each dodecamer. DNA cyclization assays show that dodecameric Dps-1 inhibits DNA bending. Taken together, the mode of DNA interaction by Dps-1 is consistent with the previously proposed layered assembly of protein and DNA that leads to DNA compaction. Using Dps-1-promoter-lacZ fusion constructs, it is shown that Dps-1 expression in D. radiodurans is relatively constant throughout both exponential and stationary phase growth. As E. coli cells expressing Dps-1 feature significant nucleoid condensation, as shown by transmission electron microscopy and nucleoid staining, a role for Dps-1 in chromosomal DNA packaging is suggested. The presence of a novel iron exit channel is most likely responsible for the inability of Dps-1 to protect DNA from hydroxyl radical-mediated DNA degradation. The release of iron from the core upon DNA binding suggests that Dps-1 may be involved in the process of DNA degradation that contributes the first response to DNA damage

Place, ethnicity and poverty in England’

Examination of the relationship between ethnicity, poverty and place has tended to focus on the spatial distribution of minority ethnic groups. This summary paper reviews some key themes in this literature, in order to review the following key questions: •Where are different ethnic groups located, and how does this location relate to their experience of poverty? •Is clustering a good or bad thing, and what is the role of location – regardless of concentration – in terms of impacts on access to housing, employment, and other resources? However, it is notable that existing research in this area continues to present ethnicity as a factor that shapes outcomes only for minority ethnic groups. A wider discussion increasingly recognises the working of ethnicity in the lives of majority communities. Some of the most consistently impoverished areas in Britain, for example, are in regions with relatively small minority ethnic communities. For example, examinations of poverty in Cornwall (Cemlyn, et al., 2002) and Wales (Kenway and Palmer, 2007) identify longstanding concentrations of poverty and social exclusion among relatively static populations. Instead of assuming that ethnic identity influences propensity to poverty when concentrated in particular places, the experiences of Cornwall and Wales encourage us to consider the manner in which places of poverty also have an ethnic character and the impact of this in the wider experience of poverty. In what follows, and in order to reflect the existing literature, we review key points in the debate about the spatial concentration of minority ethnic groups and the impact of this concentration on experiences of poverty. Where possible, we seek to extend these ideas to consider possible implications for spaces of poverty characterised by concentrations of majority ethnic groups

The N-terminal extensions of Deinococcus radiodurans Dps-1 mediate DNA major groove interactions as well as assembly of the dodecamer

Dps (DNA protection during starvation) proteins play an important role in the protection of prokaryotic macromolecules from damage by reactive oxygen species. Previous studies have suggested that the lysine-rich N-terminal tail of Dps proteins participates in DNA binding. In comparison with other Dps proteins, Dps-1 from Deinococcus radiodurans has an extended N terminus comprising 55 amino acids preceding the first helix of the 4-helix bundle monomer. In the crystal structure of Dps-1, the first ∼30 N-terminal residues are invisible, and the remaining 25 residues form a loop that harbors a novel metal-binding site. We show here that deletion of the flexible N-terminal tail obliterates DNA/Dps-1 interaction. Surprisingly, deletion of the entire N terminus also abolishes dodecameric assembly of the protein. Retention of the N-terminal metal site is necessary for formation of the dodecamer, and metal binding at this site facilitates oligomerization of the protein. Electrophoretic mobility shift assays using DNA modified with specific major/minor groove reagents further show that Dps-1 interacts through the DNA major groove. DNA cyclization assays suggest that dodecameric Dps-1 does not wrap DNA about itself. A significant decrease in DNA binding affinity accompanies a reduction in duplex length from 22 to 18 bp, but only for dodecameric Dps-1. Our data further suggest that high affinity DNA binding depends on occupancy of the N-terminal metal site. Taken together, the mode of DNA interaction by dodecameric Dps-1 suggests interaction of two metal-anchored N-terminal tails in successive DNA major grooves, leading to DNA compaction by formation of stacked protein-DNA layers. © 2007 by The American Society for Biochemistry and Molecular Biology, Inc

Revisiting ‘common-sense’ in a time of cultivated ignorance – a conversation with Errol Lawrence

An interview with Errol Lawrence, discussing the concept of common-sense racism, the adaptation of racist cultures, battles around public services and the role of the state and the continuing influence of The Empire Strikes Back

EVALUATION OF ANTIOXIDANT PROFILE AND PHYTOCHEMICAL CONSTITUENTS OF SOME HERB-SUPPLEMENTED BLACK TEA INFUSIONS

Objective: The present study was designed to adjudicate the change in contents of phytochemicals and in vitro antioxidant potential of tea infusions supplemented with herbs.Methods: The phytochemical screening of tea infusions with or without supplemented herbs was done along with their antioxidant capacities using some common in vitro assays. Infusions were prepared by soaking tea leaves and subsequent herbs in boiled water for 10 minutes.Results: ABTS radical scavenging ability did not improve after herb supplementation of the infusions, although DPPH radical scavenging ability improved in some samples, especially in ginger tea. This proves that less polar phytochemicals are supplemented mostly when herbs are added in the tea infusions. Tannin contents were mostly preserved except for the ginger tea. Most prominent effect was observed in their hydroxyl radical scavenging abilities, which commensurate with the lipid peroxidation inhibitory activities of the supplemented infusions.  Conclusion: Present study provides firm evidence to support that an augmenting effect exists between black tea and some supplemented herbs, when infusions were prepared with the both

Go home? the politics of immigration controversies

"The 2013 Go Home vans marked a turning point in government-sponsored communication designed to demonstrate control and toughness on immigration. In this study, the authors explore the effects of this toughness: on policy, public debate, pro-migrant and anti-racist activism, and on the everyday lives of people in Britain. Bringing together an authorial team of eight respected social researchers, alongside the voices of community organisations, policy makers, migrants and citizens, and with an afterword by journalist Kiri Kankhwende, this is an important intervention in one of the most heated social issues of our time.

Crystal Structure of Dps-1, a Functionally Distinct Dps Protein from Deinococcus radiodurans

DNA protection during starvation (Dps) proteins play an important role in protecting cellular macromolecules from damage by reactive oxygen species (ROS). Unlike most orthologs that protect DNA by a combination of DNA binding and prevention of hydroxyl radical formation by ferroxidation and sequestration of iron, Dps-1 from the radiation-resistant Deinococcus radiodurans fails to protect DNA from hydroxyl radical-mediated cleavage through a mechanism inferred to involve continuous release of iron from the protein core. To address the structural basis for this unusual release of Fe2+, the crystal structure of D. radiodurans Dps-1 was determined to 2.0 Å resolution. Two of four strong anomalous signals per protein subunit correspond to metal-binding sites within an iron-uptake channel and a ferroxidase site, common features related to the canonical functions of Dps homologs. Similar to Lactobacillus lactis Dps, a metal-binding site is found at the N-terminal region. Unlike other metal sites, this site is located at the base of an N-terminal coil on the outer surface of the dodecameric protein sphere and does not involve symmetric association of protein subunits. Intriguingly, a unique channel-like structure is seen featuring a fourth metal coordination site that results from 3-fold symmetrical association of protein subunits through α2 helices. The presence of this metal-binding site suggests that it may define an iron-exit channel responsible for the continuous release of iron from the protein core. This interpretation is supported by substitution of residues involved in this ion coordination and the observation that the resultant mutant protein exhibits significantly attenuated iron release. Therefore, we propose that D. radiodurans Dps-1 has a distinct iron-exit channel. © 2006 Elsevier Ltd. All rights reserved