Matt Green

Defining the Intrinsically Disordered C-Terminal Domain of SSB Reveals DNA-Mediated Compaction.

The bacterial single-stranded DNA (ssDNA) binding protein SSB is a strictly conserved and essential protein involved in diverse functions of DNA metabolism, including replication and repair. SSB comprises a well-characterized tetrameric core of N-terminal oligonucleotide binding OB folds that bind ssDNA and four intrinsically disordered C-terminal domains of unknown structure that interact with partner proteins. The generally accepted, albeit speculative, mechanistic model in the field postulates that binding of ssDNA to the OB core induces the flexible, undefined C-terminal arms to expand outwards encouraging functional interactions with partner proteins. In this structural study, we show that the opposite is true. Combined small-angle scattering with X-rays and neutrons coupled to coarse-grained modeling reveal that the intrinsically disordered C-terminal arms are relatively collapsed around the tetrameric OB core and collapse further upon ssDNA binding. This implies a mechanism of action, in which the disordered C-terminal domain collapse traps the ssDNA and pulls functional partners onto the ssDNA.

Engineering a reagentless biosensor for single-stranded DNA to measure real-time helicase activity in Bacillus

Single-stranded DNA-binding protein (SSB) is a well characterized ubiquitous and essential bacterial protein involved in almost all aspects of DNA metabolism. Using the Bacillus subtilis SSB we have generated a reagentless SSB biosensor that can be used as a helicase probe in B. subtilis and closely related gram positive bacteria. We have demonstrated the utility of the probe in a DNA unwinding reaction using a helicase from Bacillus and for the first time, characterized the B. subtilis SSBs DNA binding mode switching and stoichiometry. The importance of SSB in DNA metabolism is not limited to simply binding and protecting ssDNA during DNA replication, as previously thought. It interacts with an array of partner proteins to coordinate many different aspects of DNA metabolism. In most cases its interactions with partner proteins is species-specific and for this reason, knowing how to produce and use cognate reagentless SSB biosensors in different bacteria is critical. Here we explain how to produce a B. subtilis SSB probe that exhibits 9-fold fluorescence increase upon binding to single stranded DNA and can be used in all related gram positive firmicutes which employ drastically different DNA replication and repair systems than the widely studied Escherichia coli. The materials to produce the B. subtilis SSB probe are commercially available, so the methodology described here is widely available unlike previously published methods for the E. coli SSB.

Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity.

During Bacillus subtilis replication two replicative polymerases function at the replisome to collectively carry out genome replication. In a reconstituted in vitro replication assay, PolC is the main polymerase while the lagging strand DnaE polymerase briefly extends RNA primers synthesized by the primase DnaG prior to handing-off DNA synthesis to PolC. Here, we show in vivo that (i) the polymerase activity of DnaE is essential for both the initiation and elongation stages of DNA replication, (ii) its error rate varies inversely with PolC concentration, and (iii) its misincorporations are corrected by the mismatch repair system post-replication. We also found that the error rates in cells encoding mutator forms of both PolC and DnaE are significantly higher (up to 15-fold) than in PolC mutants. In vitro, we showed that (i) the polymerase activity of DnaE is considerably stimulated by DnaN, SSB and PolC, (ii) its error-prone activity is strongly inhibited by DnaN, and (iii) its errors are proofread by the 3′ > 5′ exonuclease activity of PolC in a stable template-DnaE–PolC complex. Collectively our data show that protein–protein interactions within the replisome modulate the activity and fidelity of DnaE, and confirm the prominent role of DnaE during B. subtilis replication.

Primase is required for helicase activity and helicase alters the specificity of primase in the enteropathogen Clostridium difficile

DNA replication is an essential and conserved process in all domains of life and may serve as a target for the development of new antimicrobials. However, such developments are hindered by subtle mechanistic differences and limited understanding of DNA replication in pathogenic microorganisms. Clostridium difficile is the main cause of healthcare-associated diarrhoea and its DNA replication machinery is virtually uncharacterized. We identify and characterize the mechanistic details of the putative replicative helicase (CD3657), helicase-loader ATPase (CD3654) and primase (CD1454) of C. difficile, and reconstitute helicase and primase activities in vitro. We demonstrate a direct and ATP-dependent interaction between the helicase loader and the helicase. Furthermore, we find that helicase activity is dependent on the presence of primase in vitro. The inherent trinucleotide specificity of primase is determined by a single lysine residue and is similar to the primase of the extreme thermophile Aquifex aeolicus. However, the presence of helicase allows more efficient de novo synthesis of RNA primers from non-preferred trinucleotides. Thus, loader–helicase–primase interactions, which crucially mediate helicase loading and activation during DNA replication in all organisms, differ critically in C. difficile from that of the well-studied Gram-positive Bacillus subtilis model.

TYPLEX® Chelate, a novel feed additive, inhibits Campylobacter jejuni biofilm formation and cecal colonization in broiler chickens.

ABSTRACT Reducing Campylobacter spp. carriage in poultry is challenging, but essential to control this major cause of human bacterial gastroenteritis worldwide. Although much is known about the mechanisms and route of Campylobacter spp. colonization in poultry, the literature is scarce on antibiotic‐free solutions to combat Campylobacter spp. colonization in poultry. In vitro and in vivo studies were conducted to investigate the role of TYPLEX® Chelate (ferric tyrosine), a novel feed additive, in inhibiting Campylobacter jejuni (C. jejuni) biofilm formation and reducing C. jejuni and Escherichia coli (E. coli) colonization in broiler chickens at market age. In an in vitro study, the inhibitory effect on C. jejuni biofilm formation using a plastic bead assay was investigated. The results demonstrated that TYPLEX® Chelate significantly reduces biofilm formation. In an in vivo study, 800 broilers (one d old) were randomly allocated to 4 dietary treatments in a randomized block design, each having 10 replicate pens with 20 birds per pen. At d 21, all birds were challenged with C. jejuni via seeded litter. At d 42, cecal samples were collected and tested for volatile fatty acid (VFA) concentrations and C. jejuni and E. coli counts. The results showed that TYPLEX® Chelate reduced the carriage of C. jejuni and E. coli in poultry by 2 and 1 log10 per gram cecal sample, respectively, and increased cecal VFA concentrations. These findings support TYPLEX® Chelate as a novel non‐antibiotic feed additive that may help produce poultry with a lower public health risk of Campylobacteriosis.

The academic study of comics within degree programmes in English literature

Across the United Kingdom comics have become part of the curricula of English university programmes. This roundtable discussion, held at the Third International Comics Conference at Bournemouth University in July 2012, examined the growing presence of comics on English literature degrees. Participants shared their experiences of introducing and designing undergraduate courses on comics, of embedding comics in modules dominated by poetry and prose literature, and of teaching students unfamiliar with the comics medium. This article ends with a collaboratively written evaluation of what the future holds for comics in higher education in Britain – on English degrees and beyond.

Preparing the perfect medical CV

Matt Green from BPP University College School of Health explores what steps you should take to ensure that your medical CV stands out for the right reasons. He will be speaking at this year’s BMJ Careers Fair

Dietary supplementation with ferric tyrosine improves zootechnical performance and reduces caecal Campylobacter spp. load in broilers

ABSTRACT 1. The objective of this study was to evaluate the effect of ferric tyrosine on the reduction of Campylobacter spp. and zootechnical performance in broilers exposed to Campylobacter spp. using a natural challenge model to simulate commercial conditions. Additionally, the minimum inhibitory concentrations (MICs) of ferric tyrosine against common enteropathogens were evaluated. 2. At the start of the trial, 840 healthy male 1-d-old birds (Ross 308) were randomly allocated to 6 replicate pens of 35 birds each and fed diets containing different concentrations of ferric tyrosine (0, 0.02, 0.05 and 0.2 g/kg) in mash form for 42 d. 3. Broilers fed diets containing ferric tyrosine showed significantly higher body weight at d 42 and weight gain compared to the control group. However, birds fed ferric tyrosine ate significantly more than the control birds so significant improvements in feed conversion rate were not observed. 4. Microbiological analyses of caecal samples collected on d 42 of the study showed, per gram of sample, 2–3 log10 reduction in Campylobacter spp. and 1 log10 reduction in Escherichia coli in the groups fed diets containing ferric tyrosine compared to the control. 5. The MICs of ferric tyrosine was >400 mg/l for C. jejuni and >200 mg/l for E. coli and Salmonella enterica, indicating that ferric tyrosine did not exert antimicrobial activity. 6. The results showed that birds fed ferric tyrosine grew faster and consumed more feed compared to the control group, indicating potential benefits of faster time to reach slaughter weight with no significant reduction on feed efficiency. Moreover, ferric tyrosine significantly reduced caecal Campylobacter spp. and E. coli indicating potential as a non-antibiotic feed additive to lower the risk of infections transmitted through the food chain.

Interactions between helicase and primase are crucial for DNA replication in the enteropathogen Clostridium difficile

DNA replication is an essential and conserved process in all domains of life and may serve as a target for the development of new antimicrobials. However, such developments are hindered by a limited understanding of DNA replication in pathogenic micro-organisms. Clostridium difficile is the main cause of health-care associated diarrhea and its DNA replication machinery is virtually uncharacterized. We identified the replicative helicase (CD3657), the helicase loader ATPase (CD3654) and primase (CD1454) of C. difficile and reconstitute helicase and primase activity in vitro. We demonstrate a direct and ATP-dependent interaction between the helicase loader and the helicase. We find that helicase activity is dependent on the presence of primase in vitro. The trinucleotide specificity of primase, which we find to be determined by a single lysine residue, is similar to extreme thermophile Aquifex aeolicus but the presence of helicase allows more efficient de novo synthesis of RNA primers from non-preferred trinucleotides. Thus, helicase-primase interactions constitute a crucial aspect of DNA replication initiation in C. difficile and helicase loading and activation in this organism differs critically from that of the Gram-positive model organism Bacillus subtilis.

‘The end of the world. That’s a bad thing right?’: Form and Function from William Blake to Alan Moore

Alan Moore’s intertextual relationship with William Blake stretches across three decades and various media. In the medium for which Moore is best known — comics and graphic novels — textual references to Blake occur in six different series: The Saga of the Swamp Thing, V for Vendetta, Watchmen, From Hell, Promethea, and The League of Extraordinary Gentlemen. Many of Moore’s essays also refer directly to Blake, including the inaugural issue of Dodgem Logic, 25,000 Years of Erotic Freedom, and the second edition of Writing for Comics. Visual references to Blake’s artwork appear in two of the graphic novels, From Hell and Promethea. Images of Blake himself appear in From Hell and, more recently, in the A3 fold-out poster, ‘Bohemia’ (based on an idea by Moore), included in Dodgem Logic 4. In the spoken word piece, Angel Passage, Moore follows Blake on a spiritual journey, ‘out of light and into history’, and references to Blake, the four-fold city, and Jerusalem also appear in an earlier performance, Snakes and Ladders. A pictorial biography of Blake will feature in the forthcoming The Moon and Serpent Bumper Book of Magic.