Rapid, DNA-induced subunit exchange by DNA gyrase

DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to form the active complex. GyrA is usually found as a dimer in solution, whereas GyrB can exist as a monomer. DNA gyrase is able to loop DNA around the C-terminal domains (CTDs) of GyrA and pass one DNA duplex through a transient double-strand break (DSB) established in another duplex. This results in the conversion of a positive loop into a negative one, thereby introducing negative supercoiling into the bacterial genome, an activity essential for DNA replication and transcription. The strong protein interface in the GyrA dimer must be broken to allow passage of the transported DNA segment and it is generally assumed that the interface is usually stable and only opens when DNA is transported, to prevent the introduction of deleterious DSBs in the genome. In this paper we show that DNA gyrase can exchange its DNA-cleaving interfaces between two active heterotetramers. This so-called “subunit exchange” can occur within a few minutes in solution. We also show that bending of DNA by gyrase is essential for cleavage but not for DNA binding per se and favors subunit exchange. Subunit exchange is also favored by DNA wrapping and an excess of GyrB. We suggest that proximity, promoted by GyrB oligomerization and binding and wrapping along a length of DNA, between two heteroteramers favors rapid interface exchange. This exchange does not require ATP, can occur in the presence of fluoroquinolones, and raises the possibility of non-homologous recombination solely through gyrase activity. The ability of gyrase to undergo subunit exchange also explains how gyrase heterodimers, containing a single active-site tyrosine, can carry out double-strand passage reactions

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Rapid, DNA-induced interface swapping by DNA gyrase

DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to form the active complex. DNA gyrase can loop DNA around the C-terminal domains (CTDs) of GyrA and pass one DNA duplex through a transient double-strand break (DSB) established in another duplex. This results in the conversion from a positive (+1) to a negative (–1) supercoil, thereby introducing negative supercoiling into the bacterial genome by steps of 2, an activity essential for DNA replication and transcription. The strong protein interface in the GyrA dimer must be broken to allow passage of the transported DNA segment and it is generally assumed that the interface is usually stable and only opens when DNA is transported, to prevent the introduction of deleterious DSBs in the genome. In this paper, we show that DNA gyrase can exchange its DNA-cleaving interfaces between two active heterotetramers. This so-called interface ‘swapping’ (IS) can occur within a few minutes in solution. We also show that bending of DNA by gyrase is essential for cleavage but not for DNA binding per se and favors IS. Interface swapping is also favored by DNA wrapping and an excess of GyrB. We suggest that proximity, promoted by GyrB oligomerization and binding and wrapping along a length of DNA, between two heterotetramers favors rapid interface swapping. This swapping does not require ATP, occurs in the presence of fluoroquinolones, and raises the possibility of non-homologous recombination solely through gyrase activity. The ability of gyrase to undergo interface swapping explains how gyrase heterodimers, containing a single active-site tyrosine, can carry out double-strand passage reactions and therefore suggests an alternative explanation to the recently proposed ‘swivelling’ mechanism for DNA gyrase (Gubaev et al., 2016)

Comparing Fly Ash Samples from Different Types of Incinerators for Their Potential as Storage Materials for Thermochemical Energy and CO2

This study aims to investigate the physical and chemical characterization of six fly ash samples obtained from different municipal solid waste incinerators (MSWIs), namely grate furnaces, rotary kiln, and fluidized bed reactor, to determine their potential for CO2 and thermochemical energy storage (TCES). Representative samples were characterized via simultaneous thermal analysis (STA) in different atmospheres, i.e., N2, air, H2O, CO2, and H2O/CO2, to identify fly ash samples that can meet the minimum requirements, i.e., charging, discharging, and cycling stability, for its consideration as TCES and CO2-storage materials and to determine their energy contents. Furthermore, other techniques, such as inductively coupled plasma optical emission spectroscopy, X-ray fluorescence (XRF) spectrometry, X-ray diffraction (XRD), scanning electron microscopy, leachability tests, specific surface area measurement based on the Brunauer–Emmett–Teller method, and particle-size distribution measurement, were performed. XRF analysis showed that calcium oxide is one of the main components in fly ash, which is a potentially suitable component for TCES systems. XRD results revealed information regarding the crystal structure and phases of various elements, including that of Ca. The STA measurements showed that the samples can store thermal heat with energy contents of 50–394 kJ/kg (charging step). For one fly ash sample obtained from a grate furnace, the release of the stored thermal heat under the selected experimental conditions (discharging step) was demonstrated. The cycling stability tests were conducted thrice, and they were successful for the selected sample. One fly ash sample could store CO2 with a storage capacity of 27 kg CO2/ton based on results obtained under the selected experimental conditions in STA. Samples from rotary kiln and fluidized bed were heated up to 1150 °C in an N2 atmosphere, resulting in complete melting of samples in crucibles; however, other samples obtained from grate furnaces formed compacted powders after undergoing the same thermal treatment in STA. Samples from different grate furnaces showed similarities in their chemical and physical characterization. The leachability test according to the standard (EN 12457-4 (2002)) using water in a ratio of 10 L/S and showed that the leachate of heavy metals is below the maximum permissible values for nonhazardous materials (except for Pb), excluding the fly ash sample obtained using fluidized bed technology. The leachate contents of Cd and Mn in the fly ash samples obtained from the rotary kiln were higher than those in other samples. Characterization performed herein helped in determining the suitable fly ash samples that can be considered as potential CO2-storage and TCES materials

Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection

Highly specific interactions between proteins are a fundamental prerequisite for life, but how they evolve remains an unsolved problem. In particular, interactions between initially unrelated proteins require that they evolve matching surfaces. It is unclear whether such surface compatibilities can only be built by selection in small incremental steps, or whether they can also emerge fortuitously. Here, we used molecular phylogenetics, ancestral sequence reconstruction and biophysical characterization of resurrected proteins to retrace the evolution of an allosteric interaction between two proteins that act in the cyanobacterial photoprotection system. We show that this interaction between the orange carotenoid protein (OCP) and its unrelated regulator, the fluorescence recovery protein (FRP), evolved when a precursor of FRP was horizontally acquired by cyanobacteria. FRP’s precursors could already interact with and regulate OCP even before these proteins first encountered each other in an ancestral cyanobacterium. The OCP–FRP interaction exploits an ancient dimer interface in OCP, which also predates the recruitment of FRP into the photoprotection system. Together, our work shows how evolution can fashion complex regulatory systems easily out of pre-existing components

Hyperphosphorylated tau self-assembles into amorphous aggregates eliciting TLR4-dependent responses.

Soluble aggregates of the microtubule-associated protein tau have been challenging to assemble and characterize, despite their important role in the development of tauopathies. We found that sequential hyperphosphorylation by protein kinase A in conjugation with either glycogen synthase kinase 3β or stress activated protein kinase 4 enabled recombinant wild-type tau of isoform 0N4R to spontaneously polymerize into small amorphous aggregates in vitro. We employed tandem mass spectrometry to determine the phosphorylation sites, high-resolution native mass spectrometry to measure the degree of phosphorylation, and super-resolution microscopy and electron microscopy to characterize the morphology of aggregates formed. Functionally, compared with the unmodified aggregates, which require heparin induction to assemble, these self-assembled hyperphosphorylated tau aggregates more efficiently disrupt membrane bilayers and induce Toll-like receptor 4-dependent responses in human macrophages. Together, our results demonstrate that hyperphosphorylated tau aggregates are potentially damaging to cells, suggesting a mechanism for how hyperphosphorylation could drive neuroinflammation in tauopathies.J.X.M. is supported by Dr. Herchel Smith Fellowship from Williams College .Y.Z. is supported by the Wellcome Trust Grant (107032AIA, R.A.F). and the Cambridge Cancer Center Pump Priming Grant and Royal Society University Research Fellowship to S.F.L. D.S. is supported by Clarendon Scholarship from Oxford University Press. A.M.H. is funded by Open Targets. G.B. Y.Y. are supported by the UK Dementia Research Institute that receives contributions from UK DRI Ltd, the UK MRC, the Alzheimer’s Society, and Alzheimer’s Research UK. C.E.B. is supported by a Wellcome Trust Investigator award (108045/Z/15/Z, C.E.B.). This work is supported by the UK Dementia Research Institute which receives its funding from DRI Ltd, funded by the UK Medical Research Council, Alzheimer’s Society and Alzheimer’s Research UK and by the Royal Society (RP150066, DK)

The beauty and complexity of the small heat shock proteins: a report on the proceedings of the fourth workshop on small heat shock proteins.

The Fourth Cell Stress Society International workshop on small heat shock proteins (sHSPs), a follow-up to successful workshops held in 2014, 2016 and 2018, took place as a virtual meeting on the 17-18 November 2022. The meeting was designed to provide an opportunity for those working on sHSPs to reconnect and discuss their latest work. The diversity of research in the sHSP field is reflected in the breadth of topics covered in the talks presented at this meeting. Here we summarise the presentations at this meeting and provide some perspectives on exciting future topics to be addressed in the field