Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding.

G-quadruplexes (G4s) are unusual stable DNA structures that cause genomic instability. To overcome the potential barriers formed by G4s, cells have evolved different families of proteins that unfold G4s. Pif1 is a DNA helicase from superfamily 1 (SF1) conserved from bacteria to humans with high G4-unwinding activity. Here, we present the first X-ray crystal structure of the Thermus oshimai Pif1 (ToPif1) complexed with a G4. Our structure reveals that ToPif1 recognizes the entire native G4 via a cluster of amino acids at domains 1B/2B which constitute a G4-Recognizing Surface (GRS). The overall structure of the G4 maintains its three-layered propeller-type G4 topology, without significant reorganization of G-tetrads upon protein binding. The three G-tetrads in G4 are recognized by GRS residues mainly through electrostatic, ionic interactions, and hydrogen bonds formed between the GRS residues and the ribose-phosphate backbone. Compared with previously solved structures of SF2 helicases in complex with G4, our structure reveals how helicases from distinct superfamilies adopt different strategies for recognizing and unfolding G4s.

Deep burn surgery of the whole dorsum of the hand: Composite skin grafting over acellular dermal matrix versus thick split-thickness skin grafting.

Preservation and restoration of hand function after burn injuries are challenging yet imperative. This study aimed to assess the curative effect of a composite skin graft over an acellular dermal matrix (ADM) and a thick split-thickness skin graft (STSG) for treating deep burns on the hand. Patients who met the inclusion criteria at the First Affiliated Hospital of Wenzhou Medical University between September 2011 and January 2020 were retrospectively identified from the operative register. We investigated patient characteristics, time from operation to the start of active motion exercise, take rates of skin graft 7 days post-surgery, donor site recovery, complications and days to complete healing. Patients were followed up for 12 months to evaluate scar quality using the Vancouver Scar Scale (VSS) and hand function through total active motion (TAM) and the Jebsen-Taylor Hand Function Test (JTHFT). A total of 38 patients (52 hands) who received thin STSG on top of the ADM or thick STSG were included. The location of the donor sites was significantly different between Group A (thick STSG) and Group B (thin STSG + ADM) (p = 0.03). There were no statistical differences in age, gender, underlying disease, cause of burn, burn area, dominant hand, patients with two hands operated on and time from burn to surgery between the two groups (p > 0.05). The time from operation to the start of active motion exercise, take rates of skin graft 7 days post-surgery and days to complete healing were not significantly different between Group A and Group B (p > 0.05). The rate of donor sites requiring skin grafting was lower in Group B than in Group A (22.2% vs. 100%, p < 0.001). There were no statistically significant differences in complications between the groups (p = 0.12). Moreover, 12 months postoperatively, the pliability subscore in the VSS was significantly lower in Group A than in Group B (p = 0.01). However, there were no statistically significant differences in vascularity (p = 0.42), pigmentation (p = 0.31) and height subscores (p = 0.13). The TAM and JTHFT results revealed no statistically significant differences between the two groups (p = 0.22 and 0.06, respectively). The ADM combined with thin STSG is a valuable approach for treating deep and extensive hand burns with low donor site morbidity. It has a good appearance and function in patients with hand burns, especially in patients with limited donor sites.

Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition.

Pif1 is an SF1B helicase that is evolutionarily conserved from bacteria to humans and plays multiple roles in maintaining genome stability in both nucleus and mitochondria. Though highly conserved, Pif1 family harbors a large mechanistic diversity. Here, we report crystal structures of Thermus oshimai Pif1 (ToPif1) alone and complexed with partial duplex or single-stranded DNA. In the apo state and in complex with a partial duplex DNA, ToPif1 is monomeric with its domain 2B/loop3 adopting a closed and an open conformation, respectively. When complexed with a single-stranded DNA, ToPif1 forms a stable dimer with domain 2B/loop3 shifting to a more open conformation. Single-molecule and biochemical assays show that domain 2B/loop3 switches repetitively between the closed and open conformations when a ToPif1 monomer unwinds DNA and, in contrast with other typical dimeric SF1A helicases, dimerization has an inhibitory effect on its helicase activity. This mechanism is not general for all Pif1 helicases but illustrates the diversity of regulation mechanisms among different helicases. It also raises the possibility that although dimerization results in activation for SF1A helicases, it may lead to inhibition for some of the other uncharacterized SF1B helicases, an interesting subject warranting further studies.

The HRDC domain oppositely modulates the unwinding activity of E. coli RecQ helicase on duplex DNA and G-quadruplex.

RecQ family helicases are highly conserved from bacteria to humans and have essential roles in maintaining genome stability. Mutations in three human RecQ helicases cause severe diseases with the main features of premature aging and cancer predisposition. Most RecQ helicases shared a conserved domain arrangement which comprises a helicase core, an RecQ C-terminal domain, and an auxiliary element helicase and RNaseD C-terminal (HRDC) domain, the functions of which are poorly understood. In this study, we systematically characterized the roles of the HRDC domain in E. coli RecQ in various DNA transactions by single-molecule FRET. We found that RecQ repetitively unwinds the 3'-partial duplex and fork DNA with a moderate processivity and periodically patrols on the ssDNA in the 5'-partial duplex by translocation. The HRDC domain significantly suppresses RecQ activities in the above transactions. In sharp contrast, the HRDC domain is essential for the deep and long-time unfolding of the G4 DNA structure by RecQ. Based on the observations that the HRDC domain dynamically switches between RecA core- and ssDNA-binding modes after RecQ association with DNA, we proposed a model to explain the modulation mechanism of the HRDC domain. Our findings not only provide new insights into the activities of RecQ on different substrates but also highlight the novel functions of the HRDC domain in DNA metabolisms.

Severity of albuminuria as an early indicator for wound healing in type 2 diabetic foot ulcers.

This study aimed to investigate the relationship between the severity of albuminuria and wound healing in type 2 diabetic foot ulcers. A total of 121 patients with diabetic foot ulcers were recruited from January 2015 to June 2017 and divided into nonproliferation and proliferation groups according to their healing status. Univariate and multivariate logistic regression were performed to assess the risk factors of wound proliferation. Skin biopsies were also taken from normal tissue near the wound in 54 participants. The microvessel density as well as the relationships among the microvessel density, albuminuria and wound proliferation were evaluated. Results showed that in a multiple linear regression model, factors including body-mass index, microalbuminuria, and macroalbuminuria showed independently significant association with wound healing in patients. The receiver operating characteristic curve analysis indicated albuminuria as a predicator for wound healing with a cutoff value of 32 mg/g. Meanwhile, normoalbuminuric patients showed significantly higher level of skin microvessels density than microalbuminuria and macroalbuminuria patients, while microalbuminuria patients also had statistically more microvessels that macroalbuminuria patients. The microvessel density were statistically significantly higher in the proliferation group than that in the nonproliferation group. In summary, this study suggested that albuminuria can be used as an independent indicator for the healing of type 2 diabetic foot ulcers.

Quantitative and real-time measurement of helicase-mediated intra-stranded G4 unfolding in bulk fluorescence stopped-flow assays.

G-Quadruplexes (G4s) are thermodynamically stable, compact, and poorly hydrated structures that pose a potent obstacle for chromosome replication and gene expression, and requiring resolution by helicases in a cell. Bulk stopped-flow fluorescence assays have provided many mechanistic insights into helicase-mediated duplex DNA unwinding. However, to date, detailed studies on intramolecular G-quadruplexes similar or comparable with those used for studying duplex DNA are still lacking. Here, we describe a method for the direct and quantitative measurement of helicase-mediated intramolecular G-quadruplex unfolding in real time. We designed a series of site-specific fluorescently double-labeled intramolecular G4s and screened appropriate substrates to characterize the helicase-mediated G4 unfolding. With the developed method, we determined, for the first time to our best knowledge, the unfolding and refolding constant of G4 (≈ 5 s-1), and other relative parameters under single-turnover experimental conditions in the presence of G4 traps. Our approach not only provides a new paradigm for characterizing helicase-mediated intramolecular G4 unfolding using stopped-flow assays but also offers a way to screen for inhibitors of G4 unfolding helicases as therapeutic drug targets. Graphical abstract.

Stimulation of ATP Hydrolysis by ssDNA Provides the Necessary Mechanochemical Energy for G4 Unfolding.

The G-quadruplex (G4) is a distinct geometric and electrophysical structure compared to classical double-stranded DNA, and its stability can impede essential cellular processes such as replication, transcription, and translation. This study focuses on the BsPif1 helicase, revealing its ability to bind independently to both single-stranded DNA (ssDNA) and G4 structures. The unfolding activity of BsPif1 on G4 relies on the presence of a single tail chain, and the covalent continuity between the single tail chain and the G4's main chain is necessary for efficient G4 unwinding. This suggests that ATP hydrolysis-driven ssDNA translocation exerts a pull force on G4 unwinding. Molecular dynamics simulations identified a specific region within BsPif1 that contains five crucial amino acid sites responsible for G4 binding and unwinding. A "molecular wire stripper" model is proposed to explain BsPif1's mechanism of G4 unwinding. These findings provide a new theoretical foundation for further exploration of the G4 development mechanism in Pif1 family helicases.

Interleukin-1ß Protection Against Experimental Sepsis in Mice.

The inflammatory response involving interleukin-1ß (IL-1ß) has been thought to play an important role in the development of late-phase sepsis. However, in this study, we wanted to explore the possibility of using IL-1ß to improve the prognosis of sepsis by triggering local differentiation of bone marrow cells (BMCs) into regulatory dendritic cells (DCs) in vivo, thereby reversing the immune paralysis in late-phase sepsis. Sepsis mouse models were induced by cecal ligation and puncture (CLP) and lethal Escherichia coli O18 infection. Mice were injected intraperitoneally with IL-1ß after CLP and after the lethal infection. Septic BMCs and liver immune cells were isolated at 0, 3, 6, 9, and 14 days post-CLP. BMCs and liver cells isolated from septic mice treated with IL-1ß were adoptively transferred into CLP mice. GFP+-C57BL/6 parabiosis models were established. Serum IL-1ß levels were determined by enzyme-linked immunosorbent assay (ELISA) kit, and the number, ratio, and phenotype of immune cells were observed by flow cytometry. IL-1ß treatment improved the survival of sepsis and increased the numbers of BMCs and liver immune cells in septic mice. Moreover, IL-1ß stimulation increased the number and the percentage of CD11c-CD45RBhigh DCs in septic BM and liver. Adoptive transfer of septic BMCs, liver immune cells, and CD11c-CD45RBhigh DCs treated with IL-1ß into CLP mice attenuated sepsis. IL-1ß triggered the redistribution of CD11c-CD45RBhigh DCs as well as BMCs in parabiosis models. IL-1ß protects against sepsis by stimulating local proliferation and differentiation of BMCs into CD11c-CD45RBhigh DCs at immune organs and non-immune organs.

Endogenous Bos taurus RECQL is predominantly monomeric and more active than oligomers.

There is broad consensus that RecQ family helicase is a high-order oligomer that dissociates into a dimer upon ATP binding. This conclusion is based mainly on studies of highly purified recombinant proteins, and the oligomeric states of RecQ helicases in living cells remain unknown. We show here that, in contrast to current models, monomeric RECQL helicase is more abundant than oligomer/dimer forms in living cells. Further characterization of endogenous BtRECQL and isolated monomeric BtRECQL using various approaches demonstrates that both endogenous and recombinant monomeric BtRECQL effectively function as monomers, displaying higher helicase and ATPase activities than dimers and oligomers. Furthermore, monomeric BtRECQL unfolds intramolecular G-quadruplex DNA as efficiently as human RECQL and BLM helicases. These discoveries have implications for understanding endogenous RECQL oligomeric structures and their regulation. It is worth revisiting oligomeric states of the other members of the RecQ family helicases in living cells.

Using competing risk and multistate model to estimate the impact of nosocomial infection on length of stay and mortality in burn patients in Southeast China.

OBJECTIVE: Due to the defects in skin barrier function and immune response, burn patients who survive the acute phase of a burn injury are at a high risk of nosocomial infection (NI). The aim of this study is to evaluate the impacts of NI on length of stay (LOS) and hospital mortality in burn patients using a multistate model. DESIGN AND SETTING: A retrospective observational study was conducted in burn unit and intensive care unit in the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China. PARTICIPANTS: Data were obtained from 1143 records of patients admitted with burn between 1 January 2013 and 31 December 2016. METHODS: Risk factors for NIs were determined by binary logistic regression. The extended Cox model with time-varying covariates was used to determine the impact of NIs on hospital mortality, and cumulative incidence functions were calculated. Multiple linear regression analysis was applied to detect the variables associated with LOS. Using a multistate model, the extra LOS due to NI were determined. RESULTS: 15.8% of total burn patients suffered from NIs and incidence density of NIs was 9.6 per 1000 patient-days. NIs significantly increased the rate of death (HR 4.266, 95% CI 2.218 to 8.208, p=0.000). The cumulative probability of death for patients with NI was greater that for those without NI. The extra LOS due to NIs was 17.68 days (95% CI 11.31 to 24.05). CONCLUSIONS: Using appropriate statistical methods, the present study further illustrated that NIs were associated with the increased cumulative incidence of burn death and increased LOS in burn patients.

Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model.

Helicase DHX36 plays essential roles in cell development and differentiation at least partially by resolving G-quadruplex (G4) structures. Here we report crystal structures of the Drosophila homolog of DHX36 (DmDHX36) in complex with RNA and a series of DNAs. By combining structural, small-angle X-ray scattering, molecular dynamics simulation, and single-molecule fluorescence studies, we revealed that positively charged amino acids in RecA2 and OB-like domains constitute an elaborate structural pocket at the nucleic acid entrance, in which negatively charged G4 DNA is tightly bound and partially destabilized. The G4 DNA is then completely unfolded through the 3'-5' translocation activity of the helicase. Furthermore, crystal structures and DNA binding assays show that G-rich DNA is preferentially recognized and in the presence of ATP, specifically bound by DmDHX36, which may cooperatively enhance the G-rich DNA translocation and G4 unfolding. On the basis of these results, a conceptual G4 DNA-resolving mechanism is proposed.