Cooperative action of separate interaction domains promotes high-affinity DNA binding of Arabidopsis thaliana ARF transcription factors.

The signaling molecule auxin coordinates many growth and development processes in plants, mainly through modulating gene expression. Transcriptional response is mediated by the family of auxin response factors (ARF). Monomers of this family recognize a DNA motif and can homodimerize through their DNA-binding domain (DBD), enabling cooperative binding to an inverted binding site. Most ARFs further contain a C-terminal PB1 domain that is capable of homotypic interactions and mediating interactions with Aux/IAA repressors. Given the dual role of the PB1 domain, and the ability of both DBD and PB1 domain to mediate dimerization, a key question is how these domains contribute to DNA-binding specificity and affinity. So far, ARF-ARF and ARF-DNA interactions have mostly been approached using qualitative methods that do not provide a quantitative and dynamic view on the binding equilibria. Here, we utilize a DNA binding assay based on single-molecule Förster resonance energy transfer (smFRET) to study the affinity and kinetics of the interaction of several Arabidopsis thaliana ARFs with an IR7 auxin-responsive element (AuxRE). We show that both DBD and PB1 domains of AtARF2 contribute toward DNA binding, and we identify ARF dimer stability as a key parameter in defining binding affinity and kinetics across AtARFs. Lastly, we derived an analytical solution for a four-state cyclic model that explains both the kinetics and the affinity of the interaction between AtARF2 and IR7. Our work demonstrates that the affinity of ARFs toward composite DNA response elements is defined by dimerization equilibrium, identifying this as a key element in ARF-mediated transcriptional activity.

Patients want to be seen: The top 3 information needs of patients with inguinal hernia.

BACKGROUND: Good patient information has shown to improve surgical outcomes. In this study we explore what kind of pre-surgical information patients need and if the provision of a 360˚ video of a surgical procedure can be of added value to the information provided by the hospital. METHODS: An explorative qualitative study using semi-structured interviews on information needs was conducted among 17 inguinal hernia patients to gain more insight in the patients' present surgical information needs. Patients either were planned to receive or already had received a surgical procedure. Questions were asked about the current information provision and, after being shown a 360˚ video of the surgery, whether this would be of added value. RESULTS: Of the total group of 17 patients (mean age 56, interquartile range 45-64) 16 were male and one was female. Most had no previous experience with virtual reality (14/17), already had undergone a surgical procedure (11/17). Patient information needs were all about "seeing" which can be viewed from three different perspectives [1] being seen as a unique person in the treatment process, [2] being seen as a partner, and [3] seeing is understanding. Patients wanted the contact with the doctor to be more personal, with the possibility to see the anesthetist in person, the surgeon to see their wound in the recovery phase, and to receive personal answers to questions about their specific situation. Patients found the 360-video not fearsome, and believed that visual content could be beneficial as it appeals more to their imagination than written or oral information and increases their understanding. It also provided them with a better understanding of their treatment options, their pre-, peri-, and post-surgical procedures and identification of the cause of post-operative side effects. CONCLUSION: To address patients' information needs, complementary tools or services are needed that increase personal contact as well as tailor it to individual patient's needs. Even though video-apps are a partial alternative, hospitals should still offer patients the possibility of having face-to-face meetings with physicians as this is highly valued by patients and leads to increased trust in physicians' performance.

Molecular mechanism of light-driven sodium pumping.

The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 Å, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools.

Early fixation versus conservative therapy of multiple, simple rib fractures (FixCon): protocol for a multicenter randomized controlled trial.

Background: Multiple rib fractures are common injuries in both the young and elderly. Rib fractures account for 10% of all trauma admissions and are seen in up to 39% of patients after thoracic trauma. With morbidity and mortality rates increasing with the number of rib fractures as well as poor quality of life at long-term follow-up, multiple rib fractures pose a serious health hazard. Operative fixation of flail chest is beneficial over nonoperative treatment regarding, among others, pneumonia and both intensive care unit (ICU) and hospital length of stay. With no high-quality evidence on the effects of multiple simple rib fracture treatment, the optimal treatment modality remains unknown. This study sets out to investigate outcome of operative fixation versus nonoperative treatment of multiple simple rib fractures. Methods: The proposed study is a multicenter randomized controlled trial. Patients will be eligible if they have three or more multiple simple rib fractures of which at least one is dislocated over one shaft width or with unbearable pain (visual analog scale (VAS) or numeric rating scale (NRS) > 6). Patients in the intervention group will be treated with open reduction and internal fixation. Pre- and postoperative care equals treatment in the control group. The control group will receive nonoperative treatment, consisting of pain management, bronchodilator inhalers, oxygen support or mechanical ventilation if needed, and pulmonary physical therapy. The primary outcome measure will be occurrence of pneumonia within 30 days after trauma. Secondary outcome measures are the need and duration of mechanical ventilation, thoracic pain and analgesics use, (recovery of) pulmonary function, hospital and ICU length of stay, thoracic injury-related and surgery-related complications and mortality, secondary interventions, quality of life, and cost-effectiveness comprising health care consumption and productivity loss. Follow-up visits will be standardized and daily during hospital admission, at 14 days and 1, 3, 6, and 12 months. Discussion: With favorable results in flail chest patients, operative treatment may also be beneficial in patients with multiple simple rib fractures. The FixCon trial will be the first study to compare clinical, functional, and economic outcome between operative fixation and nonoperative treatment for multiple simple rib fractures. Trial registration: www.trialregister.nl, NTR7248. Registered May 31, 2018.

A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125.

The activity of RING ubiquitin ligases (E3s) depends on an interaction between the RING domain and ubiquitin conjugating enzymes (E2), but posttranslational events or additional structural elements, yet largely undefined, are frequently required to enhance or regulate activity. Here, we show for the ubiquitin ligase RNF125 that, in addition to the RING domain, a C2HC Zn finger (ZnF) is crucial for activity, and a short linker sequence (Li2(120-128)) enhances activity. The contribution of these regions was first shown with truncated proteins, and the essential role of the ZnF was confirmed with mutations at the Zn chelating Cys residues. Using NMR, we established that the C2HC ZnF/Li2(120-128) region is crucial for binding of the RING domain to the E2 UbcH5a. The partial X-ray structure of RNF125 revealed the presence of extensive intramolecular interactions between the RING and C2HC ZnF. A mutation at one of the contact residues in the C2HC ZnF, a highly conserved M112, resulted in the loss of ubiquitin ligase activity. Thus, we identified the structural basis for an essential role of the C2HC ZnF and conclude that this domain stabilizes the RING domain, and is therefore required for binding of RNF125 to an E2.

Nicking activity of the pMV158 MobM relaxase on cognate and heterologous origins of transfer.

The MobM relaxase (494 amino acids) encoded by the promiscuous streptococcal plasmid pMV158 recognizes the plasmid origin of transfer, oriTpMV158, and converts supercoiled pMV158 DNA into relaxed molecules by cleavage of the phosphodiester bond of a specific dinucleotide within the sequence 5'-GTGTG/TT-3' ("/" being the nick site). After cleavage, the protein remains stably bound to the 5'-end of the nick site. Band-shift assays with single-stranded oligonucleotides and size-exclusion chromatography allowed us to show that MobM was able to generate specific complexes with one of the inverted repeats of the oriTpMV158, presumably extruded as stem-loop structure. A number of tests have been performed to attain a better characterization of the nicking activity of MobM and its linkage with its target DNA. The optimal pH for DNA relaxation was found to be 6.5. Upon nicking, gel retardation assays showed that MobM formed stable complexes with its target DNA. Moreover, MobM bound to relaxed pMV158 molecules were visualized by electron microscopy. The staphylococcal plasmids pUB110 and pE194, and the streptococcal plasmid pDL287 harbour putative oriTs and may encode Mob proteins homologous to MobM. The oriTpUB110, oriTpDL287, and oriTpE194 sequences share 100%, 70%, and 67% (in a 43-nucleotide stretch and allowing a 3-bp gap) identity to oriTpMV158, respectively. Nicking assays using supercoiled DNAs from pUB110, pDL287, and pE194 showed that MobM was able to relax, to differing degrees, all plasmid DNAs. Our results suggest that cross-recognition of heterologous oriTs by Mob proteins could play an important role in the plasmid spreading between bacteria.

Unveiling the molecular mechanism of a conjugative relaxase: The structure of TrwC complexed with a 27-mer DNA comprising the recognition hairpin and the cleavage site.

TrwC is a DNA strand transferase that catalyzes the initial and final stages of conjugative DNA transfer. We have solved the crystal structure of the N-terminal relaxase domain of TrwC in complex with a 27 base-long DNA oligonucleotide that contains both the recognition hairpin and the scissile phosphate. In addition, a series of ternary structures of protein-DNA complexes with different divalent cations at the active site have been solved. Systematic anomalous difference analysis allowed us to determine unambiguously the nature of the metal bound. Zn2+, Ni2+ and Cu2+ were found to bind the histidine-triad metal binding site. Comparison of the structures of the different complexes suggests two pathways for the DNA to exit the active pocket. They are probably used at different steps of the conjugative DNA-processing reaction. The structural information allows us to propose (i) an enzyme mechanism where the scissile phosphate is polarized by the metal ion facilitating the nucleophilic attack of the catalytic tyrosine, and (ii) a probable sequence of events during conjugative DNA processing that explains the biological function of the relaxase.