Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes

Structural maintenance of chromosomes (SMC) complexes are essential for chromatin organization and functions throughout the cell cycle. The cohesin and condensin SMCs fold and tether DNA, while Smc5/6 directly promotes DNA replication and repair. The functions of SMCs rely on their abilities to engage DNA, but how Smc5/6 binds and translocates on DNA remains largely unknown. Here, we present a 3.8 Å cryogenic electron microscopy (cryo-EM) structure of DNA-bound Saccharomyces cerevisiae Smc5/6 complex containing five of its core subunits, including Smc5, Smc6, and the Nse1-3-4 subcomplex. Intricate interactions among these subunits support the formation of a clamp that encircles the DNA double helix. The positively charged inner surface of the clamp contacts DNA in a nonsequence-specific manner involving numerous DNA binding residues from four subunits. The DNA duplex is held up by Smc5 and 6 head regions and positioned between their coiled-coil arm regions, reflecting an engaged-head and open-arm configuration. The Nse3 subunit secures the DNA from above, while the hook-shaped Nse4 kleisin forms a scaffold connecting DNA and all other subunits. The Smc5/6 DNA clamp shares similarities with DNA-clamps formed by other SMCs but also exhibits differences that reflect its unique functions. Mapping cross-linking mass spectrometry data derived from DNA-free Smc5/6 to the DNA-bound Smc5/6 structure identifies multi-subunit conformational changes that enable DNA capture. Finally, mutational data from cells reveal distinct DNA binding contributions from each subunit to Smc5/6 chromatin association and cell fitness. In summary, our integrative study illuminates how a unique SMC complex engages DNA in supporting genome regulation.

Structural maintenance of chromosomes (SMC) complexes are essential genome regulators in both prokaryotes and eukaryotes. In eukaryotes, the cohesin and condensin SMC complexes organize DNA, while the Smc5/6 complex (referred to as Smc5/6) directly regulates DNA replication and repair (1). At the structural level, SMC complexes share similarities while possessing unique attributes (1). Each complex contains a pair of SMC subunits and a set of non-SMC subunits. The SMC subunits define the tripartite filamentous architecture of the complex: their approximal 50-nm long coiled coil arm region connects their dimerized hinge and adenosine triphosphatase (ATPase) head regions (1). A non-SMC kleisin subunit uses its N- and C-terminal domains to link the head of one SMC to the head-proximal arm region (neck) of another SMC, forming a trimeric SMC-kleisin structure. In cohesin and condensin, two large U-shaped HEAT (Huntington, elongation factor 3, PR65/A, TOR) repeat HAWK (HEAT proteins associated with kleisins) subunits attach to the middle region of the kleisin. By contrast, the Smc5/6 kleisin (Nse4) binds to smaller WH (winged helix)-containing KITE (kleisin interacting tandem WH elements) subunits (Nse1 and Nse3) (2).SMC-mediated functions depend on interactions with DNA. Recent cryogenic electron microscopy (cryo-EM) structures of DNA-bound cohesin and condensin revealed that their HAWK subunits and the SMC head-neck regions form a clamp to enclose a single DNA double helix (3–7). DNA clamping can be critical for cohesin and condensin to extrude DNA loops for chromatin folding (5, 7–9). DNA loop extrusion additionally requires arm bending at a region called the elbow, which is found in both cohesin and condensin (5, 7–9). By contrast, a lack of arm bending in Smc5/6 was suggested by negative stain EM and cross-linking mass spectrometry (CLMS) data (10–14). Since Smc5/6 does not contain HAWK proteins nor shows arm-bending, it has remained unclear how Smc5/6 engages DNA to accomplish its multiple functions.Here we address the molecular mechanisms by which this unique SMC complex binds DNA using an integrative approach, coupling a cryo-EM-based structural characterization with CLMS analyses and functional investigation. Our atomic structure of a DNA-bound Saccharomyces cerevisiae Smc5/6 complex reveals that the head-neck Smc5-6 regions and the Nse1-3-4 subcomplex together form a clamp entrapping the DNA helix. The structure further reveals protein subunit folds and association, as well as how the subunits collaborate to entrap DNA. Comparison of CLMS analyses of DNA-free Smc5/6 with the structure of the DNA-bound Smc5/6 unveils large scale, multi-subunit conformational changes that enable Smc5/6 to encircle DNA. Finally, our mutational data suggest distinct contributions from each of the DNA binding regions to Smc5/6 chromatin association and cellular fitness. Comparison of our findings with those of other SMCs reveals that diverse SMC complexes use a similar DNA clamping strategy despite structural differences, and that Smc5/6 possesses unique features distinct from cohesin, condensin, and prokaryotic SMCs. Our work lays the foundation for an in-depth understanding of how Smc5/6 fulfills unique roles in genome protection.     

Domestic Violence Against Women on Yap,Federated States of Micronesia

Anecdotally there are high rates of domestic violence in the small Micronesian State of Yap, Federated States of Micronesia (FSM), but there have been no studies to quantify the prevalence or characteristics of domestic violence in Yap or in any other state of the FSM. A survey was administered to women at the Yap hospital and community health centers from February through June 2011. Survey data were on domestic violence, which was supplemented by a focus group to explore the issues involved in greater detail. A high prevalence of domestic violence was documented by the survey; perceptions about this were explored in the focus group. On the questionnaire, 148 of 194 (76%) women reported at least one form of abuse. Given the small number of adult women in Yap, these findings suggest that domestic violence is a serious, pervasive problem that Yap needs urgently to address. The issue clearly needs to be investigated throughout the other states of the FSM and addressed at the national policy level as well as at the state level.     

Pediatric Perioperative DNR Orders: A Case Series in a Children's Hospital

Context

Do-not-resuscitate (DNR) orders are common among children receiving palliative care, who may nevertheless benefit from surgery and other procedures. Although anesthesia, surgery, and pediatric guidelines recommend systematic reconsideration of DNR orders in the perioperative period, data regarding how clinicians evaluate and manage DNR orders in the perioperative period are limited.

Assessing cognition in people with severe mental disorders in low- and middle-income countries: a systematic review of assessment measures

Background

Cognitive difficulties are common in people with severe mental disorders (SMDs) and various measures of cognition are of proven validity. However, there is a lack of systematic evidence regarding the psychometric properties of these measures in low- and middle-income countries (LMICs).

Objective

To systematically review the psychometric properties of cognitive measures validated in people with SMDs in LMICs.

Methods

We conducted a systematic review of the literature by searching from four electronic databases. Two authors independently screened studies for their eligibility. Measurement properties of measures in all included studies were extracted. All eligible measures were assessed against criteria set for clinical and research recommendations. Results are summarized narratively and measures were grouped by measurement type and population.

Results

We identified 23 unique measures from 28 studies. None of these was from low-income settings. Seventeen of the measures were performance-based. The majority (n = 16/23) of the measures were validated in people with schizophrenia. The most commonly reported measurement properties were: known group, convergent, and divergent validity (n = 25/28). For most psychometric property, studies of methodological qualities were found to be doubtful. Among measures evaluated in people with schizophrenia, Brief Assessment of Cognition in Schizophrenia, Cognitive Assessment Interview, MATRICS Consensus Cognitive Battery, and CogState Schizophrenia Battery were with the highest scores for clinical and research recommendation.

Conclusions

Studies included in our review provide only limited quality evidence and future studies should consider adapting and validating measures using stronger designs and methods. Nonetheless, validated assessments of cognition could help in the management and allocating therapy in people with SMDs in LMICs.

     

The optimal management of variant histology in muscle invasive bladder cancer

Bladder cancer is a heterogenous disease that is associated with tangible mortality in muscle invasive disease. The WHO 2016 classification of urothelial tumours reflects the contemporary approach towards histological variants in bladder cancer, including variants of urothelial carcinoma (UC) and non-urothelial variants. This review focuses on variant histology in UC, and discusses the importance of accurate histological diagnosis, and subsequent risk stratification and therapeutic decision making based on proper variant recognition. Most urothelial variants are associated with poorer outcomes compared to conventional UC, although some perform reasonably better. However, high quality evidence detailing optimal treatment and survival outcomes are still lacking in literature, due to the rarity of these cases.     

Treatment of non-resectable hepatocellular carcinoma with autologous tumor-pulsed dendritic cells

BACKGROUND: The response of hepatocellular carcinoma (HCC) to therapy is often disappointing and new modalities of treatment are clearly needed. Active immunotherapy based on the injection of autologous dendritic cells (DC) co-cultured ex vivo with tumor antigens has been used in pilot studies in various malignancies such as melanoma and lymphoma with encouraging results. METHODS: In the present paper, the preparation and exposure of patient DC to autologous HCC antigens and re-injection in an attempt to elicit antitumor immune responses are described. RESULTS: Therapy was given to two patients, one with hepatitis C and one with hepatitis B, who had large, multiple HCC and for whom no other therapy was available. No significant side-effects were observed. The clinical course was unchanged in one patient, who died a few months later. The other patient, whose initial prognosis was considered poor, is still alive and well more than 3 years later with evidence of slowing of tumor growth based on organ imaging. CONCLUSIONS: It is concluded that HCC may be a malignancy worthy of DC trials and sufficient details in the present paper are given for the protocol to be copied or modified.     

Non-alcoholic fatty liver disease: is iron relevant?

Non-alcoholic fatty liver disease (NAFLD) is a common and ubiquitous disorder (Bedogni et al. in Hepatology 42:44–52, 2005; Bellentani et al. in Ann Intern Med 132:112–117, 2000) which in a proportion of subjects leads to non-alcoholic steatohepatitis (NASH), advanced liver disease and hepatocellular carcinoma. Although the factors responsible for progression of disease are still uncertain, there is evidence that insulin resistance (IR) is a key operative mechanism (Angulo et al. in Hepatology 30:1356–1362, 1999) and that two stages are involved. The first is the accumulation of triglycerides in hepatocytes followed by a “second hit” which promotes cellular oxidative stress. Several factors may be responsible for the induction of oxidative stress but hepatic iron has been implicated in various studies. The topic is controversial, however, with early studies showing an association between hepatic iron (with or without hemochromatosis gene mutations) and the progression to hepatic fibrosis. Subsequent studies, however, could not confirm an association between the presence of hepatic iron and any of the histological determinants of NAFLD or NASH. Recent studies have reactivated interest in this subject firstly, with the demonstration that hepatic iron loading increases liver cholesterol synthesis with increased lipid deposition in the liver increasing the cellular lipid burden and secondly, a large clinical study has concluded that hepatocellular iron deposition is associated with an increased risk of hepatic fibrosis, thus, strongly supporting the original observation made over a decade ago. An improvement in insulin sensitivity has been demonstrated following phlebotomy therapy but a suitably powered controlled clinical trial is required before this treatment can be implemented.