Structure of the ParM filament at 8.5Å resolution

AbstractThe actin-like protein ParM forms the cytomotive filament of the ParMRC system, a type II plasmid segregation system encoded by Escherichia coli R1 plasmid. We report an 8.5Å resolution reconstruction of the ParM filament, obtained using cryo-electron microscopy. Fitting of the 3D density reconstruction with monomeric crystal structures of ParM provides insights into dynamic instability of ParM filaments. The structural analysis suggests that a ParM conformation, corresponding to a metastable state, is held within the filament by intrafilament contacts. This filament conformation of ParM can be attained only from the ATP-bound state, and induces a change in conformation of the bound nucleotide. The structural analysis also provides a rationale for the observed stimulation of hydrolysis upon polymerisation into the filament

Towards OSGeo Best Practices for Scientific Software Citation: Integration Options for Persistent Identifiers in OSGeo Project Repositories

As a contribution to the currently ongoing larger effort to establish Open Science as best practices in academia, this article focuses on the Open Source and Open Access tiers of the Open Science triad and community software projects. The current situation of research software development and the need to recognize it as a significant contribution to science is introduced in relation to Open Science. The adoption of the Open Science paradigms occurs at different speeds and on different levels within the various fields of science and crosscutting software communities. This is paralleled by the emerging of an underlying futuresafe technical infrastructure based on open standards to enable proper recognition for published articles, data, and software. Currently the number of journal publications about research software remains low in comparison to the amount of research code published on various software repositories in the WWW. Because common standards for the citation of software projects (containers) and versions of software are lacking, the FORCE11 group and the CodeMeta project recommending to establish Persistent Identifiers (PIDs), together with suitable metadata setss to reliably cite research software. This approach is compared to the best practices implemented by the OSGeo Foundation for geospatial community software projects. For GRASS GIS, a OSGeo project and one of the oldest geospatial open source community projects, the external requirements for DOI-based software citation are compared with the projects software documentation standards. Based on this status assessment, application scenarios are derived, how OSGeo projects can approach DOI-based software citation, both as a standalone option and also as a means to foster open access journal publications as part of reproducible Open Science

Towards OSGeo Best Practices for Scientific Software Citation: Integration Options for Persistent Identifiers fn OSGeo Project Repositories

As a contribution to the currently ongoing larger effort to establish Open Science as best practices in academia, this article focuses on the Open Source and Open Access tiers of the Open Science triad and community software projects. The current situation of research software development and the need to recognize it as a significant contribution to science is introduced in relation to Open Science. The adoption of the Open Science paradigms occurs at different speeds and on different levels within the various fields of science and crosscutting software communities. This is paralleled by the emerging of an underlying futuresafe technical infrastructure based on open standards to enable proper recognition for published articles, data, and software. Currently the number of journal publications about research software remains low in comparison to the amount of research code published on various software repositories in the WWW. Because common standards for the citation of software projects (containers) and versions of software are lacking, the FORCE11 group and the CodeMeta project recommending to establish Persistent Identifiers (PIDs), together with suitable metadata setss to reliably cite research software. This approach is compared to the best practices implemented by the OSGeo Foundation for geospatial community software projects. For GRASS GIS, a OSGeo project and one of the oldest geospatial open source community projects, the external requirements for DOI-based software citation are compared with the projects software documentation standards. Based on this status assessment, application scenarios are derived, how OSGeo projects can approach DOI-based software citation, both as a standalone option and also as a means to foster open access journal publications as part of reproducible Open Science

Cryo-EM structure of the full-length Lon protease from Thermus thermophilus.

In bacteria, Lon is a large hexameric ATP-dependent protease that targets misfolded and also folded substrates, some of which are involved in cell division and survival of cellular stress. The N-terminal domain of Lon facilitates substrate recognition, but how the domains confer such activity has remained unclear. Here, we report the full-length structure of Lon protease from Thermus thermophilus at 3.9 Å resolution in a substrate-engaged state. The six N-terminal domains are arranged in three pairs, stabilized by coiled-coil segments and forming an additional channel for substrate sensing and entry into the AAA+ ring. Sequence conservation analysis and proteolysis assays confirm that this architecture is required for the degradation of both folded and unfolded substrates in bacteria

Crystal structure of the Z-ring associated cell division protein ZapC from Escherichia coli

AbstractBacterial cell division involves a contractile ring that organises downstream proteins at the division site and which contains the tubulin homologue FtsZ. ZapC has been discovered as a non-essential regulator of FtsZ. It localises to the septal ring and deletion of zapC leads to a mild phenotype, while overexpression inhibits cell division. Interference with cell division is facilitated by an interaction with FtsZ. Here, we present the 2.9Å crystal structure of ZapC from Escherichia coli. ZapC forms a dimer and comprises two domains that belong to the Royal superfamily of which many members bind methylated arginines or lysines. ZapC contains an N-terminal chromo-like domain and a Tudor-like C-terminal domain. We show by ITC that ZapC binds the C-terminal tail of FtsZ

Transport of DNA within cohesin involves clamping on top of engaged heads by Scc2 and entrapment within the ring by Scc3.

In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3. Using thiol-specific crosslinking we provide rigorous proof of entrapment activity in vitro. Scc2 alone promotes entrapment of DNAs in the E-S and E-K compartments, between ATP-bound engaged heads and the SMC hinge and associated kleisin, respectively. This does not require ATP hydrolysis nor is it accompanied by entrapment within S-K rings, which is a slower process requiring Scc3. Cryo-EM reveals that DNAs transported into E-S/E-K compartments are 'clamped' in a sub-compartment created by Scc2's association with engaged heads whose coiled coils are folded around their elbow. We suggest that clamping may be a recurrent feature of cohesin complexes active in loop extrusion and that this conformation precedes the S-K entrapment required for sister chromatid cohesion

Membraneless channels sieve cations in ammonia-oxidizing marine archaea

Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1, 2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle

The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division

ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA-adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III-dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III-dependent membrane remodeling. </p

Trauma history and depression predict incomplete adherence to antiretroviral therapies in a low income country.

As antiretroviral therapy (ART) for HIV becomes increasingly available in low and middle income countries (LMICs), understanding reasons for lack of adherence is critical to stemming the tide of infections and improving health. Understanding the effect of psychosocial experiences and mental health symptomatology on ART adherence can help maximize the benefit of expanded ART programs by indicating types of services, which could be offered in combination with HIV care. The Coping with HIV/AIDS in Tanzania (CHAT) study is a longitudinal cohort study in the Kilimanjaro Region that included randomly selected HIV-infected (HIV+) participants from two local hospital-based HIV clinics and four free-standing voluntary HIV counselling and testing sites. Baseline data were collected in 2008 and 2009; this paper used data from 36 month follow-up interviews (N = 468). Regression analyses were used to predict factors associated with incomplete self-reported adherence to ART. INCOMPLETE ART ADHERENCE WAS SIGNIFICANTLY MORE LIKELY TO BE REPORTED AMONGST PARTICIPANTS WHO EXPERIENCED A GREATER NUMBER OF CHILDHOOD TRAUMATIC EVENTS: sexual abuse prior to puberty and the death in childhood of an immediate family member not from suicide or homicide were significantly more likely in the non-adherent group and other negative childhood events trended toward being more likely. Those with incomplete adherence had higher depressive symptom severity and post-traumatic stress disorder (PTSD). In multivariable analyses, childhood trauma, depression, and financial sacrifice remained associated with incomplete adherence.\ud This is the first study to examine the effect of childhood trauma, depression and PTSD on HIV medication adherence in a low income country facing a significant burden of HIV. Allocating spending on HIV/AIDS toward integrating mental health services with HIV care is essential to the creation of systems that enhance medication adherence and maximize the potential of expanded antiretroviral access to improve health and reduce new infections

MreB filaments align along greatest principal membrane curvature to orient cell wall synthesis

MreB is essential for rod shape in many bacteria. Membrane-associated MreB filaments move around the rod circumference, helping to insert cell wall in the radial direction to reinforce rod shape. To understand how oriented MreB motion arises, we altered the shape of Bacillus subtilis. MreB motion is isotropic in round cells, and orientation is restored when rod shape is externally imposed. Stationary filaments orient within protoplasts, and purified MreB tubulates liposomes in vitro, orienting within tubes. Together, this demonstrates MreB orients along the greatest principal membrane curvature, a conclusion supported with biophysical modeling. We observed that spherical cells regenerate into rods in a local, self-reinforcing manner: rapidly propagating rods emerge from small bulges, exhibiting oriented MreB motion. We propose that the coupling of MreB filament alignment to shape-reinforcing peptidoglycan synthesis creates a locally-acting, self-organizing mechanism allowing the rapid establishment and stable maintenance of emergent rod shape