SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

<p>Abstract</p> <p>Background</p> <p>The development of complex biochemical models has been facilitated through the standardization of machine-readable representations like SBML (Systems Biology Markup Language). This effort is accompanied by the ongoing development of the human-readable diagrammatic representation SBGN (Systems Biology Graphical Notation). The graphical SBML editor CellDesigner allows direct translation of SBGN into SBML, and vice versa. For the assignment of kinetic rate laws, however, this process is not straightforward, as it often requires manual assembly and specific knowledge of kinetic equations.</p> <p>Results</p> <p>SBMLsqueezer facilitates exactly this modeling step via automated equation generation, overcoming the highly error-prone and cumbersome process of manually assigning kinetic equations. For each reaction the kinetic equation is derived from the stoichiometry, the participating species (e.g., proteins, mRNA or simple molecules) as well as the regulatory relations (activation, inhibition or other modulations) of the SBGN diagram. Such information allows distinctions between, for example, translation, phosphorylation or state transitions. The types of kinetics considered are numerous, for instance generalized mass-action, Hill, convenience and several Michaelis-Menten-based kinetics, each including activation and inhibition. These kinetics allow SBMLsqueezer to cover metabolic, gene regulatory, signal transduction and mixed networks. Whenever multiple kinetics are applicable to one reaction, parameter settings allow for user-defined specifications. After invoking SBMLsqueezer, the kinetic formulas are generated and assigned to the model, which can then be simulated in CellDesigner or with external ODE solvers. Furthermore, the equations can be exported to SBML, LaTeX or plain text format.</p> <p>Conclusion</p> <p>SBMLsqueezer considers the annotation of all participating reactants, products and regulators when generating rate laws for reactions. Thus, for each reaction, only applicable kinetic formulas are considered. This modeling scheme creates kinetics in accordance with the diagrammatic representation. In contrast most previously published tools have relied on the stoichiometry and generic modulators of a reaction, thus ignoring and potentially conflicting with the information expressed through the process diagram. Additional material and the source code can be found at the project homepage (URL found in the Availability and requirements section).</p

Antagonistic Roles of SEPALLATA3, FT and FLC Genes as Targets of the Polycomb Group Gene CURLY LEAF

In Arabidopsis, mutations in the Pc-G gene CURLY LEAF (CLF) give early flowering plants with curled leaves. This phenotype is caused by mis-expression of the floral homeotic gene AGAMOUS (AG) in leaves, so that ag mutations largely suppress the clf phenotype. Here, we identify three mutations that suppress clf despite maintaining high AG expression. We show that the suppressors correspond to mutations in FPA and FT, two genes promoting flowering, and in SEPALLATA3 (SEP3) which encodes a co-factor for AG protein. The suppression of the clf phenotype is correlated with low SEP3 expression in all case and reveals that SEP3 has a role in promoting flowering in addition to its role in controlling floral organ identity. Genetic analysis of clf ft mutants indicates that CLF promotes flowering by reducing expression of FLC, a repressor of flowering. We conclude that SEP3 is the key target mediating the clf phenotype, and that the antagonistic effects of CLF target genes masks a role for CLF in promoting flowering

Circulating Nucleosomes as Potential Markers to Monitor COVID-19 Disease Progression.

peer reviewedThe severity of coronavirus disease 2019 (COVID-19) varies significantly with cases spanning from asymptomatic to lethal with a subset of individuals developing Severe Acute Respiratory Syndrome (SARS) and death from respiratory failure. To determine whether global nucleosome and citrullinated nucleosome levels were elevated in COVID-19 patients, we tested two independent cohorts of COVID-19 positive patients with quantitative nucleosome immunoassays and found that nucleosomes were highly elevated in plasma of COVID-19 patients with a severe course of the disease relative to healthy controls and that both histone 3.1 variant and citrullinated nucleosomes increase with disease severity. Elevated citrullination of circulating nucleosomes is indicative of neutrophil extracellular trap formation, neutrophil activation and NETosis in severely affected individuals. Importantly, using hospital setting (outpatient, inpatient or ICU) as a proxy for disease severity, nucleosome levels increased with disease severity and may serve as a guiding biomarker for treatment. Owing to the limited availability of mechanical ventilators and extracorporal membrane oxygenation (ECMO) equipment, there is an urgent need for effective tools to rapidly assess disease severity and guide treatment selection. Based on our studies of two independent cohorts of COVID-19 patients from Belgium and Germany, we suggest further investigation of circulating nucleosomes and citrullination as biomarkers for clinical triage, treatment allocation and clinical drug discovery

Molecular Architecture of the Human Prp19/CDC5L Complex▿ †

Protein complexes containing Prp19 play a central role during catalytic activation of the spliceosome, and Prp19 and its related proteins are major components of the spliceosome's catalytic core RNP. To learn more about the spatial organization of the human Prp19 (hPrp19)/CDC5L complex, which is comprised of hPrp19, CDC5L, PRL1, AD002, SPF27, CTNNBL1, and HSP73, we purified native hPrp19/CDC5L complexes from HeLa cells stably expressing FLAG-tagged AD002 or SPF27. Stoichiometric analyses indicated that, like Saccharomyces cerevisiae NTC (nineteen complex), the human Prp19/CDC5L complex contains four copies of hPrp19. Salt treatment identified a stable core comprised of CDC5L, hPrp19, PRL1, and SPF27. Protein-protein interaction studies revealed that SPF27 directly interacts with each component of the hPrp19/CDC5L complex core and also elucidated several additional, previously unknown interactions between hPrp19/CDC5L complex components. Limited proteolysis of the hPrp19/CDC5L complex revealed a protease-resistant complex comprised of SPF27, the C terminus of CDC5L, and the N termini of PRL1 and hPrp19. Under the electron microscope, purified hPrp19/CDC5L complexes exhibit an elongated, asymmetric shape with a maximum dimension of ∼20 nm. Our findings not only elucidate the molecular organization of the hPrp19/CDC5L complex but also provide insights into potential protein-protein interactions at the core of the catalytically active spliceosome

Methylation of Lysine 9 in Histone H3 Directs Alternative Modes of Highly Dynamic Interaction of Heterochromatin Protein hHP1β with the Nucleosome

CAPSULE: BACKGROUND: Chromatin-HP1 (heterochromatin protein 1) interaction is crucial for heterochromatin assembly. RESULTS: hHP1β uses alternative interfaces to bind nucleosomes depending on histone 3 methylation within a highly dynamic complex. CONCLUSION: hHP1β explores chromatin for sites of methyl-mark enrichment where it can bind histone 3 tails from adjacent nucleosomes. SIGNIFICANCE: We provide a conceptual framework to understand the molecular basis of dynamic interactions regulated by histone modification.Binding of heterochromatin protein 1 (HP1) to the histone H3 lysine 9 trimethylation (H3K9me3) mark is a hallmark of establishment and maintenance of heterochromatin. Although genetic and cell biological aspects have been elucidated, the molecular details of HP1 binding to H3K9me3 nucleosomes are unknown. Using a combination of NMR spectroscopy and biophysical measurements on fully defined recombinant experimental systems, we demonstrate that H3K9me3 works as an on/off switch regulating distinct binding modes of hHP1β to the nucleosome. The methyl-mark determines a highly flexible and very dynamic interaction of the chromodomain of hHP1β with the H3-tail. There are no other constraints of interaction or additional multimerization interfaces. In contrast, in the absence of methylation, the hinge region and the N-terminal tail form weak nucleosome contacts mainly with DNA. In agreement with the high flexibility within the hHP1β-H3K9me3 nucleosome complex, the chromoshadow domain does not provide a direct binding interface. Our results report the first detailed structural analysis of a dynamic protein-nucleosome complex directed by a histone modification and provide a conceptual framework for understanding similar interactions in the context of chromatin

HErZ: The German Hans-Ertel Centre for Weather Research

In 2011, the German Federal Ministry of Transport, Building and Urban Development laid the foundation of the Hans-Ertel Centre for Weather Research [Hans-Ertel-Zentrum für Wetterforschung (HErZ)] in order to better connect fundamental meteorological research and teaching at German universities and atmospheric research centers with the needs of the German national weather service Deutscher Wetterdienst (DWD). The concept for HErZ was developed by DWD and its scientific advisory board with input from the entire German meteorological community. It foresees core research funding of about €2,000,000 yr−1 over a 12-yr period, during which time permanent research groups must be established and DWD subjects strengthened in the university curriculum. Five priority research areas were identified: atmospheric dynamics and predictability, data assimilation, model development, climate monitoring and diagnostics, and the optimal use of information from weather forecasting and climate monitoring for the benefit of society. Following an open call, five groups were selected for funding for the first 4-yr phase by an international review panel. A dual project leadership with one leader employed by the academic institute and the other by DWD ensures that research and teaching in HErZ is attuned to DWD needs and priorities, fosters a close collaboration with DWD, and facilitates the transfer of fundamental research into operations. In this article, we describe the rationale behind HErZ and the road to its establishment, present some scientific highlights from the initial five research groups, and discuss the merits and future development of this new concept to better link academic research with the needs and challenges of a national weather service

Ecological role of volatiles produced by Epichloë: differences in antifungal toxicity

Species of Epichloë (Ascomycota, Clavicipitaceae) are endophytic symbionts of pooid grasses. Sexual reproduction of the fungus depends on gamete-transferring Botanophila flies, which in earlier studies were shown to be specifically attracted by the fungal volatiles chokol K and methyl (Z)-3-methyldodec-2-enoate. As several Epichloë volatiles are known to have antimicrobial properties, it was hypothesised that the original function of insect-attracting volatiles is microbial deterrence. However, the origin of volatile compounds and their toxicity within an ecological context has not yet been clarified. We examined the inhibitory effect of chokol K and methyl (Z)-3-methyldodec-2-enoate on mycoparasites, plant pathogenic fungi and on Epichloë itself at ecologically relevant concentrations, and assessed volatile production in pure cultures of Epichloë on complex and defined media supplemented with inorganic sources of carbon and nitrogen. Chokol K reduced the spore germination of all tested fungi, whereas methyl (Z)-3-methyldodec-2-enoate had no inhibitory effect. Moreover, only chokol K was produced in culture, confirming its fungal origin. Our findings are consistent with the proposed scenario that fungal volatile substances have followed an evolutionary pathway from defence to attraction