More than a bystander: RNAs specify multifaceted behaviors of liquid-liquid phase-separated biomolecular condensates

Cells contain a myriad of membraneless ribonucleoprotein (RNP) condensates with distinct compositions of proteins and RNAs. RNP condensates participate in different cellular activities, including RNA storage, mRNA translation or decay, stress response, etc. RNP condensates are assembled via liquid-liquid phase separation (LLPS) driven by multivalent interactions. Transition of RNP condensates into bodies with abnormal material properties, such as solid-like amyloid structures, is associated with the pathogenesis of various diseases. In this review, we focus on how RNAs regulate multiple aspects of RNP condensates, such as dynamic assembly and/or disassembly and biophysical properties. RNA properties – including concentration, sequence, length and structure – also determine the phase behaviors of RNP condensates. RNA is also involved in specifying autophagic degradation of RNP condensates. Unraveling the role of RNA in RNPs provides novel insights into pathological accumulation of RNPs in various diseases. This new understanding can potentially be harnessed to develop therapeutic strategies.     

Poly(ADP-ribose) drives condensation of FUS via a transient interaction

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The role of DNA replication in chromosome condensation

At metaphase, DNA in a human chromosome is estimated to be compacted at least 10,000 fold in length. However, the higher order mechanisms by which the chromosomes are organized in interphase and subsequently further condensed in mitosis have largely remained elusive. One generally overlooked participant in chromosome condensation is DNA replication. Many early studies of eukaryotic chromosome organization and cell fusions have suggested that DNA replication plays a role in chromosome compaction. Recent phenotypic analysis of Drosophila DNA replication mutants has revitalized this old idea. In this review, the role of DNA replication in chromosome condensation will be examined.     

The minor spliceosome could be the major key for FUS/TLS mutants in ALS

Despite its name, minor spliceosome alterations are often involved in human disease origin. Work by Reber et al ( 2016 ) in this issue of The EMBO Journal now demonstrates a connection between minor spliceosome components and FUS/TLS, one of the major proteins aggregating in the brain of patients affected by amyotrophic lateral sclerosis (ALS). This finding has important implications as it extends the spectrum of diseases where minor spliceosome plays a role. It may also represent a new opportunity for specific therapeutic targets.     

The A-kinase-anchoring protein AKAP95 is a multivalent protein with a key role in chromatin condensation at mitosis

Protein kinase A (PKA) and the nuclear A-kinase-anchoring protein AKAP95 have previously been shown to localize in separate compartments in interphase but associate at mitosis. We demonstrate here a role for the mitotic AKAP95-PKA complex. In HeLa cells, AKAP95 is associated with the nuclear matrix in interphase and redistributes mostly into a chromatin fraction at mitosis. In a cytosolic extract derived from mitotic cells, AKAP95 recruits the RIIalpha regulatory subunit of PKA onto chromatin. Intranuclear immunoblocking of AKAP95 inhibits chromosome condensation at mitosis and in mitotic extract in a PKA-independent manner. Immunodepletion of AKAP95 from the extract or immunoblocking of AKAP95 at metaphase induces premature chromatin decondensation. Condensation is restored in vitro by a recombinant AKAP95 fragment comprising the 306-carboxy-terminal amino acids of the protein. Maintenance of condensed chromatin requires PKA binding to chromatin-associated AKAP95 and cAMP signaling through PKA. Chromatin-associated AKAP95 interacts with Eg7, the human homologue of Xenopus pEg7, a component of the 13S condensin complex. Moreover, immunoblocking nuclear AKAP95 inhibits the recruitment of Eg7 to chromatin in vitro. We propose that AKAP95 is a multivalent molecule that in addition to anchoring a cAMP/PKA-signaling complex onto chromosomes, plays a role in regulating chromosome structure at mitosis.     

Expression of human FUS/TLS in yeast leads to protein aggregation and cytotoxicity,recapitulating key features of FUS proteinopathy

Mutations in the fused in sarcoma/translocated in liposarcoma (FUS/TLS) gene have been associated with amyotrophic lateral sclerosis (ALS). FUS-positive neuropathology is reported in a range of neurodegenerative diseases, including ALS and fronto-temporal lobar degeneration with ubiquitin-positive pathology (FTLD-U). To examine protein aggregation and cytotoxicity, we expressed human FUS protein in yeast. Expression of either wild type or ALS-associated R524S or P525L mutant FUS in yeast cells led to formation of aggregates and cytotoxicity, with the two ALS mutants showing increased cytotoxicity. Therefore, yeast cells expressing human FUS protein recapitulate key features of FUS-positive neurodegenerative diseases. Interestingly, a significant fraction of FUS expressing yeast cells stained by propidium iodide were without detectable protein aggregates, suggesting that membrane impairment and cellular damage caused by FUS expression may occur before protein aggregates become microscopically detectable and that aggregate formation might protect cells from FUS-mediated cytotoxicity. The N-terminus of FUS, containing the QGSY and G rich regions, is sufficient for the formation of aggregates but not cytotoxicity. The C-terminal domain, which contains a cluster of mutations, did not show aggregation or cytotoxicity. Similar to TDP-43 when expressed in yeast, FUS protein has the intrinsic property of forming aggregates in the absence of other human proteins. On the other hand, the aggregates formed by FUS are thioflavin T-positive and resistant to 0.5% sarkosyl, unlike TDP-43 when expressed in yeast cells. Furthermore, TDP-43 and FUS display distinct domain requirements in aggregate formation and cytotoxicity.     

Reaction equilibrium for lipase-catalyzed condensation in organic solvent systems

Lipase-catalyzed condensation in an organic solvent is useful for the syntheses of esters. To reasonably design and optimize the reaction conditions, knowledge of the reaction equilibrium is required. The interaction of water with other reactants and the quantitative predictions for adsorption of water by a desiccant are discussed. The solvent effects on the reaction equilibrium are also elucidated in mixtures of nitrile and tert-alcohol.     

Reaction equilibrium for lipase-catalyzed condensation in organic solvent systems

Lipase-catalyzed condensation in an organic solvent is useful for the syntheses of esters. To reasonably design and optimize the reaction conditions, knowledge of the reaction equilibrium is required. The interaction of water with other reactants and the quantitative predictions for adsorption of water by a desiccant are discussed. The solvent effects on the reaction equilibrium are also elucidated in mixtures of nitrile and tert-alcohol.     

The evolutionary significance of phase-separated microsystems

The source, preparation, and properties of phase-separated systems such as lipid layers, coacervate droplets, sulphobes, and proteinoid microspheres are reviewed. These microsystems are of interest as partial models for the cell and as partial or total models for the protocell. Conceptual benefits from study of such models are: clues to experiments on origins, insights into principles of action and, in some instances, presumable models of the origin of the protocell. The benefits to evolution of organized chemical units are many, and can in part be analyzed. Ease of formation suggests that such units would have arisen early in primordial organic evolution. Integration of these various concepts and the results of consequent experiments have contributed to the developing theory of the origins of primordial and of contemporary life.Invited paper. Presented at the International Seminar Origin of Life, 2–7 August 1974, Moscow, U.S.S.R.     

DNA condensation by cobalt hexaammine(III) in alcohol–water mixtures: Dielectric constant and other solvent effects

DNA molecules condense into compact structures in the presence of a critical concentration of multivalent cations. To probe the contribution ofelectrostatic forces to condensation, we used mixtures of water with methanol (MeOH), ethanol (EtOH), and isopropanol (iPrOH) to vary the dielectric constant ? from 80 to 50. The condensation of pUC18 plasmids by hexaammine cobalt (III), Co(NH₃), was monitored by total intensity and dynamic light scattering, electron microscopy, andCD. The total scattering intensity increased as ? went from 80 to 70, and then decreased as ? decreased further. Ultraviolet spectrophotometry confirmed that the loss of intensity at low ? was not due to the particles' settling out of solution. The rate as well as the extent of condensation increased as? was lowered from 80 to 70, and also depended on the species of alcohol (MeOH < EtOH < iPrOH). The hydrodynamic radii R_H of the particles, however, remained roughly the same at 300–350 A and was independent of the species of alcohol. R_H increased below ? = 70. The critical concentration of Co(NH₃) required to induce DNA condensation decreased from 21 μM to about 16 μM as the dielectric constant decreased from 80 to 70, and decreased moderately with the nonpolarity of the alcohol. The fraction of DNA charge neutralized at the onset of DNA condensation was calculated by a modification of Manning's two-variable counterion condensation theory to be 0.90 ± 0.01, independent of ?. By electron microscopy we observed that the condensed particles changed from about 93% toroids at ? = 80 to 89% rods at ? = 70 and 98% rods at ? = 65. At epsi; lower than 65, DNA collapsed into a network of multistranded fibers. The morphology of condensed DNA particles, whether toroids, rods, or fibers, was independent of the alcohol species. CD spectra in ethanol–water mixtures indicated that both closed circular and linearized plasmids were in the B conformation when condensed with Co(NH₃)³⁺₆ at ?≥ 70, although the closed circular molecules exhibited a weak Ψ-DNA spectrum. A transition from the B to A formtook place between ? = 70 and 60, well above the normal dielectric constant of ? = 40 for this transition, indicating that ethanol and Co(NH₃) synergistically promote the B–A transition. We interpret these results to mean that alcohols have both electrostatic and structural effects on DNA, leading to three regimes of condensation. At the lowest alcohol concentrations the B conformation is stableand condensation is relatively slow, allowing time for the packing adjustments necessary to form toroids. At intermediate alcohol concentrations condensation is faster, and the combined effects of solvent and Co(NH₃) locally destabilize the double helix, permitting DNA foldbacks that lead to rodlike condensates. Rods become shorter as wellas more numerous as ? decreases from 80 to 65–60, indicatingincreasing destabilization as alcohol increases. At the lowest dielectric constants, alcohol and Co(NH₃) produce A-DNA, which strongly self-adheres and rapidly aggregates intofibrous networks, not allowing time for more compact condensates to form. © 1995 John Wiley & Sons, Inc.     

The key role of lignin decomposing fungi in the decay of roofs thatched with water reed

We investigated the involvement of microorganisms in the rapid reed decay of roofs thatched with water reed. Numerous bacteria and fungi were isolated by enrichment cultures from reed samples and from fungal fruit bodies on roofs. All strains were characterised in respect to their abilities to degrade cellulose, hemicelluloses and the lignin model substance Poly-R-478. Only 15 of the 92 isolated bacterial strains were capable of degrading cellulose and hemicelluloses. However, nearly all 61 of the identified fungal isolates had these abilities. Nevertheless, only 14 of the isolated fungal strains as well as a reference isolate of Trametes versicolor were capable of degrading Poly-R-478. The ability of the microorganisms to attack complete reed was assessed using a newly developed test system which measures the loss of dry weight during the incubation. A significant loss of dry weight was apparent only in tests using the ligninolytic fungi Pycnoporus cinnabarinus, Trametes versicolor, Phlebia tremellosa and some Mycena species, but not in the case of the majority of cellulolytic bacteria and fungi. From these results, we conclude that ligninolytic fungi are capable of destroying complete reed structure and that they play the key role in the process of the rapid decay of roofs thatched with reed. Directly after the initial lignin attack, cellulose and hemicellulose were degraded to a great extent, evidenced by the large loss of dry weight (up to 72 %), which significantly exceeds the lignin content of reed (ca. 15 %). However, after the initial attack by ligninolytic fungi, bacteria or other fungi capable of degrading cellulose and hemicelluloses may contribute to the progressive decay of reed under natural conditions. Furthermore, we show that the rate of decay depends on the source of the reed and on the reed quality.     

The key role of behaviour in animal camouflage

Animal camouflage represents one of the most important ways of preventing (or facilitating) predation. It attracted the attention of the earliest evolutionary biologists, and today remains a focus of investigation in areas ranging from evolutionary ecology, animal decision‐making, optimal strategies, visual psychology, computer science, to materials science. Most work focuses on the role of animal morphology per se, and its interactions with the background in affecting detection and recognition. However, the behaviour of organisms is likely to be crucial in affecting camouflage too, through background choice, body orientation and positioning; and strategies of camouflage that require movement. A wealth of potential mechanisms may affect such behaviours, from imprinting and self‐assessment to genetics, and operate at several levels (species, morph, and individual). Over many years there have been numerous studies investigating the role of behaviour in camouflage, but to date, no effort to synthesise these studies and ideas into a coherent framework. Here, we review key work on behaviour and camouflage, highlight the mechanisms involved and implications of behaviour, discuss the importance of this in a changing world, and offer suggestions for addressing the many important gaps in our understanding of this subject.     

The possible role of solid surface area in condensation reactions during chemical evolution: Reevaluation

Summary Published data on adsorption and condensation of amino acids, purine and pyrimidine bases, sugars, nucleosides, and nucleotides are analyzed in connection with Bernal's hypothesis that clays and other minerals may have provided the most likely surface for adsorption and condensation of these molecules in prebiotic times. Using surface concentration and reaction rate as the main criteria for the feasibility of condensation reactions, four types of prebiotic environments were analyzed: (1) an ocean-sediment system, (2) a dehydrated lagoon bed produced by evaporation, (3) the surface of a frozen sediment, and (4) a fluctuating system where hydration (rainstorms, tidal variations, flooding) and dehydration (evaporation) take place in a cyclic manner. With the possible exception of nucleotides, low adsorption of organomonomers on sediment surfaces of a prebiotic ocean (pH 8) is expected, and significant condensation is considered unlikely. In dehydrated and frozen systems, high surface concentrations are probable and condensation is more likely. In fluctuating environments, condensation rates will be enhanced and the size distribution of the oligomers formed during dehydration may be influenced by a redistribution mechanism in which adsorbed oligomers and monomers are desorbed and redistributed on the solid surface during the next hydration-dehydration cycle.On leave from the Faculty of Agriculture, Rehovot, The Hebrew University of Jerusalem, Israel.     

The protective role of small heat shock proteins in cardiac diseases: key role in atrial fibrillation

Atrial fibrillation (AF) is the most common tachyarrhythmia which is associated with increased morbidity and mortality. AF usually progresses from a self-terminating paroxysmal to persistent disease. It has been recognized that AF progression is driven by structural remodeling of cardiomyocytes, which results in electrical and contractile dysfunction of the atria. We recently showed that structural remodeling is rooted in derailment of proteostasis, i.e., homeostasis of protein production, function, and degradation. Since heat shock proteins (HSPs) play an important role in maintaining a healthy proteostasis, the role of HSPs was investigated in AF. It was found that especially small heat shock protein (HSPB) levels get exhausted in atrial tissue of patients with persistent AF and that genetic or pharmacological induction of HSPB protects against cardiomyocyte remodeling in experimental models for AF. In this review, we provide an overview of HSPBs as a potential therapeutic target for normalizing proteostasis and suppressing the substrates for AF progression in experimental and clinical AF and discuss HSP activators as a promising therapy to prevent AF onset and progression.     

The key role of residue 5 in angiotensin II

The conformation–biological activity relationships in a series of angiotensin II analogs substituted in position 5 were studied. Results indicated that only analogs with β-branched residue in position 5 possess spectral and biological properties identical to that of parent angiotensin II.     

Enzymatic esterification in organic media: role of water and organic solvent in kinetics and yield of butyl butyrate synthesis

Summary The respective roles of organic solvent and of water in butyl butyrate synthesis from n-butanol and n-butyric acid in n-hexane by Mucor miehei lipase have been investigated by analysis of the kinetics and the reaction balances. Esterificaton was found to take place in both low water systems containing solid enzyme in hexane and in biphasic aqueous enzyme solution/hexane systems. In the solid enzyme system, the enzyme adsorbed the water produced, thus delaying the appearance of a discrete aqueous phase. As expected, the presence of some water was indispensable for this system, as its removal or exclusion by various means (adsorption, distillation) affected enzyme activity. However, water removal had little effect on the final yield of esterification. Reaction velocities were quite similar for the solid enzyme/hexane system and for the biphasic aqueous enzyme solution/hexane system. In the latter case, the butyl butyrate formed was almost exclusively found in the organic phase. Ethyl butyrate, a more polar compound, was synthesized with a lower yield. These results allow the conclusion that the reaction took place in a phase consisting of either solid hydrated enzyme with no discrete aqueous phase or of an aqueous enzyme solution by basically similar mechanisms according to the amount of water available to the system, the esterification being driven to completion by transfer of the ester into the organic phase because of a favourable partition coefficient. Offprint requests to: F. Monot