INO80 and SWR1 complexes: the non-identical twins of chromatin remodelling

The INO80 family of chromatin remodellers are multisubunit complexes that perform a variety of tasks on nucleosomes. Family members are built around a heterohexamer of RuvB-like protein, an ATP-dependent DNA translocase,nuclear actin and actin-related proteins, and a few complex-specific subunits. They modify chromatin in a number of ways including nucleosome sliding and exchange of variant histones. Recent structural information on INO80 and SWR1 complexes has revealed similarities in the basic architecture of the complexes. However, structural and biochemical data on the complexes bound to nucleosomes reveal these similarities to be somewhat superficial and their biochemical activities and mechanisms are very different. Consequently, the INO80 family displays a surprising diversity of function that is based upon a similar structural framework

Wellcome Witnesses to Twentieth Century Medicine: Volume 1

Annotated and edited transcript of four Witness Seminars. Introduction by E M Tansey First published by the Wellcome Trust, 1997. ©The Trustee of the Wellcome Trust, London, 1997.In Volume One (Occasional Publication no. 4, 1997).All volumes are freely available online at: www.history.qmul.ac.uk/research/modbiomed/wellcome_witnesses/Annotated and edited transcript of four Witness Seminars. Introduction by E M Tansey.Annotated and edited transcript of four Witness Seminars. Introduction by E M Tansey.Annotated and edited transcript of four Witness Seminars. Introduction by E M Tansey.Annotated and edited transcript of four Witness Seminars. Introduction by E M Tansey.Four Witness Seminar transcripts of meetings held between 1993 and 1996: ‘Technology Transfer in Britain: The case of Monoclonal Antibodies’ (E M Tansey and P P Catterall, eds); ‘Self and Non-Self: A History of Autoimmunity’ (E M Tansey, S V Willhoft and D A Christie, eds); ‘Endogenous Opiates’ (E M Tansey and D A Christie, eds); ‘The Committee on Safety of Drugs’ (E M Tansey and L A Reynolds, eds). Introduction by E M Tansey, ‘What is a Witness Seminar’, separate index for each meeting. Tansey E M, Catterall P P, Christie D A, Willhoft S V, Reynolds L A. (eds) (1997) Wellcome Witnesses to Twentieth Century Medicine, volume 1. London: The Wellcome Trust.The Wellcome Trust is a registered charity, no. 210183

Perceptual justification and the phenomenology of experience

This thesis seeks to provide an explanation of what I call the Basic Principle about Perceptual Justification which states that if a subject S has a perceptual experience as of a mind-independent object x being F (or in which it appears to him as if an x is F), and forms the belief that an x is F on the basis of having an experience of this phenomenological sort, then (perhaps provided certain further conditions obtain) S‘s belief that an x is F is prima facie justified for S. I distinguish between two conceptions of epistemic justification. Roughly, on an objective conception, a subject S has a justified belief that p if he bases this belief on grounds that entail or make likely the truth of p, while on a subjective conception a subject S has a justified belief that p if he forms this belief on the basis of his occupying a perspective from which a situation obtains that entails or makes likely the truth of p. I argue that the truth of the Basic Principle can be derived, in part, from facts about the phenomenal character of perceptual experience. In particular, I argue that the Basic Principle can be explained by saying that the subject‘s perceptual experience can provide him with justification for believing that an x is F in the subjective sense and that it does so, in part, in virtue of its phenomenal character. I also address the question of whether perceptual experiences can provide us with immediate justification for believing propositions about our environment, that is, with justification that does not depend on our having independent justification for believing other propositions such as the proposition that perceptual experiences are generally reliable. To this end, I consider the so-called problem of easy knowledge and argue that the issues concerning this problem should not compel us into thinking that perceptual justification cannot be immediate

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

This work was funded by Wellcome Senior Fellowship 095062, Wellcome Trust grants 094090, 099149 and 097945. ALH was funded by an EMBO long term fellowship ALTF 380–2015 co-funded by the European Commission (LTFCOFUND2013, GA-2013–609409).ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.Publisher PDFPeer reviewe

Repair or destruction: an intimate liaison between ubiquitin ligases and molecular chaperones in proteostasis

Cellular differentiation, developmental processes, and environmental factors challenge the integrity of the proteome in every eukaryotic cell. The maintenance of protein homeostasis, or proteostasis, involves folding and degradation of damaged proteins, and is essential for cellular function, organismal growth, and viability [1, 2]. Misfolded proteins that cannot be refolded by chaperone machineries are degraded by specialized proteolytic systems. A major degradation pathway regulating cellular proteostasis is the ubiquitin/proteasome-system (UPS), which regulates turnover of damaged proteins that accumulate upon stress and during aging. Despite the large number of structurally unrelated substrates, ubiquitin conjugation is remarkably selective. Substrate selectivity is mainly provided by the group of E3 enzymes. Several observations indicate that numerous E3 ubiquitin ligases intimately collaborate with molecular chaperones to maintain the cellular proteome. In this Review, we provide an overview of specialized quality control E3 ligases playing a critical role in the degradation of damaged proteins. The process of substrate recognition and turnover, the type of chaperones they team up with, and the potential pathogeneses associated with their malfunction will be further discusse

Synergy and antagonism in regulation of recombinant human INO80 chromatin remodeling complex

We have purified a minimal core human Ino80 complex from recombinant protein expressed in insect cells. The complex comprises one subunit each of an N-terminally truncated Ino80, actin, Arp4, Arp5, Arp8, Ies2 and Ies6, together with a single heterohexamer of the Tip49a and Tip49b proteins. This core complex has nucleosome sliding activity that is similar to that of endogenous human and yeast Ino80 complexes and is also inhibited by inositol hexaphosphate (IP6). We show that IP6 is a non-competitive inhibitor that acts by blocking the stimulatory effect of nucleosomes on the ATPase activity. The IP6 binding site is located within the C-terminal region of the Ino80 subunit. We have also prepared complexes lacking combinations of Ies2 and Arp5/Ies6 subunits that reveal regulation imposed by each of them individually and synergistically that couples ATP hydrolysis to nucleosome sliding. This coupling between Ies2 and Arp5/Ies6 can be overcome in a bypass mutation of the Arp5 subunit that is active in the absence of Ies2. These studies reveal several underlying mechanisms for regulation of ATPase activity involving a complex interplay between these protein subunits and IP6 that in turn controls nucleosome sliding