Protein Solubility and Protein Homeostasis: A Generic View of Protein Misfolding Disorders

According to the “generic view” of protein aggregation, the ability to self-assemble into stable and highly organized structures such as amyloid fibrils is not an unusual feature exhibited by a small group of peptides and proteins with special sequence or structural properties, but rather a property shared by most proteins. At the same time, through a wide variety of techniques, many of which were originally devised for applications in other disciplines, it has also been established that the maintenance of proteins in a soluble state is a fundamental aspect of protein homeostasis. Taken together, these advances offer a unified framework for understanding the molecular basis of protein aggregation and for the rational development of therapeutic strategies based on the biological and chemical regulation of protein solubility.Virtually every complex biochemical process taking place in living cells depends on the ability of the molecules involved to self-assemble into functional structures (Dobson 2003; Robinson et al. 2007; Russel et al. 2009), and a sophisticated quality control system is responsible for regulating the reactions leading to this organization within the cellular environment (Dobson 2003; Balch et al. 2008; Hartl and Hayer-Hartl 2009; Powers et al. 2009; Vendruscolo and Dobson 2009). Proteins are the molecules that are essential for enabling, regulating, and controlling almost all the tasks necessary to maintain such a balance. To function, the majority of our proteins need to fold into specific three-dimensional structures following their biosynthesis in the ribosome (Hartl and Hayer-Hartl 2002). The wide variety of highly specific structures that results from protein folding, and which serve to bring key functional groups into close proximity, has enabled living systems to develop an astonishing diversity and selectivity in their underlying chemical processes by using a common set of just 20 basic molecular components, the amino acids (Dobson 2003). Given the central importance of protein folding, it is not surprising that the failure of proteins to fold correctly, or to remain correctly folded, is at the origin of a wide variety of pathological conditions, including late-onset diabetes, cystic fibrosis, and Alzheimer’s and Parkinson’s diseases (Dobson 2003; Chiti and Dobson 2006; Haass and Selkoe 2007). In many of these disorders proteins self-assemble in an aberrant manner into large molecular aggregates, notably amyloid fibrils (Chiti and Dobson 2006; Ramirez-Alvarado et al. 2010).     

What Was the Real Contribution of Endosymbionts to the Eukaryotic Nucleus? Insights from Photosynthetic Eukaryotes

Eukaryotic genomes are composed of genes of different evolutionary origins. This is especially true in the case of photosynthetic eukaryotes, which, in addition to typical eukaryotic genes and genes of mitochondrial origin, also contain genes coming from the primary plastids and, in the case of secondary photosynthetic eukaryotes, many genes provided by the nuclei of red or green algal endosymbionts. Phylogenomic analyses have been applied to detect those genes and, in some cases, have led to proposing the existence of cryptic, no longer visible endosymbionts. However, detecting them is a very difficult task because, most often, those genes were acquired a long time ago and their phylogenetic signal has been heavily erased. We revisit here two examples, the putative cryptic endosymbiosis of green algae in diatoms and chromerids and of Chlamydiae in the first photosynthetic eukaryotes. We show that the evidence sustaining them has been largely overestimated, and we insist on the necessity of careful, accurate phylogenetic analyses to obtain reliable results.Today it is widely accepted that photosynthesis originated in eukaryotes by the endosymbiosis of a cyanobacterium within a heterotrophic eukaryotic host. This occurred in a lineage that subsequently diversified to give rise to the three contemporary groups of primary photosynthetic eukaryotes: Viridiplantae (including green algae and land plants), Rhodophyta and Glaucophyta, grouped collectively within a unique eukaryotic superphylum called Archaeplastida (Adl et al. 2005) or Plantae (Cavalier-Smith 1982). Recently, a second case of primary endosymbioses has been unveiled thanks to the characterization of Paulinella chromatophora, a filose amoeba that hosts a cyanobacterium with a reduced genome that has been described as “a plastid in the making” (Marin et al. 2005; Keeling and Archibald 2008; Nowack et al. 2008). Primary endosymbioses resulted in the establishment of plastids with two membranes. However, a vast variety of eukaryotes possess plastids with three or more membranes. They derive from the endosymbioses of primary photosynthetic eukaryotes within other eukaryotic cells (Delwiche 1999; Keeling 2013). Such secondary endosymbioses have spread photosynthesis across the eukaryotic tree, either by the endosymbiosis of red or of green algae. Whereas it is almost certain that secondary endosymbioses of green algae occurred twice (in euglenids and chlorarachniophytes), secondary red algal plastids are found in a variety of alveolates, stramenopiles, cryptophytes, and haptophytes, and the number of red algal endosymbioses at the origin of these groups has been matter of intense debate (Baurain et al. 2010; Keeling 2010, 2013; Burki et al. 2012b). Moreover, the existence of tertiary endosymbioses (namely, the symbiosis of a secondary photosynthetic eukaryote within another eukaryotic cell) and of plastid replacements makes the picture of plastid evolution in eukaryotes even more complex. Dinoflagellates, some of which have replaced their ancestral red algal plastids by green algae, diatoms, haptophytes, or cryptophytes, are paradigmatic examples of such complex situations (Keeling 2013).The evolution of plastids has been studied using genes from the plastid genome as well as typical eukaryotic nuclear genes, which allow inferring the phylogenies of both the plastids and their hosts. The use of those markers has led to interesting discoveries, such as the monophyly of the Archaeplastida (Moreira et al. 2000; Rodríguez-Ezpeleta et al. 2005) or the difficulties in reconciling the plastid and host histories in eukaryotes with red algal plastids (Baurain et al. 2010; Burki et al. 2012b). However, a third class of genes can also provide useful complementary information: the genes of plastid origin retrieved within the nuclear genome of the host. In fact, contemporary plastids have small genomes, which is due to the fact that most of the original cyanobacterial symbiont genes were lost or transferred to the host nucleus (by a process called endosymbiotic gene transfer, EGT) during the evolution of plastids (Weeden 1981; Martin et al. 1998). These transfer events are not restricted to plastid endosymbioses—the same phenomenon occurred during the endosymbiosis that gave rise to the mitochondria (Gray et al. 1999; Burger et al. 2003).EGT genes may serve to study the evolutionary history of plastids and, in particular, the presence of cryptic endosymbioses. In fact, species that had a plastid in the past but lost photosynthesis may have conserved genes of plastid origin in their nuclear genomes. This has been shown for a variety of nonphotosynthetic eukaryotes, such as, for example, apicomplexan parasites (Fast et al. 2001; Roos et al. 2002; Williams and Keeling 2003; Huang et al. 2004), perkinsids (Stelter et al. 2007; Matsuzaki et al. 2008; Fernández Robledo et al. 2011) or nonphotosynthetic dinoflagellates (Sanchez-Puerta et al. 2007; Slamovits and Keeling 2008), and green algae (de Koning and Keeling 2004). Although much more controversial, potential EGTs have also been used to propose a photosynthetic ancestry for ciliates (Reyes-Prieto et al. 2008) or that algae with secondary plastids of red algal origin, such as diatoms and chromerids, may have contained green algal endosymbionts in their past (Moustafa et al. 2009; Woehle et al. 2011). Likewise, several dozens of potential EGTs have been detected in algae and plants that appear to have been acquired from Chlamydiae, a group of parasitic bacteria (Huang and Gogarten 2007; Becker et al. 2008; Moustafa et al. 2008), which led to proposing that cryptic chlamydial endosymbionts may have helped to establish the first plastids, in particular, by providing essential functions for plastid activity (Greub and Raoult 2003; Ball et al. 2013; Baum 2013).We revise here some of these cases of cryptic endosymbiosis, with special attention on the difficulties in accurately detecting EGT and the importance of proper phylogenetic analysis and of an adequate taxonomic sampling to achieve that task.     

Endoreplication

Developmentally programmed polyploidy occurs by at least four different mechanisms, two of which (endoreduplication and endomitosis) involve switching from mitotic cell cycles to endocycles by the selective loss of mitotic cyclin-dependent kinase (CDK) activity and bypassing many of the processes of mitosis. Here we review the mechanisms of endoreplication, focusing on recent results from Drosophila and mice.Eukaryotic cells proliferate by undergoing a sequence of events termed the “mitotic cell cycle” in which the genome is duplicated once and only once between cell divisions. The result is a population of cells with two copies of each chromosome (diploid, or 2C). Agents that interfere with the mechanisms that govern genome duplication frequently induce reinitiation of nuclear DNA replication during S phase. This phenomenon, termed “DNA rereplication,” is an aberrant event that produces a population of cells with a heterogeneous DNA content that reflects incomplete chromosome duplication, stalled replication forks, and DNA damage. In most cells, these events can lead to inducing the cell’s DNA damage response and can lead to apoptosis (Lee et al. 2010).Remarkably, some cells are developmentally programmed to exit their mitotic cell cycle in response either to environmental signals or to injury or stress, and then differentiate into nonproliferating, viable, polyploid cells. This phenomenon, termed “developmentally programmed polyploidy,” is a normal part of animal and plant development that occurs frequently in ferns, flowering plants, mollusks, arthropods, amphibians, and fish, although rarely in mammals. In contrast to DNA rereplication, developmentally programmed polyploidy produces cells with a DNA content of >4C, but in integral multiples of 4C (e.g., 8C, 16C, 32C, etc.), consistent with multiple S phases in the absence of cytokinesis. These cells typically stop proliferating but remain viable in a terminally differentiated state that may serve to regulate tissue size or organization, to trigger cell differentiation or morphogenesis, to increase the number of genes dedicated to tissue-specific functions without increasing the number of cells, or to adapt to environmental conditions. Mitotic divisions of polyploid cells are common for plant species, but they are rarely found in animals. Although known for decades, polyploid mitosis in insects remained mostly unstudied until it was recently shown that the cells of the rectal papilla in Drosophila undergo mitosis after executing two or more endocycles (Fox et al. 2010). Thus, polyploidy is not an irreversible process, although the benefit of this cell cycle variant remains to be elucidated.Developmentally programmed polyploidy occurs by at least four different mechanisms (Ullah et al. 2009). Proliferating cells in the syncytial blastoderm of Drosophila embryos and some hepatocytes in the postnatal liver of mammals become multinucleated and therefore polyploid by failing to undergo cytokinesis after mitosis (“acytokinetic mitosis”). Differentiation of skeletal muscle myoblasts into myotubes, monocytes into osteoclasts, and formation of placental syncytiotrophoblasts involves “cell fusion” to produce multinucleated, terminally differentiated cells that are similarly polyploid. Alternatively, cells may exit their mitotic cell cycle by arresting mitosis during anaphase and failing to undergo cytokinesis. This phenomenon, termed “endomitosis,” produces cells with a single giant nucleus that may subsequently fragment into a multinuclear appearance. Endomitosis occurs in mammals when megakaryoblasts differentiate into megakaryocytes (Bluteau et al. 2009), and in some plant cells (Weingartner et al. 2004). However, the primary mechanism for developmentally programmed polyploidy in arthropods (Smith and Orr-Weaver 1991; Edgar and Orr-Weaver 2001), plants (de la Paz Sanchez et al. 2012), and possibly mammals (Ullah et al. 2009) is “endoreplication” (also referred to as “endoreduplication”). Endoreplication occurs when a cell exits the mitotic cell cycle in G₂ phase and undergoes multiple S phases without entering mitosis and undergoing cytokinesis. The result is a giant cell with a single, enlarged, polyploid nucleus.     

Microglia Function in Central Nervous System Development and Plasticity

The nervous system comprises a remarkably diverse and complex network of different cell types, which must communicate with one another with speed, reliability, and precision. Thus, the developmental patterning and maintenance of these cell populations and their connections with one another pose a rather formidable task. Emerging data implicate microglia, the resident myeloid-derived cells of the central nervous system (CNS), in the spatial patterning and synaptic wiring throughout the healthy, developing, and adult CNS. Importantly, new tools to specifically manipulate microglia function have revealed that these cellular functions translate, on a systems level, to effects on overall behavior. In this review, we give a historical perspective of work to identify microglia function in the healthy CNS and highlight exciting new work in the field that has identified roles for these cells in CNS development, maintenance, and plasticity.Microglia are one of the most enigmatic and understudied populations in the brain. Until recently, most of what was known about their function has been associated with their rapid and robust responses to disease and injury (Ransohoff and Perry 2009; Graeber 2010; Ransohoff and Cardona 2010). The idea that microglia could be performing normal, homeostatic functions is a relatively new concept, galvanized by pioneering in vivo imaging studies, which revealed that the processes of “resting” microglia are highly motile in the intact, healthy adult brain (Davalos et al. 2005; Nimmerjahn et al. 2005). Remarkably, it is estimated that these microglial processes survey the entire brain parenchyma within a matter of hours, raising many questions about the significance of this immune surveillance system.Since these initial findings, there has been a surge in the field to examine functional roles of microglia in the healthy central nervous system (CNS), with a primary focus on postnatal development. This focus was, to a large extent, incited by a landmark fate-mapping study in the mouse showing that microglia develop from primitive myeloid progenitors in the embryonic yolk sac and begin to colonize the brain during early embryonic development (approximately embryonic day 9.5 [∼E9.5] in the mouse) (Ginhoux et al. 2010). Given this early colonization, microglia are poised to play important roles in shaping the developing CNS and contributing to overall nervous system function. Indeed, recent work has shown that microglia in the developing CNS can physically interact with neuronal soma and synapses in response to changes in neural activity, and data implicate microglia in many functions required to build and wire the developing CNS ranging from neurogenesis to synaptic pruning (Tremblay 2011; Tremblay et al. 2011; Kettenmann et al. 2013; Schafer et al. 2013; Wake et al. 2013; Salter and Beggs 2014). Furthermore, emerging work in the juvenile and adult reveal that these interactions and functions observed in the postnatal brain occur more broadly to affect plasticity over the life span of the animal, ultimately affecting behavior.In this chapter, we review the latest findings in the field on microglia function in CNS development and plasticity. Our goal is to give a comprehensive and critical perspective of this relatively new area of research and highlight new questions. Furthermore, we discuss novel strategies to manipulate microglia function that will contribute to our understanding of these cells in the healthy nervous system and, ultimately, help to identify mechanisms of disease.     

Extracellular Matrix in Development: Insights from Mechanisms Conserved between Invertebrates and Vertebrates

The extracellular matrix (ECM) and its receptors make diverse contributions to development. The ECM comes in a variety of forms, including the more “standard” ECM that is internal to the animal and on the basal side of epithelial sheets, as well as the apical ECM, which is especially elaborated in the invertebrates to form the exoskeleton. ECM proteins accumulate adjacent to particular target tissues in the developing animal by a variety of mechanisms: local synthesis in the target tissue; local synthesis by migrating cells; and secretion from a distant source and capture by the target tissue. The diverse developmental functions of the ECM are discussed, including the generation of a road for cell migration, creation of morphogenetic checkpoints for differentiation, modulation of morphogen gradients, insulation of organs, gluing together cell layers, and providing structure for the organism.This article will discuss the many functions of the ECM that are important in animal development. First, I will discuss the production of ECM in the developing animal (see Adams and Lawler 2011, Barros et al. 2011; Chiquet-Ehrismann and Tucker 2011; Schwarzbauer and DeSimone 2011; Watt and Fujiwara 2011; Wickstrom et al. 2011; Yurchenco 2011), and then describe briefly the range of ways that the ECM contributes to development. Given the space constraints of this article, I will not attempt to be exhaustive in my coverage, but instead will seek to identify examples that show the different kinds of ECM function that have been revealed from studies of development. My examples will be focused on developmental processes shared between invertebrates and vertebrates, as many vertebrate-specific roles of the ECM are covered in other references that are part of this subject collection. The somewhat different compositions, arrangements, and developmental changes in invertebrate ECMs provide an illuminating perspective from which to consider ECM function more generally.     

Autophagy and Neuronal Cell Death in Neurological Disorders

Autophagy is implicated in the pathogenesis of major neurodegenerative disorders although concepts about how it influences these diseases are still evolving. Once proposed to be mainly an alternative cell death pathway, autophagy is now widely viewed as both a vital homeostatic mechanism in healthy cells and as an important cytoprotective response mobilized in the face of aging- and disease-related metabolic challenges. In Alzheimer’s, Parkinson’s, Huntington’s, amyotrophic lateral sclerosis, and other diseases, impairment at different stages of autophagy leads to the buildup of pathogenic proteins and damaged organelles, while defeating autophagy’s crucial prosurvival and antiapoptotic effects on neurons. The differences in the location of defects within the autophagy pathway and their molecular basis influence the pattern and pace of neuronal cell death in the various neurological disorders. Future therapeutic strategies for these disorders will be guided in part by understanding the manifold impact of autophagy disruption on neurodegenerative diseases.Soon after the discovery of lysosomes by de Duve in the 1950s, electron microscopists recognized the presence of cytoplasmic organelles within membrane-limited vacuoles (Clark 1957) and observed what appeared to be the progressive breakdown of these contents (Ashford and Porter 1962). Proposing that “prelysosomes” containing sequestered cytoplasm matured to autolysosomes by fusion with primary lysosomes, de Duve and colleagues (de Duve 1963; de Duve and Wattiaux 1966) named this process “autophagy” (self-eating). Neurons, as cells particularly rich in acid phosphatase-positive lysosomes, were a preferred model in the initial investigations of autophagy. Early studies of pathologic states such as neuronal chromatolysis (Holtzman and Novikoff 1965; Holtzman et al. 1967) linked neurodegenerative phenomena to robust proliferation of autophagic vacuoles (AVs) and lysosomes. Although de Duve appreciated the importance of lysosomes for maintaining cell homeostasis, he was especially intrigued with their potential as “suicide bags” capable of triggering cell death by releasing proteases into the cytoplasm. Despite some support for this notion (Brunk and Brun 1972), the concept was not significantly embraced until many decades later. Instead, for many years, lysosomes and autophagy were mainly considered to perform cellular housekeeping and to scavenge and clean up debris during neurodegeneration in preparation for regenerative processes. The connection between autophagy and neuronal cell death reemerged in the 1970s from observations of Clarke and colleagues, who presented evidence that the developing brain deployed autophagy as a form of programmed neuronal cell death during which autophagy was massively up-regulated to eliminate cytoplasmic components, at once killing the neuron and reducing its cell mass for easy removal. Self-degradation was suggested as a more efficient elimination mechanism than apoptosis, which requires a large population of phagocytic cells and access of these cells to the dying region (Baehrecke 2005). Indeed, the best evidence for this process is in the context of massive cell death, as in metamorphosis and involutional states (Das et al. 2012).Clarke proposed that autophagic cell death (ACD)—type 2 programmed cell death (PCD)—could be a relatively common alternative route to death distinct from apoptosis—type 1 PCD (Clarke 1990)—or caspase-independent cell death—type 3 PCD (Fig. 1). The distinguishing features of ACD are marked proliferation of AVs and progressive disappearance of organelles but relative preservation of cytoskeletal and nuclear integrity until late in the process (Schweichel and Merker 1973; Hornung et al. 1989). In this original concept of ACD or type 2 PCD, death is achieved by autophagic digestion of organelles and essential regulatory molecules and elimination of death inhibitory factors (Baehrecke 2005). With the advent of the molecular era of autophagy research in the 1990s, it became possible to verify the most important implication of ACD, namely, that the death could be prevented by inhibiting autophagy genetically or pharmacologically. Meanwhile, reports of prominent lysosomal/autophagic pathology in Alzheimer’s disease (AD) (Cataldo et al. 1997; Nixon et al. 2000, 2005) and other neuropathic states (Anglade et al. 1997; Rubinsztein et al. 2005) raised important questions about whether autophagy pathology signifies a prodeath program or an attempt to maintain survival—a critical question for any potential therapy based on autophagy modulation. In this article, we will examine evidence for the various neuroprotective roles of autophagy and review our current understanding of how specific stages of autophagy may become disrupted and influence the neurodegenerative pattern seen in major adult-onset neurological diseases. We will particularly focus on how neurons regulate the balance between prosurvival autophagy and well-established cell death mechanisms in making life or death decisions.Open in a separate windowFigure 1.Neuronal cell death: three general morphological types of dying cells in the developing nervous system, as initially classified by Schweichel and Merker (1973) and later Clarke (1990). (A,B) Type 1 (“apoptotic”) cell death: (A) A neuron, from the brain of a postnatal day 6 mouse pup, in the middle of apoptotic degeneration showing cell shrinkage, cytoplasmic condensation, ruffled plasma membrane, and a highly electron-dense nucleus. Endoplasmic reticulum (ER) is still recognizable and some are dilated. A small number of autophagic vacuoles (AVs) can be seen (arrows). (B) A late-stage apoptotic neuron displaying electron-dense chromatin balls (CB), each surrounded by a small amount of highly condensed cytoplasm. (Panel from Yang et al. 2008; reprinted, with permission, from the American Association of Pathologists and Bacteriologists.) (C) Type 2 (“autophagic”) cell death: a deafferented isthmo-optic neuron in developing chick brain after uptake of horseradish peroxidase to highlight (electron dense) endocytic and autophagic compartments. The cell death pattern features pyknosis, abundant AVs, and sometimes dilated ER and mitochondria. (Panel from Hornung et al. 1989; reproduced, with permission, from John Wiley & Sons) (D) Type 3 (“cytoplasmic, nonlysosomal”) cell death: a motoneuron displaying markedly dilated rough ER, Golgi, and nuclear envelope, late vacuolization, and increased chromatin granularity. (Panel from Chu-Wang and Oppenheim 1978; reproduced, with permission, from John Wiley & Sons) Scale bars, 1 µm (A,B); 2 µm (C,D).     

Cellular Mechanisms Controlling Caspase Activation and Function

Caspases are the primary drivers of apoptotic cell death, cleaving cellular proteins that are critical for dismantling the dying cell. Initially translated as inactive zymogenic precursors, caspases are activated in response to a variety of cell death stimuli. In addition to factors required for their direct activation (e.g., dimerizing adaptor proteins in the case of initiator caspases that lie at the apex of apoptotic signaling cascades), caspases are regulated by a variety of cellular factors in a myriad of physiological and pathological settings. For example, caspases may be modified posttranslationally (e.g., by phosphorylation or ubiquitylation) or through interaction of modulatory factors with either the zymogenic or active form of a caspase, altering its activation and/or activity. These regulatory events may inhibit or enhance enzymatic activity or may affect activity toward particular cellular substrates. Finally, there is emerging literature to suggest that caspases can participate in a variety of cellular processes unrelated to apoptotic cell death. In these settings, it is particularly important that caspases are maintained under stringent control to avoid inadvertent cell death. It is likely that continued examination of these processes will reveal new mechanisms of caspase regulation with implications well beyond control of apoptotic cell death.Apoptosis is a form of programmed cell death that eliminates individual cells within an organism while preserving the overall structure of surrounding tissue. Many of the prominent morphological features of apoptosis were first described in 1972 by Kerr, Wyllie, and Currie (Kerr et al. 1972). However, it was not until the mid-1990s that apoptosis was linked to the activation of the cysteine-dependent aspartate-driven proteases (caspases), which cleave key intracellular substrates to promote cell death (Cerretti et al. 1992; Nicholson et al. 1995; Alnemri et al. 1996; Liu et al. 1996; Thornberry and Lazebnik 1998). Given the critical role that caspases play in dismantling the cell during apoptosis, their activation and subsequent activity are highly regulated. Failure of a cell to properly modulate caspase activity can cause aberrant or untimely apoptotic cell death, potentially leading to carcinogenesis, autoimmunity, neurodegeneration, and immunodeficiency (Thompson 1995; Hanahan and Weinberg 2000; Yuan and Yankner 2000; Li and Yuan 2008).Caspases are synthesized within the cell as inactive zymogens that lack significant protease activity. Thus, caspases are, in essence, regulated from the moment of protein synthesis in that they are not activated until receipt of specific death stimuli (Earnshaw et al. 1999). The primary structure of a caspase is an amino-terminal prodomain and a carboxy-terminal protease domain, which contains the key catalytic cysteine residue. Caspases are categorized as initiator or effector caspases, based on their position in apoptotic signaling cascades. The initiator caspases (caspase-2, -8, -9, and -10) act apically in cell death pathways and all share long, structurally similar prodomains. This group of enzymes is activated through “induced proximity” when adaptor proteins interact with the prodomains and promote caspase dimerization (Boatright et al. 2003; Baliga et al. 2004; Pop et al. 2006; Riedl and Salvesen 2007; Wachmann et al. 2010). In contrast, the effector caspases (caspase-3, -6, and -7) have shorter prodomains and exist in the cell as preformed, but inactive, homodimers. Following cleavage mediated by an initiator caspase, effector caspases act directly on specific cellular substrates to dismantle the cell. Although many individual caspase substrates have been implicated in specific aspects of cellular destruction (e.g., lamin cleavage is required for the efficient packaging of nuclei into small membrane-bound vesicles), recent proteomic approaches have greatly expanded the known repertoire of proteolytic products generated during apoptosis (Van Damme et al. 2005; Dix et al. 2008; Mahrus et al. 2008). Further work will be needed to confirm these findings and to determine how (or if) all of these substrates participate in the apoptotic process (see Poreba et al. 2013), especially as new details emerge on the relationship between posttranslational modifications, like phosphorylation, and caspase cleavage (Dix et al. 2012).     

Origin of Microglia: Current Concepts and Past Controversies

Microglia are the resident macrophages of the central nervous system (CNS), which sit in close proximity to neural structures and are intimately involved in brain homeostasis. The microglial population also plays fundamental roles during neuronal expansion and differentiation, as well as in the perinatal establishment of synaptic circuits. Any change in the normal brain environment results in microglial activation, which can be detrimental if not appropriately regulated. Aberrant microglial function has been linked to the development of several neurological and psychiatric diseases. However, microglia also possess potent immunoregulatory and regenerative capacities, making them attractive targets for therapeutic manipulation. Such rationale manipulations will, however, require in-depth knowledge of their origins and the molecular mechanisms underlying their homeostasis. Here, we discuss the latest advances in our understanding of the origin, differentiation, and homeostasis of microglial cells and their myelomonocytic relatives in the CNS.Microglia are the resident macrophages of the central nervous system (CNS), which are uniformly distributed throughout the brain and spinal cord with increased densities in neuronal nuclei, including the Substantia nigra in the midbrain (Lawson et al. 1990; Perry 1998). They belong to the nonneuronal glial cell compartment and their function is crucial to maintenance of the CNS in both health and disease (Ransohoff and Perry 2009; Perry et al. 2010; Ransohoff and Cardona 2010; Prinz and Priller 2014).Two key functional features define microglia: immune defense and maintenance of CNS homeostasis. As part of the innate immune system, microglia constantly sample their environment, scanning and surveying for signals of external danger (Davalos et al. 2005; Nimmerjahn et al. 2005; Lehnardt 2010), such as those from invading pathogens, or internal danger signals generated locally by damaged or dying cells (Bessis et al. 2007; Hanisch and Kettenmann 2007). Detection of such signals initiates a program of microglial responses that aim to resolve the injury, protect the CNS from the effects of the inflammation, and support tissue repair and remodeling (Minghetti and Levi 1998; Goldmann and Prinz 2013).Microglia are also emerging as crucial contributors to brain homeostasis through control of neuronal proliferation and differentiation, as well as influencing formation of synaptic connections (Lawson et al. 1990; Perry 1998; Hughes 2012; Blank and Prinz 2013). Recent imaging studies revealed dynamic interactions between microglia and synaptic connections in the healthy brain, which contributed to the modification and elimination of synaptic structures (Perry et al. 2010; Tremblay et al. 2010; Bialas and Stevens 2013). In the prenatal brain, microglia regulate the wiring of forebrain circuits, controlling the growth of dopaminergic axons in the forebrain and the laminar positioning of subsets of neocortical interneurons (Squarzoni et al. 2014). In the postnatal brain, microglia-mediated synaptic pruning is similarly required for the remodeling of neural circuits (Paolicelli et al. 2011; Schafer et al. 2012). In summary, microglia occupy a central position in defense and maintenance of the CNS and, as a consequence, are a key target for the treatment of neurological and psychiatric disorders.Although microglia have been studied for decades, a long history of experimental misinterpretation meant that their true origins remained debated until recently. Although we knew that microglial progenitors invaded the brain rudiment at very early stages of embryonic development (Alliot et al. 1999; Ransohoff and Perry 2009), it has now been established that microglia arise from yolk sac (YS)-primitive macrophages, which persist in the CNS into adulthood (Davalos et al. 2005; Nimmerjahn et al. 2005; Ginhoux et al. 2010, 2013; Kierdorf and Prinz 2013; Kierdorf et al. 2013a). Moreover, early embryonic brain colonization by microglia is conserved across vertebrate species, implying that it is essential for early brain development (Herbomel et al. 2001; Bessis et al. 2007; Hanisch and Kettenmann 2007; Verney et al. 2010; Schlegelmilch et al. 2011; Swinnen et al. 2013). In this review, we will present the latest findings in the field of microglial ontogeny, which provide new insights into their roles in health and disease.     

Receptor Tyrosine Kinases: Legacy of the First Two Decades

Receptor tyrosine kinases (RTKs) and their cellular signaling pathways play important roles in normal development and homeostasis. Aberrations in their activation or signaling leads to many pathologies, especially cancers, motivating the development of a variety of drugs that block RTK signaling that have been successfully applied for the treatment of many cancers. As the current field of RTKs and their signaling pathways are covered by a very large amount of literature, spread over half a century, I am focusing the scope of this review on seminal discoveries made before tyrosine phosphorylation was discovered, and on the early days of research into RTKs and their cellular signaling pathways. I review the history of the early days of research in the field of RTKs. I emphasize key early findings, which provided conceptual frameworks for addressing the questions of how RTKs are activated and how they regulate intracellular signaling pathways.The family of cell-surface receptors designated receptor tyrosine kinases (RTK) received their name more that a decade after the same molecules were already known as the cell-surface receptors for insulin (insulin receptor), epidermal growth factor (EGFR), and many other growth factor receptors. Following the pioneering discoveries of nerve growth factor and epidermal growth factor (EGF; Levi-Montalcini and Booker 1960; Cohen 1962) and the establishment of the important roles of these two growth factors in the control of neuronal differentiation and cell proliferation in vivo and in vitro, it became clear that these cytokines bind specifically to cell-surface receptors. Insulin had already been discovered by this time, and had been applied successfully to treat diabetes patients since the early twentieth century. The resulting homogenous preparations of pure insulin enabled the quantitative characterization of insulin binding to its receptor on intact cells or to solubilized insulin receptor preparations using radiolabeled insulin (De Meyts et al. 1973). These studies greatly advanced understanding of the ligand binding characteristics of insulin receptor and, later on EGFR (Carpenter et al. 1975), including the establishment of negative cooperativity in insulin binding to its receptor expressed on the surface of living cells (De Meyts et al. 1973). Moreover, these studies shed important light on the dynamic nature of the cellular behavior of these receptors. The capacities of insulin receptor and EGFR to undergo ligand-dependent down-regulation and desensitization through receptor-mediated internalization and degradation (Carpenter and Cohen 1976; Gordon et al. 1978; Schlessinger et al. 1978a,b; Carpentier et al. 1979; Haigler et al. 1979) were also established well before the realization that growth factors receptors are endowed with intrinsic protein tyrosine kinase activities (Fig. 1).Open in a separate windowFigure 1.A time line of key findings during the history of RTKs, with emphasis on findings and discoveries that produced the conceptual framework in the development of the RTK field and its application for cancer therapy. References for the key findings are also presented in the text (Lee et al. 1985; Libermann et al. 1985; Margolis et al. 1990; Bottaro et al. 1991; Bae et al. 2009).Progress was also made in elucidating the role of growth factors in normal embryonic development, wound healing, and pathological conditions such as cancer. Early studies in the 1960s and 1970s showed that growth factors play an important role in oncogenesis induced by retroviruses and in the proliferation of tumor-derived cancer cells. Pioneering studies performed by Howard Temin (1966, 1967) showed that cancer cells need less insulin and serum growth factors for cell proliferation compared with normal cells, suggesting that cancer cells produce and use their own growth factors and/or use cellular processes that in normal cells are regulated by exogenously supplied growth factors; both predictions were subsequently confirmed. A variety of new polypeptide growth factors that stimulate cell proliferation by binding to receptors at the cell surface were subsequently discovered. Those include a growth factor isolated from human platelets designated platelet-derived growth factor (PDGF; Antoniades et al. 1979; Heldin et al. 1979), a growth factor isolated from bovine brain designated fibroblast growth factor (FGF; Gospodarowicz et al. 1978), a growth factor isolated from rat platelets that stimulates the proliferation of mature hepatocytes, designated hepatocyte growth factor (HGF; Nakamura et al. 1986). In addition to EGF, another growth factor that binds selectively to cells expressing EGFR was isolated from virally and chemically transformed cells, suggesting that this growth factor—designated transforming growth factor α—may play a role in oncogenesis by an autocrine mechanism (Roberts et al. 1980, 1982). This discovery provided further support to the earlier finding that transformation by murine and feline sarcoma viruses selectively interferes with EGF binding to EGFR in transformed cells (Todaro et al. 1976). Together with many other studies published since the 1980s, this work showed that growth factors and their receptors play numerous important roles during development and in many normal cellular processes as well as in pathologies such as cancer, diabetes, atherosclerosis, severe bone disorders, and tumor angiogenesis.Visualization of dynamic cellular redistribution of ligand/receptor complexes, and rapid receptor-mediated internalization of growth factors such as insulin or EGF, led to the proposal that cell-surface receptors for these ligands may play a passive role in delivering them to intracellular compartments in which internalized EGF or insulin molecules exert their actions (Vigneri et al. 1978; Podlecki et al. 1986; Jiang and Schindler 1990). In other words, according to this hypothesis, the biological signals induced by insulin or EGF were thought to be mediated by binding of the ligands themselves to intracellular target(s) in the cytoplasm or nucleus, with the role of the cell-surface receptor being to act as a “carrier” that delivers them directly to these targets. An alternative hypothesis was that insulin or EGF activates their cognate receptors at the cell surface, which in turn stimulate the production of an intracellular second messenger molecule analogous to cAMP in signaling by the G-protein-activating β-adrenergic receptor. Indeed, several potential second messengers that are generated in cells on stimulation with insulin or other growth factors were proposed before (and even after) it became clear that insulin receptor, EGFR, and other RTKs are endowed with intrinsic tyrosine kinase activity (Larner et al. 1979; Das 1980; Saltiel and Cuatrecasas 1986).A demonstration that anti-insulin receptor antibodies from the serum of certain diabetic patients could mimic cellular responses of insulin (Flier et al. 1977; Van Obberghen et al. 1979) provided the first conclusive answer to the question of whether the biological activity of growth factors is mediated directly or indirectly through their membrane receptors. This experiment ruled out the possibility that insulin receptor functions as a passive carrier that delivers insulin to an intracellular target to induce cellular responses. Studies showing that intact, bivalent antibodies against the insulin receptor can activate its signaling, whereas monovalent Fab fragments of the same antibodies cannot further argued that ligand-induced receptor dimerization or stimulation of a particular arrangement between two receptor molecules in a dimer can activate the insulin receptor (Kahn et al. 1978).A similar conclusion was reached using certain monoclonal antibodies that bind to the extracellular region of EGFR and block ligand binding (Schreiber et al. 1981). Whereas intact antibodies were able to mimic EGF in stimulating a variety of EGF-like responses including cell proliferation, monovalent Fab fragments of the same monoclonal EGFR antibodies failed to do so—and acted instead as EGFR antagonists (Schreiber et al. 1981, 1983). These experiments provided strong evidence both that EGFR plays a crucial role in mediating EGF-induced cellular responses and that EGFR is activated by ligand-induced receptor dimerization (Schreiber 1981, 1983).     

Origin and Evolution of the Self-Organizing Cytoskeleton in the Network of Eukaryotic Organelles

The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity and, in many aspects, prefigure the self-organizing properties of the eukaryotic cytoskeleton. Here, the dynamic properties of the prokaryotic and eukaryotic cytoskeleton are compared, and how these relate to function and evolution of organellar networks is discussed. The evolution of new aspects of filament dynamics in eukaryotes, including severing and branching, and the advent of molecular motors converted the eukaryotic cytoskeleton into a self-organizing “active gel,” the dynamics of which can only be described with computational models. Advances in modeling and comparative genomics hold promise of a better understanding of the evolution of the self-organizing cytoskeleton in early eukaryotes, and its role in the evolution of novel eukaryotic functions, such as amoeboid motility, mitosis, and ciliary swimming.The eukaryotic cytoskeleton organizes space on the cellular scale and this organization influences almost every process in the cell. Organization depends on the mechanochemical properties of the cytoskeleton that dynamically maintain cell shape, position organelles, and macromolecules by trafficking, and drive locomotion via actin-rich cellular protrusions, ciliary beating, or ciliary gliding. The eukaryotic cytoskeleton is best described as an “active gel,” a cross-linked network of polymers (gel) in which many of the links are active motors that can move the polymers relative to each other (Karsenti et al. 2006). Because prokaryotes have only cytoskeletal polymers but lack motor proteins, this “active gel” property clearly sets the eukaryotic cytoskeleton apart from prokaryotic filament systems.Prokaryotes contain elaborate systems of several cytomotive filaments (Löwe and Amos 2009) that share many structural and dynamic features with eukaryotic actin filaments and microtubules (Löwe and Amos 1998; van den Ent et al. 2001). Prokaryotic cytoskeletal filaments may trace back to the first cells and may have originated as higher-order assemblies of enzymes (Noree et al. 2010; Barry and Gitai 2011). These cytomotive filaments are required for the segregation of low copy number plasmids, cell rigidity and cell-wall synthesis, cell division, and occasionally the organization of membranous organelles (Komeili et al. 2006; Thanbichler and Shapiro 2008; Löwe and Amos 2009). These functions are performed by dynamic filament-forming systems that harness the energy from nucleotide hydrolysis to generate forces either via bending or polymerization (Löwe and Amos 2009; Pilhofer and Jensen 2013). Although the identification of actin and tubulin homologs in prokaryotes is a major breakthrough, we are far from understanding the origin of the structural and dynamic complexity of the eukaryotic cytoskeleton.Advances in genome sequencing and comparative genomics now allow a detailed reconstruction of the cytoskeletal components present in the last common ancestor of eukaryotes. These studies all point to an ancestrally complex cytoskeleton, with several families of motors (Wickstead and Gull 2007; Wickstead et al. 2010) and filament-associated proteins and other regulators in place (Jékely 2003; Richards and Cavalier-Smith 2005; Rivero and Cvrcková 2007; Chalkia et al. 2008; Eme et al. 2009; Fritz-Laylin et al. 2010; Eckert et al. 2011; Hammesfahr and Kollmar 2012). Genomic reconstructions and comparative cell biology of single-celled eukaryotes (Raikov 1994; Cavalier-Smith 2013) allow us to infer the cellular features of the ancestral eukaryote. These analyses indicate that amoeboid motility (Fritz-Laylin et al. 2010; although, see Cavalier-Smith 2013), cilia (Cavalier-Smith 2002; Mitchell 2004; Jékely and Arendt 2006; Satir et al. 2008), centrioles (Carvalho-Santos et al. 2010), phagocytosis (Cavalier-Smith 2002; Jékely 2007; Yutin et al. 2009), a midbody during cell division (Eme et al. 2009), mitosis (Raikov 1994), and meiosis (Ramesh et al. 2005) were all ancestral eukaryotic cellular features. The availability of functional information from organisms other than animals and yeasts (e.g., Chlamydomonas, Tetrahymena, Trypanosoma) also allow more reliable inferences about the ancestral functions of cytoskeletal components (i.e., not only their ancestral presence or absence) and their regulation (Demonchy et al. 2009; Lechtreck et al. 2009; Suryavanshi et al. 2010).The ancestral complexity of the cytoskeleton in eukaryotes leaves a huge gap between prokaryotes and the earliest eukaryote we can reconstruct (provided that our rooting of the tree is correct) (Cavalier-Smith 2013). Nevertheless, we can attempt to infer the series of events that happened along the stem lineage, leading to the last common ancestor of eukaryotes. Meaningful answers will require the use of a combination of gene family history reconstructions (Wickstead and Gull 2007; Wickstead et al. 2010), transition analyses (Cavalier-Smith 2002), and computer simulations relevant to cell evolution (Jékely 2008).     

Structure and Biochemistry of Cadherins and Catenins

Classical cadherins mediate specific adhesion at intercellular adherens junctions. Interactions between cadherin ectodomains from apposed cells mediate cell–cell contact, whereas the intracellular region functionally links cadherins to the underlying cytoskeleton. Structural, biophysical, and biochemical studies have provided important insights into the mechanism and specificity of cell–cell adhesion by classical cadherins and their interplay with the cytoskeleton. Adhesive binding arises through exchange of β strands between the first extracellular cadherin domains (EC1) of partner cadherins from adjacent cells. This “strand-swap” binding mode is common to classical and desmosomal cadherins, but sequence alignments suggest that other cadherins will bind differently. The intracellular region of classical cadherins binds to p120 and β-catenin, and β-catenin binds to the F-actin binding protein α-catenin. Rather than stably bridging β-catenin to actin, it appears that α-catenin actively regulates the actin cytoskeleton at cadherin-based cell–cell contacts.Cadherins constitute a large family of cell surface proteins, many of which participate in Ca²⁺-dependent cell adhesion that plays a fundamental role in the formation of solid tissues (Takeichi 1995; Tepass 1999; Gumbiner 2005). Many events in the development of multicellular assemblies are associated with changes in cadherin expression (Takeichi 1995; Honjo et al. 2000; Price et al. 2002). Expression of particular cadherins often correlates with formation of discrete tissue structures, and in mature tissues discrete cell layers or other cell assemblies are often demarcated by particular cadherins (Gumbiner 1996). Conversely, down-regulation or loss of cadherins correlates with an increased metastatic potential of the affected cells that arises from the loss of their adhesive properties (Hajra and Fearon 2002; Gumbiner 2005).The cadherins of vertebrates, and some of their invertebrate homologs, are the most highly characterized. “Classical” cadherins, associated with the adherens junction, and the closely related desmosomal cadherins feature an amino-terminal extracellular region or ectodomain that is followed by a transmembrane anchor and a carboxy-terminal intracellular region. Interactions between ectodomains on apposed cells mediate specific cell–cell contacts, whereas the intracellular region functionally links cadherins to the underlying cytoskeleton. This article focuses on structural, biophysical, and biochemical studies that have provided important mechanistic insights into the specificity of cell–cell adhesion and its interplay with the cytoskeleton (see also Meng and Takeichi 2009; Cavey and Lecuit 2009).     

Unconventional Functions for Clathrin,ESCRTs, and Other Endocytic Regulators in the Cytoskeleton,Cell Cycle,Nucleus, and Beyond: Links to Human Disease

The roles of clathrin, its regulators, and the ESCRT (endosomal sorting complex required for transport) proteins are well defined in endocytosis. These proteins can also participate in intracellular pathways that are independent of endocytosis and even independent of the membrane trafficking function of these proteins. These nonendocytic functions involve unconventional biochemical interactions for some endocytic regulators, but can also exploit known interactions for nonendocytic functions. The molecular basis for the involvement of endocytic regulators in unconventional functions that influence the cytoskeleton, cell cycle, signaling, and gene regulation are described here. Through these additional functions, endocytic regulators participate in pathways that affect infection, glucose metabolism, development, and cellular transformation, expanding their significance in human health and disease.The discovery and characterization of clathrin (Pearse 1975) initiated molecular definition of the many endocytosis regulators described in this collection, which mediate the clathrin-dependent and -independent pathways for membrane internalization (see Kirchhausen et al. 2014; Mayor et al. 2014; Merrifield and Kaksonen 2014). In accompanying reviews, we have seen how these endocytic pathways influence nutrition and metabolism (see Antonescu et al. 2014), signal transduction (see Bökel and Brand 2014; Di Fiore and von Zastrow 2014), neuronal function (see Morgan et al. 2013; Cosker and Segal 2014), infection and immunity (see ten Broeke et al. 2013; Cossart and Helenius 2014), tissue polarity and development (see Eaton and Martin-Belmonte 2014; Gonzalez-Gaitan and Jülicher 2014), and migration and metastasis (see Mellman and Yarden 2013). Recently, it has been established that some endocytic regulators have molecular properties that expand their functions beyond endocytosis. These include molecular interactions that affect the microtubule and actin cytoskeletons, nuclear translocation that influences gene regulation, and the formation of membrane-associated scaffolds that serve as signaling and sorting platforms. Through these diverse nonendocytic functions, endocytosis regulators play additional roles in cell division, pathogen infection, cell adhesion, and oncogenesis. In this article, we review the nonconventional behavior of endocytic regulators, first discussing the molecular properties that enable their moonlighting functions and then discussing the cellular processes and disease states that are influenced by these functions.     

Is Sexual Conflict an “Engine of Speciation”?

At the end of the last century, sexual conflict was identified as a powerful engine of speciation, potentially even more important than ecological selection. Earlier work that followed—experimental, comparative, and mathematical—provided strong initial support for this assertion. However, as the field matures, both the power of sexual conflict and constraints on the evolution of reproductive isolation as driven by sexual conflict are becoming better understood. From theoretical studies, we now know that speciation is only one of several possible evolutionary outcomes of sexual conflict. In line with these predictions, both experimental evolution studies and comparative analyses of fertilization proteins and of species richness show that sexual conflict leads to, or is associated with, reproductive isolation and speciation in some cases but not in others. Increased genetic variation (especially in females) without reproductive isolation is an underappreciated consequence of sexually antagonistic selection.By the end of 1990s, studies of sexual conflict and sexually antagonistic coevolution moved to the forefront of experimental and theoretical research in evolutionary biology (Rice and Holland 1997; Holland and Rice 1998; Rice 1998). Although the potential evolutionary importance of sexual conflict was anticipated and articulated from a theoretical point of view by Geoff Parker 20 years earlier (Parker 1979), the explosive interest in this topic was a result of groundbreaking experimental work with Drosophila melanogaster by Bill Rice (1993, 1996), which directly showed high potential for sexually antagonistic coevolution.Sexual conflict is a special case of intragenomic conflict (Rice and Holland 1997; Rice 1998; Crespi and Nosil 2013). Sexual conflict occurs if the interests of the sexes with regard to certain aspects of reproduction differ (Parker 1979; Arnqvist and Rowe 2005). Ultimately, sexual conflict arises because of the differences in the roles played by the sexes in the process of reproduction, which in turn lead to the differences between the sexes in the costs and benefits of mating and reproduction (Bateman 1948; Trivers 1972; Parker 1979). Sexual conflict can occur over mating rate (Rice and Holland 1997; Holland and Rice 1998; Rice 1998), offspring size (Haig 2000), parental care (Smith and Härdling 2000; Barta et al. 2002), the use of sperm (Ball and Parker 2003), epigenetic control of development (Rice et al. 2012), etc.Sexual conflict can occur through two genetic routes (Chapman and Partridge 1996; Parker and Partridge 1998). Within-locus conflict occurs when the locus controls a trait expressed in both sexes and the optimum trait values differ between the sexes. As a result, optimizing the trait value in one sex will lead to a fitness reduction in the other sex. Within-locus conflict can be resolved via a number of mechanisms, including the evolution of sex linkage, sex-specific expression of genes, gene duplication, and condition dependence (Bonduriansky and Chenoweth 2009; van Doorn 2009). Between-locus conflict occurs when there are two different (sets of) traits each expressed in one sex only but affecting the fitness of both sexes in opposite directions. In this case, adaptive changes in a trait of one sex cause deleterious fitness consequences for the other sex, which can be negated by the evolution in a trait of the other sex, which in turn will cause deleterious fitness consequences for the first sex. For example, males can evolve adaptations increasing their mating rate, which would be detrimental for females who would then evolve some counteradaptations to decrease the mating rate (Rice 1996).One particularly exciting idea that has emerged from studies of sexual conflict and sexually antagonistic coevolution is that sexual conflict can be an important “engine of speciation” (Rice 1996, 1998; Howard et al. 1998; Parker and Partridge 1998). In standard modern perspective, speciation is a result of genetic divergence between populations accompanied by the evolution of reproductive isolation (Howard and Berlocher 1998; Schluter 2000; Coyne and Orr 2004; Dieckmann et al. 2004; Gavrilets 2004). Genetic divergence can be driven by a variety of evolutionary factors, including mutation, random genetic drift, and natural, sexual, and social selection. Reproductive isolation can follow from a variety of mechanisms, resulting in incompatibilities (including genetic, developmental, morphological, ecological, and behavioral) of males and females from diverging populations or in a reduced fitness of their offspring. As was argued by Rice (1998), Parker and Partridge (1998), and others (e.g., Howard et al. 1998), sexual conflict can contribute to these processes in a number of ways.Below, I briefly summarize several, mostly verbal, theories of biological diversification caused by sexual conflict and then move to discussing some of the more concrete mathematical models and empirical data and patterns.     

The Biochemistry of Mitosis

In this article, we will discuss the biochemistry of mitosis in eukaryotic cells. We will focus on conserved principles that, importantly, are adapted to the biology of the organism. It is vital to bear in mind that the structural requirements for division in a rapidly dividing syncytial Drosophila embryo, for example, are markedly different from those in a unicellular yeast cell. Nevertheless, division in both systems is driven by conserved modules of antagonistic protein kinases and phosphatases, underpinned by ubiquitin-mediated proteolysis, which create molecular switches to drive each stage of division forward. These conserved control modules combine with the self-organizing properties of the subcellular architecture to meet the specific needs of the cell. Our discussion will draw on discoveries in several model systems that have been important in the long history of research on mitosis, and we will try to point out those principles that appear to apply to all cells, compared with those in which the biochemistry has been specifically adapted in a particular organism.The aim of mitosis is to separate the genome and ensure that the two daughter cells inherit an equal and identical complement of chromosomes (Yanagida 2014). To achieve this, eukaryotic cells completely reorganize their microtubules to build a mitotic spindle that pulls apart the sister chromatids after the cohesin complexes are cut (see Cheeseman 2014; Hirano 2015; Reber and Hyman 2015; Westhorpe and Straight 2015) and, subsequently, use the actin cytoskeleton to divide the cell into two (cytokinesis) (see D’Avino et al. 2015). In some cells, such as in budding and fission yeasts, the spindle is built within the nucleus (closed mitosis), whereas in others, the nuclear envelope breaks down and the condensed chromosomes are captured by microtubules in the cytoplasm (open mitosis). This difference in the spatial organization of the mitotic cell has ramifications for the machinery controlling mitosis. In particular, the breakdown of the nuclear compartment disrupts the guanosine triphosphate (GTP)–guanosine diphosphate (GDP) gradient of the small GTPase called Ran. Ran usually controls nuclear-cytoplasmic transport through the importin chaperones; Ran-GDP in the cytoplasm promotes binding to nuclear transport substrates, whereas Ran-GTP in the nucleus promotes their dissociation (Güttler and Görlich 2011). As a result of nuclear envelope breakdown (NEBD), another Ran-GTP gradient is generated around the chromosomes, to which the RCC1 GTP-exchange factor binds (Clarke 2008). This Ran-GTP gradient is important for the interaction between microtubules and chromosomes because the high Ran-GTP levels around chromosomes promote the dissociation between the importin β chaperone and its binding partners, several of which help to stabilize or nucleate microtubules (Carazo-Salas et al. 1999; Kalab et al. 1999; Gruss et al. 2001; Wilde et al. 2001; Yokoyama et al. 2008).The dramatic reorganization of the cell at mitosis must be coordinated in both time and space. There are several key temporal events: entry to mitosis, sister chromatid separation, and mitotic exit, and these are effectively made unidirectional by the biochemical machinery. We will discuss the biochemistry behind each of these temporal events, in turn, but it is important to emphasize that the control mechanisms are also spatially organized. Our understanding of this spatial organization has improved dramatically with advances in the technology to detect gradients of activity in cells, and this has revealed the importance of local gradients of antagonistic protein kinases and phosphatases, GTP-binding protein regulators, and ubiquitin ligases and deubiquitylases, to name only a few of the more prominent examples (reviewed in Pines and Hagan 2011).     

The Immunogenetic Architecture of Autoimmune Disease

The development of most autoimmune diseases includes a strong heritable component. This genetic contribution to disease ranges from simple Mendelian inheritance of causative alleles to the complex interactions of multiple weak loci influencing risk. The genetic variants responsible for disease are being discovered through a range of strategies from linkage studies to genome-wide association studies. Despite the rapid advances in genetic analysis, substantial components of the heritable risk remain unexplained, either owing to the contribution of an as-yet unidentified, “hidden,” component of risk, or through the underappreciated effects of known risk loci. Surprisingly, despite the variation in genetic control, a great deal of conservation appears in the biological processes influenced by risk alleles, with several key immunological pathways being modified in autoimmune diseases covering a broad spectrum of clinical manifestations. The primary translational potential of this knowledge is in the rational design of new therapeutics to exploit the role of these key pathways in influencing disease. With significant further advances in understanding the genetic risk factors and their biological mechanisms, the possibility of genetically tailored (or “personalized”) therapy may be realized.Autoimmune diseases affect a significant proportion of the population, with >4% of the European population suffering from one or more of these disorders (Vyse and Todd 1996; Cooper et al. 2009; Eaton et al. 2010). Although all autoimmune diseases share similarities in the basic immunological mechanisms, in other aspects, such as clinical manifestation and age of onset, individual diseases vary widely. A few rare autoimmune diseases with Mendelian inheritance patterns within families occur including APS-1 (autoimmune polyendocrine syndrome type 1), IPEX (immunodysregulation, polyendocrinopathy, and enteropathy X-linked) syndrome, and ALPS (autoimmune lymphoproliferative syndrome). Most autoimmune diseases are, however, multifactorial in nature, with susceptibility controlled by multiple genetic and environmental factors.The genetic component of more common autoimmune diseases can be calculated in several different manners, including the sibling recurrence risk (λ_s) and the twin concordance rate. The sibling recurrence risk is the ratio of the lifetime risk in siblings of patients to the lifetime population risk, whereas the twin concordance rate measures the proportion of the siblings of affected twins that are also affected. Most common autoimmune diseases, such as multiple sclerosis (MS), type 1 diabetes (T1D), rheumatoid arthritis (RA), and inflammatory bowel disease (IBD) are characterized by a sibling recurrence risk between 6 and 20 (Vyse and Todd 1996), and concordance rates of 25%–50% in monozygotic twins and 2%–12% in dizygotic twins (Cooper et al. 1999). A substantial proportion of relatives may also have subclinical evidence of autoimmunity without developing clinically overt disease. For example, 19% of healthy siblings of MS patients show antibody production in the cerebrospinal fluid, compared to 4% of unrelated healthy controls (Haghighi et al. 2000), whereas 4% of healthy first-degree relatives display lesions that are indistinguishable from those seen in patients and are not seen in unrelated healthy controls (De Stefano et al. 2006). Furthermore, comorbidity with the development of several autoimmune diseases in the same patient and clustering of several autoimmune diseases within families above what is expected by chance appear common (Cooper et al. 2009; Zhernakova et al. 2009). Together these data show a strong genetic component to autoimmune disease development.     

Endocytosis of Viruses and Bacteria

Of the many pathogens that infect humans and animals, a large number use cells of the host organism as protected sites for replication. To reach the relevant intracellular compartments, they take advantage of the endocytosis machinery and exploit the network of endocytic organelles for penetration into the cytosol or as sites of replication. In this review, we discuss the endocytic entry processes used by viruses and bacteria and compare the strategies used by these dissimilar classes of pathogens.Many of the most widespread and devastating diseases in humans and livestock are caused by viruses and bacteria that enter cells for replication. Being obligate intracellular parasites, viruses have no choice. They must transport their genome to the cytosol or nucleus of infected cells to multiply and generate progeny. Bacteria and eukaryotic parasites do have other options; most of them can replicate on their own. However, some have evolved to take advantage of the protected environment in the cytosol or in cytoplasmic vacuoles of animal cells as a niche favorable for growth and multiplication. In both cases (viruses and intracellular bacteria), the outcome is often destructive for the host cell and host organism. The mortality and morbidity caused by infectious diseases worldwide provide a strong rationale for research into pathogen–host cell interactions and for pursuing the detailed mechanisms of transmission and dissemination. The study of viruses and bacteria can, moreover, provide invaluable insights into fundamental aspects of cell biology.Here, we focus on the mechanisms by which viral and bacterial pathogens exploit the endocytosis machinery for host cell entry and replication. Among recent reviews on this topic, dedicated uniquely to either mammalian viruses or bacterial pathogens, we recommend the following: Cossart and Sansonetti (2004); Pizarro-Cerda and Cossart (2006); Kumar and Valdivia (2009); Cossart and Roy (2010); Mercer et al. (2010b); Grove and Marsh (2011); Kubo et al. (2012); Vazquez-Calvo et al. (2012a); Sun et al. (2013).The term “endocytosis” is used herein in its widest sense, that is, to cover all processes whereby fluid, solutes, ligands, and components of the plasma membrane as well as particles (including pathogenic agents) are internalized by cells through the invagination of the plasma membrane and the scission of membrane vesicles or vacuoles. This differs from current practice in the bacterial pathogenesis field, where the term “endocytosis” is generally reserved for the internalization of molecules or small objects, whereas the uptake of bacteria into nonprofessional phagocytes is called “internalization” or “bacterial-induced phagocytosis.” In addition, the term “phagocytosis” is reserved for internalization of bacteria by professional phagocytes (macrophages, polymorphonuclear leucocytes, dendritic cells, and amoebae), a process that generally but not always leads to the destruction of the ingested bacteria (Swanson et al. 1999; May and Machesky 2001; Henry et al. 2004; Zhang et al. 2010). With a few exceptions, we will not discuss phagocytosis of bacteria or the endocytosis of protozoan parasites such as Toxoplasma and Plasmodium (Robibaro et al. 2001).