Annual Review of Cell and Developmental Biology - Volume 23, 2007

I have been fascinated by chromosomes for longer than I care to mention; their beautiful structure, cell-type-specific changes in morphology, and elegant movements delight me. Shortly before I began graduate study, the development of nucleic acid hybridization made it possible to compare two nucleic acids whether or not their sequences were known. From this stemmed a progression of development in tools and techniques that continues to enhance our understanding of how chromosomes function. As my PhD project I contributed to this progression by developing in situ hybridization, a technique for hybridization to nucleic acids within their cellular context. Early studies with this technique initiated several lines of research, two of which I describe here, that I have pursued to this day. First, analysis of RNA populations by hybridization to polytene chromosomes (a proto-microarray-type experiment) led us to characterize levels of regulation during heat shock beyond those recognizable by puffing studies. We found also that one still-undeciphered major heat shock puff encodes a novel set of RNAs for which we propose a regulatory role. Second, localization of various multicopy DNA sequences has suggested roles for them in chromosome structure: Most recently we have found that Drosophila telomeres consist of and are maintained by special non-LTR (long terminal repeat) retrotransposons.

Although the precise mechanism by which nonenveloped viruses penetrate biological membranes is unclear, a more coherent understanding of this process is starting to emerge. To initiate membrane penetration, nonenveloped viruses engage host cell factors that impart conformational changes on the viral particles, resulting in the exposure of a hydrophobic moiety or the release of a lytic factor. The viruses' interactions with the limiting membrane subsequently compromise the bilayer integrity. This reaction presumably perforates the bilayer to enable the virus to cross the membrane and reach the cytosol. Valuable insights into this process can be gleaned from the membrane transport mechanisms of enveloped viruses and bacterial toxins. To identify systematically the cellular components that facilitate nonenveloped virus membrane penetration, sensitive assays that monitor the transport event directly must first be established. Moreover, higher-resolution structures of penetration intermediates, particularly those solved in complex with membranes, would provide important molecular details into this process.

In this review we discuss the major morphogenetic and regulative events that control myocardial progenitor cells from the time that they delaminate from the epiblast in the primitive streak to their differentiation into cardiomyocytes in the heart tube. During chick and mouse embryogenesis, myocardial progenitor cells go through four specific processes that are sequential but overlapping: specification of the cardiogenic mesoderm, determination of the bilaterally symmetric heart fields, patterning of the heart field, and finally cardiomyocyte differentiation and formation of the heart tube. We describe the morphological and molecular events that play a pivotal role in each of these four processes.

Injury to the skin initiates a complex process of events involving inflammation as well as the formation and remodeling of new tissue. These processes result in at least partial reconstitution of the injured skin. However, wounds in adult mammals heal with a scar, which is accompanied by functional and aesthetic impairments. In addition to this problem, a large number of patients, in particular in the aged population, suffer from chronic, nonhealing ulcers. Therefore, there is a strong need to improve the wound healing process. This requires a thorough understanding of the underlying molecular and cellular mechanisms. During the past several years, important regulators of the wound healing process have been identified. In particular, the growth factors and matrix proteins, which orchestrate skin repair, have been characterized in detail. By contrast, much less is known about the transcription factors, which regulate gene expression at the wound site. This review summarizes recent data on the expression of transcription factors in skin wounds and their functions in the repair process.

The epidermis is a stratified epithelium that functions as a barrier protecting the organism from dehydration, mechanical trauma, and microbial insults. This barrier function is established during embryogenesis through a complex and tightly controlled stratification program. Whereas the morphological changes that occur during epidermal development have been extensively studied, the molecular mechanisms that govern this process remain poorly understood. In this review we summarize the current advances that have been made in understanding the molecular mechanisms that regulate epidermal morphogenesis.

Chaperonins are large ring assemblies that assist protein folding to the native state by binding nonnative proteins in their central cavities and then, upon binding ATP, release the substrate protein into a now-encapsulated cavity to fold productively. Two families of such components have been identified: type I in mitochondria, chloroplasts, and the bacterial cytosol, which rely on a detachable “lid” structure for encapsulation, and type II in archaea and the eukaryotic cytosol, which contain a built-in protrusion structure. We discuss here a number of issues under current study. What is the range of substrates acted on by the two classes of chaperonin, in particular by GroEL in the bacterial cytoplasm and CCT in the eukaryotic cytosol, and are all these substrates subject to encapsulation? What are the determinants for substrate binding by the type II chaperonins? And is the encapsulated chaperonin cavity a passive container that prevents aggregation, or could it be playing an active role in polypeptide folding?

In yeast and animal cells, members of the superfamily of N-ethylmaleimide-sensitive factor adaptor protein receptor (SNARE)-domain-containing proteins are key players in vesicle-associated membrane fusion events during transport processes between individual compartments of the endomembrane system, including exocytosis and endocytosis. Compared with genomes of other eukaryotes, genomes of monocotyledonous and dicotyledonous plants encode a surprisingly high number of SNARE proteins, suggesting vital roles for this protein class in higher plant species. Although to date it remains elusive whether plant SNARE proteins function like their yeast and animal counterparts, genetic screens have recently begun to unravel the variety of biological tasks in which plant SNAREs are involved. These duties involve fundamental processes such as cytokinesis, shoot gravitropism, pathogen defense, symbiosis, and abiotic stress responses, suggesting that SNAREs contribute essentially to many facets of plant biology.

microRNAs (miRNAs) are small noncoding RNAs that play important roles in posttranscriptional gene regulation. In animal cells, miRNAs regulate their targets by translational inhibition and mRNA destabilization. Here, we review recent work in animal models that provide insight into the diverse roles of miRNAs in vivo.

Early embryonic development in the flowering plant Arabidopsis thaliana follows a predictable sequence of cell divisions. Anatomical hallmarks and the expression of marker genes in dynamic patterns indicate that new cell fates are established with virtually every round of mitosis. Although some of the factors regulating these early patterning events have been identified, the overall process remains relatively poorly understood. Starting at the globular stage, when the embryo has approximately 100 cells, the organization of development appears to be taken over by programs that regulate postembryonic patterning throughout the life cycle.

Cadherins are Ca²⁺-dependent cell adhesion molecules found in several kinds of cell-cell contact, including adherens junctions and desmosomes. In the presence of Ca²⁺, cells expressing the same type of cadherin form stable contacts with one another, a phenomenon designated homophilic, or homotypic, adhesion. Most cadherins are single-pass transmembrane proteins whose extracellular regions mediate specific cell-cell interactions. The intracellular faces of these contacts are associated with the actin cytoskeleton in adherens junctions or the intermediate-filament system in desmosomes. The close coordination of the transmembrane adhesion molecules with the cytoskeleton is believed to be essential in coordinating morphogenetic movements of tissues during development and in conferring the appropriate mechanical properties to cell-cell contacts. Structural, biochemical, and biophysical analysis of the molecules that comprise these contacts has provided unique mechanistic insights into the specificity of homophilic adhesion, the functional connection to the underlying cytoskeleton, and the dynamics of junction formation.

Semaphorin proteins, although initially characterized as repulsive neuronal guidance cues, are now appreciated as major contributors to morphogenesis and homeostasis for a wide range of tissue types. Semaphorin-mediated long- and short-range repulsive, and attractive, guidance has profound influences on cellular morphology. The diversity of semaphorin receptor complexes utilized by various semaphorin ligands, the ability of semaphorins themselves to serve as receptors, and the myriad of intracellular signaling components that comprise semaphorin signaling cascades all contribute to cell-type-specific responses to semaphorins. Analysis of the molecular and cellular mechanisms underlying semaphorin function in neural and vascular systems provides insight into principles governing how this large protein family contributes to organogenesis, function, and disease.

The positioning and elaboration of ectodermal veins in the wing of Drosophila melanogaster rely on widely utilized developmental signals, including those mediated by EGF, BMP, Hedgehog, Notch, and Wnt. Analysis of vein patterning mutants, using the molecular and genetic mosaic techniques available in Drosophila, has provided important insights into how a combination of short-range and long-range signaling can pattern a simple epidermal tissue. Moreover, venation has become a powerful system for isolating and analyzing novel components in these signaling pathways. I here review the basic events of vein patterning and give examples of how changes in venation have been used to identify important features of cell signaling pathways.

Eukaryotic cells divide their metabolic labor between functionally distinct, membrane-enveloped organelles, each precisely tailored for a specific set of biochemical reactions. Peroxisomes are ubiquitous, endoplasmic reticulum–derived organelles that perform requisite biochemical functions intimately connected to lipid metabolism. Upon cell division, cells have to strictly control peroxisome division and inheritance to maintain an appropriate number of peroxisomes in each cell. Peroxisome division follows a specific sequence of events that include peroxisome elongation, membrane constriction, and peroxisome fission. Pex11 proteins mediate the elongation step of peroxisome division, whereas dynamin-related proteins execute the final fission. The mechanisms responsible for peroxisome membrane constriction are poorly understood. Molecular players involved in peroxisome inheritance are just beginning to be elucidated. Inp1p and Inp2p are two recently identified peroxisomal proteins that perform antagonistic functions in regulating peroxisome inheritance in budding yeast. Inp1p promotes the retention of peroxisomes in mother cells and buds by attaching peroxisomes to as-yet-unidentified cortical structures. Inp2p is implicated in the motility of peroxisomes by linking them to the Myo2p motor, which then propels their movement along actin cables. The functions of Inp1p and Inp2p are cell cycle regulated and coordinated to ensure a fair distribution of peroxisomes at cytokinesis.

Recent studies have revealed unexpected connections between the mammalian Hedgehog (Hh) signal transduction pathway and the primary cilium, a microtubule-based organelle that protrudes from the surface of most vertebrate cells. Intraflagellar transport proteins, which are required for the construction of cilia, are essential for all responses to mammalian Hh proteins, and proteins required for Hh signal transduction are enriched in primary cilia. The phenotypes of different mouse mutants that affect ciliary proteins suggest that cilia may act as processive machines that organize sequential steps in the Hh signal transduction pathway. Cilia on vertebrate cells are likely to be important in additional developmental signaling pathways and are required for PDGF receptor α signaling in cultured fibroblasts. Cilia are not essential for either canonical or noncanonical Wnt signaling, although cell-type-specific modulation of cilia components may link cilia and Wnt signaling in some tissues. Because ciliogenesis in invertebrates is limited to a very small number of specialized cell types, the role of cilia in developmental signaling pathways is likely a uniquely vertebrate phenomenon.

Neuronal motility is a fundamental feature that underlies the development, regeneration, and plasticity of the nervous system. Two major developmental events—directed migration of neuronal precursor cells to the proper positions and guided elongation of axons to their target cells—depend on large-scale neuronal motility. At a finer scale, motility is also manifested in many aspects of neuronal structures and functions, ranging from differentiation and refinement of axonal and dendritic morphology during development to synapse remodeling associated with learning and memory in the adult brain. As a primary second messenger that conveys the cytoplasmic actions of electrical activity and many neuroactive ligands, Ca²⁺ plays a central role in the regulation of neuronal motility. Recent studies have revealed common Ca²⁺-dependent signaling pathways that are deployed for regulating cytoskeletal dynamics associated with neuronal migration, axon and dendrite development and regeneration, and synaptic plasticity.

The Caenorhabditis elegans germ line provides an exceptional model for analysis of the molecular controls governing stem cell maintenance, the cell cycle transition from mitosis to meiosis, and the choice of sexual identity—sperm or oocyte. Germline stem cells are maintained in an undifferentiated state within a well-defined niche formed by a single somatic cell, the distal tip cell (DTC). In both sexes, the DTC employs GLP-1/Notch signaling and FBF/PUF RNA-binding proteins to maintain stem cells and promote mitotic divisions, three additional RNA regulators (GLD-1/quaking, GLD-2/poly(A) polymerase, and GLD-3/Bicaudal-C) control entry into meiosis, and FOG-1/CPEB and FOG-3/Tob proteins govern sperm specification. These key regulators are part of a robust regulatory network that controls germ cell proliferation, stem cell maintenance, and sex determination. Parallels with controls in other organisms include the use of PUF proteins for stem cell maintenance and the prominence of mRNA regulation for the control of germline development.

A hallmark of tissue injury and repair is the turnover of extracellular matrix components. This review focuses on the role of the glycosaminoglycan hyaluronan in tissue injury and repair. Both the synthesis and degradation of extracellular matrix are critical contributors to tissue repair and remodeling. Fragmented hyaluronan accumulates during tissue injury and functions in ways distinct from the native polymer. There is accumulating evidence that hyaluronan degradation products can stimulate the expression of inflammatory genes by a variety of immune cells at the injury site. CD44 is the major cell-surface hyaluronan receptor and is required to clear hyaluronan degradation products produced during lung injury; impaired clearance of hyaluronan results in persistent inflammation. However, hyaluronan fragment stimulation of inflammatory gene expression is not dependent on CD44 in inflammatory macrophages. Instead, hyaluronan fragments utilize both Toll-like receptor (TLR) 4 and TLR2 to stimulate inflammatory genes in macrophages. Hyaluronan also is present on the cell surface of lung alveolar epithelial cells and provides protection against tissue damage by interacting with TLR2 and TLR4 on these parenchymal cells. The simple repeating structure of hyaluronan appears to be involved in a number of important aspects of noninfectious tissue injury and repair that are dependent on the size and location of the polymer as well as the interacting cells. Thus, the interactions between the endogenous matrix component hyaluronan and its signaling receptors initiate inflammatory responses, maintain structural cell integrity, and promote recovery from tissue injury.

Like all hematopoietic cells, T lymphocytes are derived from bone-marrow-resident stem cells. However, whereas most blood lineages are generated within the marrow, the majority of T cell development occurs in a specialized organ, the thymus. This distinction underscores the unique capacity of the thymic microenvironment to support T lineage restriction and differentiation. Although the identity of many of the contributing thymus-derived signals is well established and rooted in highly conserved pathways involving Notch, morphogenetic, and protein tyrosine kinase signals, the manner in which the ensuing cascades are integrated to orchestrate the underlying processes of T cell development remains under investigation. This review focuses on the current definition of the early stages of T cell lymphopoiesis, with an emphasis on the nature of thymus-derived signals delivered to T cell progenitors that support the commitment and differentiation of T cells toward the αβ and γδ T cell lineages.

Cytotoxic T lymphocytes (CTLs) play a critical role in the immune system; they are able to recognize and destroy virally infected and tumorigenic cells. Specific recognition of MHC class I–peptide complexes by the T cell receptor (TcR) results in precise delivery of lytic granules to the target cell, sparing neighboring cells and the CTL itself. Over the past 10 years various studies have eludicated the mechanisms that lead to the rapid polarization of the secretory apparatus in CTLs. These studies highlight similarities and differences between polarity and secretory mechanisms seen in other cell types and developmental systems. This review focuses on recent advances in our understanding of the molecular basis of polarized secretion from CTLs and the novel mechanism used by these cells to deliver their lethal hit.