Recent Journal Articles: Developmental Biology -- Neurotransmitter.net

Recent Articles in Annual Review of Cell and Developmental Biology

Zheng JQ, Poo MM
Calcium signaling in neuronal motility.
Annu Rev Cell Dev Biol. 2007;23375-404.
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, Ca(2+) plays a central role in the regulation of neuronal motility. Recent studies have revealed common Ca(2+)-dependent signaling pathways that are deployed for regulating cytoskeletal dynamics associated with neuronal migration, axon and dendrite development and regeneration, and synaptic plasticity. [Abstract]

Lobo NA, Shimono Y, Qian D, Clarke MF
The biology of cancer stem cells.
Annu Rev Cell Dev Biol. 2007;23675-99.
Cancers originally develop from normal cells that gain the ability to proliferate aberrantly and eventually turn malignant. These cancerous cells then grow clonally into tumors and eventually have the potential to metastasize. A central question in cancer biology is, which cells can be transformed to form tumors? Recent studies elucidated the presence of cancer stem cells that have the exclusive ability to regenerate tumors. These cancer stem cells share many characteristics with normal stem cells, including self-renewal and differentiation. With the growing evidence that cancer stem cells exist in a wide array of tumors, it is becoming increasingly important to understand the molecular mechanisms that regulate self-renewal and differentiation because corruption of genes involved in these pathways likely participates in tumor growth. This new paradigm of oncogenesis has been validated in a growing list of tumors. Studies of normal and cancer stem cells from the same tissue have shed light on the ontogeny of tumors. That signaling pathways such as Bmi1 and Wnt have similar effects in normal and cancer stem cell self-renewal suggests that common molecular pathways regulate both populations. Understanding the biology of cancer stem cells will contribute to the identification of molecular targets important for future therapies. [Abstract]

Jenik PD, Gillmor CS, Lukowitz W
Embryonic patterning in Arabidopsis thaliana.
Annu Rev Cell Dev Biol. 2007;23207-36.
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. [Abstract]

Tran TS, Kolodkin AL, Bharadwaj R
Semaphorin regulation of cellular morphology.
Annu Rev Cell Dev Biol. 2007;23263-92.
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. [Abstract]

Pokutta S, Weis WI
Structure and mechanism of cadherins and catenins in cell-cell contacts.
Annu Rev Cell Dev Biol. 2007;23237-61.
Cadherins are Ca(2+)-dependent cell adhesion molecules found in several kinds of cell-cell contact, including adherens junctions and desmosomes. In the presence of Ca(2+), 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. [Abstract]

Gillingham AK, Munro S
The small G proteins of the Arf family and their regulators.
Annu Rev Cell Dev Biol. 2007;23579-611.
Small G proteins play a central role in the organization of the secretory and endocytic pathways. The majority of such small G proteins are members of the Rab family, which are anchored to the bilayer by C-terminal prenyl groups. However, the recruitment of some effectors, including vesicle coat proteins, is mediated by a second class of small G proteins that is unique in having an N-terminal amphipathic helix that becomes available for membrane insertion upon GTP binding. Sar1, Arf1, and Arf6 are the best-characterized members of this ADP-ribosylation factor (Arf) family. In addition, all eukaryotes contain additional distantly related G proteins, often called Arf like, or Arls. The complete Arf family in humans has 29 members. The roles of these related G proteins are poorly understood, but recent work has shown that some are involved in membrane traffic or organizing the cytoskeleton. Here we review what is known about all the members of the Arf family, along with the known regulatory molecules that convert them between GDP- and GTP-bound states. [Abstract]

Fagarasanu A, Fagarasanu M, Rachubinski RA
Maintaining peroxisome populations: a story of division and inheritance.
Annu Rev Cell Dev Biol. 2007;23321-44.
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. [Abstract]

Stinchcombe JC, Griffiths GM
Secretory mechanisms in cell-mediated cytotoxicity.
Annu Rev Cell Dev Biol. 2007;23495-517.
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. [Abstract]

Blair SS
Wing vein patterning in Drosophila and the analysis of intercellular signaling.
Annu Rev Cell Dev Biol. 2007;23293-319.
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. [Abstract]

Shepherd JD, Huganir RL
The cell biology of synaptic plasticity: AMPA receptor trafficking.
Annu Rev Cell Dev Biol. 2007;23613-43.
The cellular processes that govern neuronal function are highly complex, with many basic cell biological pathways uniquely adapted to perform the elaborate information processing achieved by the brain. This is particularly evident in the trafficking and regulation of membrane proteins to and from synapses, which can be a long distance away from the cell body and number in the thousands. The regulation of neurotransmitter receptors, such as the AMPA-type glutamate receptors (AMPARs), the major excitatory neurotransmitter receptors in the brain, is a crucial mechanism for the modulation of synaptic transmission. The levels of AMPARs at synapses are very dynamic, and it is these plastic changes in synaptic function that are thought to underlie information storage in the brain. Thus, understanding the cellular machinery that controls AMPAR trafficking will be critical for understanding the cellular basis of behavior as well as many neurological diseases. Here we describe the life cycle of AMPARs, from their biogenesis, through their journey to the synapse, and ultimately through their demise, and discuss how the modulation of this process is essential for brain function. [Abstract]

Kimble J, Crittenden SL
Controls of germline stem cells, entry into meiosis, and the sperm/oocyte decision in Caenorhabditis elegans.
Annu Rev Cell Dev Biol. 2007;23405-33.
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. [Abstract]

Piper RC, Katzmann DJ
Biogenesis and function of multivesicular bodies.
Annu Rev Cell Dev Biol. 2007;23519-47.
The two major cellular sites for membrane protein degradation are the proteasome and the lysosome. Ubiquitin attachment is a sorting signal for both degradation routes. For lysosomal degradation, ubiquitination triggers the sorting of cargo proteins into the lumen of late endosomal multivesicular bodies (MVBs)/endosomes. MVB formation occurs when a portion of the limiting membrane of an endosome invaginates and buds into its own lumen. Intralumenal vesicles are degraded when MVBs fuse to lysosomes. The proper delivery of proteins to the MVB interior relies on specific ubiquitination of cargo, recognition and sorting of ubiquitinated cargo to endosomal subdomains, and the formation and scission of cargo-filled intralumenal vesicles. Over the past five years, a number of proteins that may directly participate in these aspects of MVB function and biogenesis have been identified. However, major questions remain as to exactly what these proteins do at the molecular level and how they may accomplish these tasks. [Abstract]

Pardue ML
Following the chromosome path to the garden of the genome.
Annu Rev Cell Dev Biol. 2007;231-22.
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. [Abstract]

Bushati N, Cohen SM
microRNA functions.
Annu Rev Cell Dev Biol. 2007;23175-205.
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. [Abstract]

Lipka V, Kwon C, Panstruga R
SNARE-ware: the role of SNARE-domain proteins in plant biology.
Annu Rev Cell Dev Biol. 2007;23147-74.
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. [Abstract]

Ciofani M, Z��iga-Pfl�cker JC
The thymus as an inductive site for T lymphopoiesis.
Annu Rev Cell Dev Biol. 2007;23463-93.
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 alphabeta and gammadelta T cell lineages. [Abstract]

Poo MM, Zheng J
Calcium Signaling and Neuronal Motility.
Annu Rev Cell Dev Biol. 2006 Sep 8;
Neuronal motility is a fundamental feature of the nervous system that underlies its development, regeneration and plasticity. 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, Ca(2+) plays a central role in the regulation of neuronal motility. Recent studies have revealed common Ca(2+)-dependent signaling pathways that are deployed for regulating cytoskeletal dynamics associated with neuronal migration, axon and dendrite development and regeneration, and synaptic plasticity. Expected final online publication date for the Annual Review of Cell and Developmental Biology Volume 23 is October 6, 2007. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates. [Abstract]

Eggenschwiler JT, Anderson KV
Cilia and developmental signaling.
Annu Rev Cell Dev Biol. 2007;23345-73.
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 alpha 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. [Abstract]

Jiang D, Liang J, Noble PW
Hyaluronan in tissue injury and repair.
Annu Rev Cell Dev Biol. 2007;23435-61.
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. [Abstract]

Buckingham M, Relaix F
The role of Pax genes in the development of tissues and organs: Pax3 and Pax7 regulate muscle progenitor cell functions.
Annu Rev Cell Dev Biol. 2007;23645-73.
Pax genes play key roles in the formation of tissues and organs during embryogenesis. Pax3 and Pax7 mark myogenic progenitor cells and regulate their behavior and their entry into the program of skeletal muscle differentiation. Recent results have underlined the importance of the Pax3/7 population of cells for skeletal muscle development and regeneration. We present our current understanding of different aspects of Pax3/7 function in myogenesis, focusing on the mouse model. This is compared with that of other Pax proteins in the emergence of tissue specific lineages and their differentiation as well as in cell survival, proliferation, and migration. Finally, we consider the molecular mechanisms that underlie the function of Pax transcription factors, including the cofactors and regulatory networks with which they interact. [Abstract]

Sillitoe RV, Joyner AL
Morphology, molecular codes, and circuitry produce the three-dimensional complexity of the cerebellum.
Annu Rev Cell Dev Biol. 2007;23549-77.
The most noticeable morphological feature of the cerebellum is its folded appearance, whereby fissures separate its anterior-posterior extent into lobules. Each lobule is molecularly coded along the medial-lateral axis by parasagittal stripes of gene expression in one cell type, the Purkinje cells (PCs). Additionally, within each lobule distinct combinations of afferents terminate and supply the cerebellum with synchronized sensory and motor information. Strikingly, afferent terminal fields are organized into parasagittal domains, and this pattern bears a close relationship to PC molecular coding. Thus, cerebellum three-dimensional complexity obeys a basic coordinate system that can be broken down into morphology and molecular coding. In this review, we summarize the sequential stages of cerebellum development that produce its laminar structure, foliation, and molecular organization. We also introduce genes that regulate morphology and molecular coding, and discuss the establishment of topographical circuits within the context of the two coordinate systems. Finally, we discuss how abnormal cerebellar organization may result in neurological disorders like autism. [Abstract]

Horwich AL, Fenton WA, Chapman E, Farr GW
Two families of chaperonin: physiology and mechanism.
Annu Rev Cell Dev Biol. 2007;23115-45.
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? [Abstract]

Koster MI, Roop DR
Mechanisms regulating epithelial stratification.
Annu Rev Cell Dev Biol. 2007;2393-113.
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. [Abstract]

Sch�fer M, Werner S
Transcriptional control of wound repair.
Annu Rev Cell Dev Biol. 2007;2369-92.
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. [Abstract]

Abu-Issa R, Kirby ML
Heart field: from mesoderm to heart tube.
Annu Rev Cell Dev Biol. 2007;2345-68.
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. [Abstract]

Tsai B
Penetration of nonenveloped viruses into the cytoplasm.
Annu Rev Cell Dev Biol. 2007;2323-43.
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. [Abstract]

Mombaerts P
Axonal wiring in the mouse olfactory system.
Annu Rev Cell Dev Biol. 2006;22713-37.
The main olfactory epithelium of the mouse is a mosaic of 2000 populations of olfactory sensory neurons (OSNs). Each population expresses one allele of one of the 1000 intact odorant receptor (OR) genes. An OSN projects a single unbranched axon to a single glomerulus, from an array of 1600-1800 glomeruli in the main olfactory bulb. Within a glomerulus the OSN axon synapses with the dendrites of second-order neurons and interneurons. Axons of OSNs that express the same OR project to the same glomeruli-typically one glomerulus per half-bulb and thus four glomeruli per mouse. These glomeruli are located at characteristic positions within the glomerular layer of the bulb. ORs determine both the odorant response profile of the OSN and the projection of its axon to a specific glomerulus. I focus on genetic approaches to the axonal wiring problem, particularly on how ORs may function in axonal wiring. [Abstract]

Dickson BJ, Gilestro GF
Regulation of commissural axon pathfinding by slit and its Robo receptors.
Annu Rev Cell Dev Biol. 2006;22651-75.
Commissural axons grow along complex pathways toward, across, and beyond the midline of the central nervous system. Taking commissural axons in the vertebrate spinal cord and the Drosophila ventral nerve cord as examples, we examine how commissural axon pathfinding is regulated by the Slit family of guidance cues and their Robo family receptors. We extract several principles that seem likely to apply to other axons and other contexts, such as the reiterative use of the same guidance molecules in distinct pathfinding decisions, the transcriptional specification of a pathway, the posttranscriptional regulation of growth along the pathway, and the possible role of feedback mechanisms to ensure the fidelity of pathfinding choices. Such mechanisms may help explain how a relatively small number of guidance molecules can generate complex and stereotyped wiring patterns. We also highlight the many gaps in our understanding of commissural axon pathfinding and question some widely accepted views. We hope that this review encourages further efforts to tackle these questions, in the expectation that this system will continue to reveal the general principles of axon pathfinding. [Abstract]

Hay BA, Guo M
Caspase-dependent cell death in Drosophila.
Annu Rev Cell Dev Biol. 2006;22623-50.
Cell death plays many roles during development, in the adult, and in the genesis of many pathological states. Much of this death is apoptotic in nature and requires the activity of members of the caspase family of proteases. It is now possible uniquely in Drosophila to carry out genetic screens for genes that determine the fate-life or death-of any population of cells during development and adulthood. This, in conjunction with the ability to obtain biochemical quantities of material, has made Drosophila a useful organism for exploring the mechanisms by which apoptosis is carried out and regulated. This review summarizes our knowledge of caspase-dependent cell death in Drosophila and compares that knowledge with what is known in worms and mammals. We also discuss the significance of recent work showing that a number of key cell death activators also play nonapoptotic roles. We highlight opportunities and outstanding questions along the way. [Abstract]

Stewart SA, Weinberg RA
Telomeres: cancer to human aging.
Annu Rev Cell Dev Biol. 2006;22531-57.
The cell phenotypes of senescence and crisis operate to circumscribe the proliferative potential of mammalian cells, suggesting that both are capable of operating in vivo to suppress the formation of tumors. The key regulators of these phenotypes are the telomeres, which are located at the ends of chromosomes and operate to protect the chromosomes from end-to-end fusions. Telomere erosion below a certain length can trigger crisis. The relationship between senescence and telomere function is more complex, however: Cell-physiological stresses as well as dysfunction of the complex molecular structures at the ends of telomeric DNA can trigger senescence. Cells can escape senescence by inactivating the Rb and p53 tumor suppressor proteins and can surmount crisis by activating a telomere maintenance mechanism. The resulting cell immortalization is an essential component of the tumorigenic phenotype of human cancer cells. Here we discuss how telomeres are monitored and maintained and how loss of a functional telomere influences biological functions as diverse as aging and carcinogenesis. [Abstract]

Recent Articles in Genes & Development

Peden E, Kimberly E, Gengyo-Ando K, Mitani S, Xue D
Control of sex-specific apoptosis in C. elegans by the BarH homeodomain protein CEH-30 and the transcriptional repressor UNC-37/Groucho.
Genes Dev. 2007 Dec 1;21(23):3195-207.
Apoptosis is essential for proper development and tissue homeostasis in metazoans. It plays a critical role in generating sexual dimorphism by eliminating structures that are not needed in a specific sex. The molecular mechanisms that regulate sexually dimorphic apoptosis are poorly understood. Here we report the identification of the ceh-30 gene as a key regulator of sex-specific apoptosis in Caenorhabditis elegans. Loss-of-function mutations in ceh-30 cause the ectopic death of male-specific CEM neurons. ceh-30 encodes a BarH homeodomain protein that acts downstream from the terminal sex determination gene tra-1, but upstream of, or in parallel to, the cell-death-initiating gene egl-1 to protect CEM neurons from undergoing apoptosis in males. The second intron of the ceh-30 gene contains two adjacent cis-elements that are binding sites for TRA-1A and a POU-type homeodomain protein UNC-86 and acts as a sensor to regulate proper specification of the CEM cell fate. Surprisingly, the N terminus of CEH-30 but not its homeodomain is critical for CEH-30's cell death inhibitory activity in CEMs and contains a conserved eh1/FIL domain that is important for the recruitment of the general transcriptional repressor UNC-37/Groucho. Our study suggests that ceh-30 defines a critical checkpoint that integrates the sex determination signal TRA-1 and the cell fate determination and survival signal UNC-86 to control the sex-specific activation of the cell death program in CEMs through the general transcription repressor UNC-37. [Abstract]

Schwartz HT, Horvitz HR
The C. elegans protein CEH-30 protects male-specific neurons from apoptosis independently of the Bcl-2 homolog CED-9.
Genes Dev. 2007 Dec 1;21(23):3181-94.
The developmental control of apoptosis is fundamental and important. We report that the Caenorhabditis elegans Bar homeodomain transcription factor CEH-30 is required for the sexually dimorphic survival of the male-specific CEM (cephalic male) sensory neurons; the homologous cells of hermaphrodites undergo programmed cell death. We propose that the cell-type-specific anti-apoptotic gene ceh-30 is transcriptionally repressed by the TRA-1 transcription factor, the terminal regulator of sexual identity in C. elegans, to cause hermaphrodite-specific CEM death. The established mechanism for the regulation of specific programmed cell deaths in C. elegans is the transcriptional control of the BH3-only gene egl-1, which inhibits the Bcl-2 homolog ced-9; similarly, most regulation of vertebrate apoptosis involves the Bcl-2 superfamily. In contrast, ceh-30 acts within the CEM neurons to promote their survival independently of both egl-1 and ced-9. Mammalian ceh-30 homologs can substitute for ceh-30 in C. elegans. Mice lacking the ceh-30 homolog Barhl1 show a progressive loss of sensory neurons and increased sensory-neuron cell death. Based on these observations, we suggest that the function of Bar homeodomain proteins as cell-type-specific inhibitors of apoptosis is evolutionarily conserved. [Abstract]

Junion G, Bataill� L, Jagla T, Da Ponte JP, Tapin R, Jagla K
Genome-wide view of cell fate specification: ladybird acts at multiple levels during diversification of muscle and heart precursors.
Genes Dev. 2007 Dec 1;21(23):3163-80.
Correct diversification of cell types during development ensures the formation of functional organs. The evolutionarily conserved homeobox genes from ladybird/Lbx family were found to act as cell identity genes in a number of embryonic tissues. A prior genetic analysis showed that during Drosophila muscle and heart development ladybird is required for the specification of a subset of muscular and cardiac precursors. To learn how ladybird genes exert their cell identity functions we performed muscle and heart-targeted genome-wide transcriptional profiling and a chromatin immunoprecipitation (ChIP)-on-chip search for direct Ladybird targets. Our data reveal that ladybird not only contributes to the combinatorial code of transcription factors specifying the identity of muscle and cardiac precursors, but also regulates a large number of genes involved in setting cell shape, adhesion, and motility. Among direct ladybird targets, we identified bric-a-brac 2 gene as a new component of identity code and inflated encoding alphaPS2-integrin playing a pivotal role in cell-cell interactions. Unexpectedly, ladybird also contributes to the regulation of terminal differentiation genes encoding structural muscle proteins or contributing to muscle contractility. Thus, the identity gene-governed diversification of cell types is a multistep process involving the transcriptional control of genes determining both morphological and functional properties of cells. [Abstract]

P�yry TA, Kaminski A, Connell EJ, Fraser CS, Jackson RJ
The mechanism of an exceptional case of reinitiation after translation of a long ORF reveals why such events do not generally occur in mammalian mRNA translation.
Genes Dev. 2007 Dec 1;21(23):3149-62.
The subgenomic mRNA of feline caliciviruses is bicistronic with the two cistrons overlapping by four nucleotides, ..AUGA. The upstream cistron encodes a 75-kDa major capsid protein precursor (pre-VP1), and the downstream cistron a 10-kDa minor capsid protein. The kinetics of translation in reticulocyte lysates show that the downstream cistron is translated by a termination-reinitiation process, which is unusual in not requiring eIF4G or the eIF4F complex. Reinitiation requires the 3'-terminal 87 nucleotides (nt) of the pre-VP1 ORF, but no other viral sequences. The reinitiation site is selected by virtue of its proximity to this 87-nt element, and not its proximity to the pre-VP1 ORF stop codon, although this must be located not more than approximately 30 nt downstream from the restart codon. This 87-nt element was shown to bind 40S ribosomal subunits and initiation factor eIF3, and addition of supplementary eIF3 enhanced reinitiation efficiency. Mutants defective in reinitiation showed reduced affinity for eIF3 or defective 40S subunit binding (or both). These results suggest a mechanism in which some of the eIF3/40S complexes formed during disassembly of post-termination ribosomes bind to this 87-nt element in a position appropriate for reinitiation following acquisition of an eIF2/GTP/Met-tRNA i ternary complex. [Abstract]

Funakoshi Y, Doi Y, Hosoda N, Uchida N, Osawa M, Shimada I, Tsujimoto M, Suzuki T, Katada T, Hoshino S
Mechanism of mRNA deadenylation: evidence for a molecular interplay between translation termination factor eRF3 and mRNA deadenylases.
Genes Dev. 2007 Dec 1;21(23):3135-48.
In eukaryotes, shortening of the 3'-poly(A) tail is the rate-limiting step in the degradation of most mRNAs, and two major mRNA deadenylase complexes--Caf1-Ccr4 and Pan2-Pan3--play central roles in this process, referred to as deadenylation. However, the molecular mechanism triggering deadenylation remains elusive. Previously, we demonstrated that eukaryotic releasing factor eRF3 mediates deadenylation and decay of mRNA in a manner coupled to translation termination. Here, we report the mechanism of mRNA deadenylation. The eRF3-mediated deadenylation is catalyzed by both Caf1-Ccr4 and Pan2-Pan3. Interestingly, translation termination complexes eRF1-eRF3, Pan2-Pan3, and Caf1-Ccr4 competitively interact with polyadenylate-binding protein PABPC1. In each complex, eRF3, Pan3, and Tob, respectively, mediate PABPC1 binding, and a combination of a PAM2 motif and a PABC domain is commonly utilized for their contacts. A translation-dependent exchange of eRF1-eRF3 for the deadenylase occurs on PABPC1. Consequently, PABPC1 binding leads to the activation of Pan2-Pan3 and Caf1-Ccr4. From these results, we suggest a mechanism of mRNA deadenylation by Pan2-Pan3 and Caf1-Ccr4 in cooperation with eRF3 and PABPC1. [Abstract]

Linhart HG, Lin H, Yamada Y, Moran E, Steine EJ, Gokhale S, Lo G, Cantu E, Ehrich M, He T, Meissner A, Jaenisch R
Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing.
Genes Dev. 2007 Dec 1;21(23):3110-22.
Increased methylation of CpG islands and silencing of affected target genes is frequently found in human cancer; however, in vivo the question of causality has only been addressed by loss-of-function studies. To directly evaluate the role and mechanism of de novo methylation in tumor development, we overexpressed the de novo DNA methyltransferases Dnmt3a1 and Dnmt3b1 in Apc Min/+ mice. We found that Dnmt3b1 enhanced the number of colon tumors in Apc Min/+ mice approximately twofold and increased the average size of colonic microadenomas, whereas Dnmt3a1 had no effect. The overexpression of Dnmt3b1 caused loss of imprinting and increased expression of Igf2 as well as methylation and transcriptional silencing of the tumor suppressor genes Sfrp2, Sfrp4, and Sfrp5. Importantly, we found that Dnmt3b1 but not Dnmt3a1 efficiently methylates the same set of genes in tumors and in nontumor tissues, demonstrating that de novo methyltransferases can initiate methylation and silencing of specific genes in phenotypically normal cells. This suggests that DNA methylation patterns in cancer are the result of specific targeting of at least some tumor suppressor genes rather than of random, stochastic methylation followed by clonal selection due to a proliferative advantage caused by tumor suppressor gene silencing. [Abstract]

Leu JI, George DL
Hepatic IGFBP1 is a prosurvival factor that binds to BAK, protects the liver from apoptosis, and antagonizes the proapoptotic actions of p53 at mitochondria.
Genes Dev. 2007 Dec 1;21(23):3095-109.
Liver is generally refractory to apoptosis induced by the p53 tumor suppressor protein, but the molecular basis remains poorly understood. Here we show that p53 transcriptional activation leads to enhanced expression of hepatic IGFBP1 (insulin-like growth factor-binding protein-1). Exhibiting a previously unanticipated role, a portion of intracellular IGFBP1 protein localizes to mitochondria where it binds to the proapoptotic protein BAK and hinders BAK activation and apoptosis induction. Interestingly, in many cells and tissues p53 also has a direct apoptotic function at mitochondria that includes BAK binding and activation. When IGFBP1 is in a complex with BAK, formation of a proapoptotic p53/BAK complex and apoptosis induction are impaired, both in cultured cells and in liver. In contrast, livers of IGFBP1-deficient mice exhibit spontaneous apoptosis that is accompanied by p53 mitochondrial accumulation and evidence of BAK oligomerization. These data support the importance of BAK as a mediator of p53's mitochondrial function. The results also identify IGFBP1 as a negative regulator of the BAK-dependent pathway of apoptosis, whose expression integrates the transcriptional and mitochondrial functions of the p53 tumor suppressor protein. [Abstract]

Hogg JR, Collins K
Human Y5 RNA specializes a Ro ribonucleoprotein for 5S ribosomal RNA quality control.
Genes Dev. 2007 Dec 1;21(23):3067-72.
Humans express four distinct non-protein-coding Y RNAs (ncRNAs). To investigate Y RNA functional diversification, we exploited an RNA-based affinity purification method to isolate ribonucleoproteins (RNPs) assembled on individual human Y RNAs. Silver staining and mass spectrometry revealed that the Ro and La proteins assemble with all Y RNAs, while additional proteins associate with specific Y RNAs. Unexpectedly, Y5 RNA uniquely copurified ribosomal protein L5 and its binding partner 5S RNA. These findings reveal a contribution of Y5 to 5S surveillance and suggest that interactions between Ro-Y5 and L5-5S RNPs establish 5S RNA as a target of quality control. [Abstract]

Juh�sz G, Erdi B, Sass M, Neufeld TP
Atg7-dependent autophagy promotes neuronal health, stress tolerance, and longevity but is dispensable for metamorphosis in Drosophila.
Genes Dev. 2007 Dec 1;21(23):3061-6.
Autophagy, a cellular process of cytoplasmic degradation and recycling, is induced in Drosophila larval tissues during metamorphosis, potentially contributing to their destruction or reorganization. Unexpectedly, we find that flies lacking the core autophagy regulator Atg7 are viable, despite severe defects in autophagy. Although metamorphic cell death is perturbed in Atg7 mutants, the larval-adult midgut transition proceeds normally, with extended pupal development compensating for reduced autophagy. Atg7-/- adults are short-lived, hypersensitive to nutrient and oxidative stress, and accumulate ubiquitin-positive aggregates in degenerating neurons. Thus, normal levels of autophagy are crucial for stress survival and continuous cellular renewal, but not metamorphosis. [Abstract]

Martinez-Agosto JA, Mikkola HK, Hartenstein V, Banerjee U
The hematopoietic stem cell and its niche: a comparative view.
Genes Dev. 2007 Dec 1;21(23):3044-60.
Stem cells have been identified as a source of virtually all highly differentiated cells that are replenished during the lifetime of an animal. The critical balance between stem and differentiated cell populations is crucial for the long-term maintenance of functional tissue types. Stem cells maintain this balance by choosing one of several alternate fates: self-renewal, commitment to differentiate, and senescence or cell death. These characteristics comprise the core criteria by which these cells are usually defined. The self-renewal property is important, as it allows for extended production of the corresponding differentiated cells throughout the life span of the animal. A microenvironment that is supportive of stem cells is commonly referred to as a stem cell niche. In this review, we first present some general concepts regarding stem cells and their niches, comparing stem cells of many different kinds from diverse organisms, and in the second part, we compare specific aspects of hematopoiesis and the niches that support hematopoiesis in Drosophila, zebrafish and mouse. [Abstract]

Schneider R, Grosschedl R
Dynamics and interplay of nuclear architecture, genome organization, and gene expression.
Genes Dev. 2007 Dec 1;21(23):3027-43.
The organization of the genome in the nucleus of a eukaryotic cell is fairly complex and dynamic. Various features of the nuclear architecture, including compartmentalization of molecular machines and the spatial arrangement of genomic sequences, help to carry out and regulate nuclear processes, such as DNA replication, DNA repair, gene transcription, RNA processing, and mRNA transport. Compartmentalized multiprotein complexes undergo extensive modifications or exchange of protein subunits, allowing for an exquisite dynamics of structural components and functional processes of the nucleus. The architecture of the interphase nucleus is linked to the spatial arrangement of genes and gene clusters, the structure of chromatin, and the accessibility of regulatory DNA elements. In this review, we discuss recent studies that have provided exciting insight into the interplay between nuclear architecture, genome organization, and gene expression. [Abstract]

Branzei D, Foiani M
RecQ helicases queuing with Srs2 to disrupt Rad51 filaments and suppress recombination.
Genes Dev. 2007 Dec 1;21(23):3019-26. [Abstract]

Adler AS, Sinha S, Kawahara TL, Zhang JY, Segal E, Chang HY
Motif module map reveals enforcement of aging by continual NF-{kappa}B activity.
Genes Dev. 2007 Nov 30;
Aging is characterized by specific alterations in gene expression, but their underlying mechanisms and functional consequences are not well understood. Here we develop a systematic approach to identify combinatorial cis-regulatory motifs that drive age-dependent gene expression across different tissues and organisms. Integrated analysis of 365 microarrays spanning nine tissue types predicted fourteen motifs as major regulators of age-dependent gene expression in human and mouse. The motif most strongly associated with aging was that of the transcription factor NF-kappaB. Inducible genetic blockade of NF-kappaB for 2 wk in the epidermis of chronologically aged mice reverted the tissue characteristics and global gene expression programs to those of young mice. Age-specific NF-kappaB blockade and orthogonal cell cycle interventions revealed that NF-kappaB controls cell cycle exit and gene expression signature of aging in parallel but not sequential pathways. These results identify a conserved network of regulatory pathways underlying mammalian aging and show that NF-kappaB is continually required to enforce many features of aging in a tissue-specific manner. [Abstract]

Wendel HG, Silva RL, Malina A, Mills JR, Zhu H, Ueda T, Watanabe-Fukunaga R, Fukunaga R, Teruya-Feldstein J, Pelletier J, Lowe SW
Dissecting eIF4E action in tumorigenesis.
Genes Dev. 2007 Nov 30;
Genetically engineered mouse models are powerful tools for studying cancer genes and validating targets for cancer therapy. We previously used a mouse lymphoma model to demonstrate that the translation initiation factor eIF4E is a potent oncogene in vivo. Using the same model, we now show that the oncogenic activity of eIF4E correlates with its ability to activate translation and become phosphorylated on Ser 209. Furthermore, constitutively activated MNK1, an eIF4E Ser 209 kinase, promotes tumorigenesis in a manner similar to eIF4E, and a dominant-negative MNK mutant inhibits the in vivo proliferation of tumor cells driven by mutations that deregulate translation. Phosphorylated eIF4E promotes tumorigenesis primarily by suppressing apoptosis and, accordingly, the anti-apoptotic protein Mcl-1 is one target of both phospho-eIF4E and MNK1 that contributes to tumor formation. Our results provide insight into how eIF4E contributes to tumorigenesis and pinpoint a level of translational control that may be suitable for therapeutic intervention. [Abstract]

Garcia SM, Casanueva MO, Silva MC, Amaral MD, Morimoto RI
Neuronal signaling modulates protein homeostasis in Caenorhabditis elegans post-synaptic muscle cells.
Genes Dev. 2007 Nov 15;21(22):3006-16.
Protein homeostasis maintains proper intracellular balance by promoting protein folding and clearance mechanisms while minimizing the stress caused by the accumulation of misfolded and damaged proteins. Chronic expression of aggregation-prone proteins is deleterious to the cell and has been linked to a wide range of conformational disorders. The molecular response to misfolded proteins is highly conserved and generally studied as a cell-autonomous process. Here, we provide evidence that neuronal signaling is an important modulator of protein homeostasis in post-synaptic muscle cells. In a forward genetic screen in Caenorhabditis elegans for enhancers of polyglutamine aggregation in muscle cells, we identified unc-30, a neuron-specific transcription factor that regulates the synthesis of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA). We used additional sensors of protein conformational states to show that defective GABA signaling or increased acetylcholine (ACh) signaling causes a general imbalance in protein homeostasis in post-synaptic muscle cells. Moreover, exposure to GABA antagonists or ACh agonists has a similar effect, which reveals that toxins that act at the neuromuscular junction are potent modifiers of protein conformational disorders. These results demonstrate the importance of intercellular communication in intracellular homeostasis. [Abstract]

Sikder D, Kodadek T
The neurohormone orexin stimulates hypoxia-inducible factor-1 activity.
Genes Dev. 2007 Nov 15;21(22):2995-3005.
Orexin A and Orexin B (also known as hypocretins) are neuropeptides that bind two related G-coupled protein receptors (OXR1 and OXR2) and thus induce wakefulness, food consumption, and locomotion. Conversely, deletion of the orexin gene in mice produces a condition similar to canine and human narcolepsy. Despite the central importance of the orexin system in regulating wakefulness and feeding behavior, little is known about the downstream signaling mechanisms that achieve these effects. In this study, genomics techniques are used to probe this question and reveal that orexin activates the hypoxia-inducible factor 1 (HIF-1), a heterodimeric transcription factor whose pathogenic role in stimulating angiogenesis in hypoxic tumors has been the focus of intense investigation. Orexin-stimulated HIF-1 activity is due to both increased HIF-1alpha gene transcription and a down-regulation of von Hippel-Lindau (VHL), the E3 ubiquitin ligase that mediates the turnover of HIF-1 via the ubiquitin-proteasome pathway. Orexin-mediated activation of HIF-1 results in increased glucose uptake and higher glycolytic activity, as expected from studies of hypoxic cells. However, orexin receptor-expressing cells somehow override the HIF-1-mediated preference for funneling pyruvate into anaerobic glycolysis and instead favor ATP production through the tricarboxylic acid cycle and oxidative phosphorylation. These findings implicate HIF-1 as an important transcription factor in the hormone-mediated regulation of hunger and wakefulness. [Abstract]

Samuelson AV, Carr CE, Ruvkun G
Gene activities that mediate increased life span of C. elegans insulin-like signaling mutants.
Genes Dev. 2007 Nov 15;21(22):2976-94.
Genetic and RNA interference (RNAi) screens for life span regulatory genes have revealed that the daf-2 insulin-like signaling pathway plays a major role in Caenorhabditis elegans longevity. This pathway converges on the DAF-16 transcription factor and may regulate life span by controlling the expression of a large number of genes, including free-radical detoxifying genes, stress resistance genes, and pathogen resistance genes. We conducted a genome-wide RNAi screen to identify genes necessary for the extended life span of daf-2 mutants and identified approximately 200 gene inactivations that shorten daf-2 life span. Some of these gene inactivations dramatically shorten daf-2 mutant life span but less dramatically shorten daf-2; daf-16 mutant or wild-type life span. Molecular and behavioral markers for normal aging and for extended life span in low insulin/IGF1 (insulin-like growth factor 1) signaling were assayed to distinguish accelerated aging from general sickness and to examine age-related phenotypes. Detailed demographic analysis, molecular markers of aging, and insulin signaling mutant test strains were used to filter progeric gene inactivations for specific acceleration of aging. Highly represented in the genes that mediate life span extension in the daf-2 mutant are components of endocytotic trafficking of membrane proteins to lysosomes. These gene inactivations disrupt the increased expression of the DAF-16 downstream gene superoxide dismutase sod-3 in a daf-2 mutant, suggesting trafficking between the insulin-like receptor and DAF-16. The activities of these genes may normally decline during aging. [Abstract]

Xu YX, Manley JL
Pin1 modulates RNA polymerase II activity during the transcription cycle.
Genes Dev. 2007 Nov 15;21(22):2950-62.
The C-terminal domain of the RNA polymerase (RNAP) II largest subunit (CTD) plays a critical role in coordinating multiple events in pre-mRNA transcription and processing. Previously we reported that the peptidyl prolyl isomerase Pin1 modulates RNAP II function during the cell cycle. Here we provide evidence that Pin1 affects multiple aspects of RNAP II function via its regulation of CTD phosphorylation. Using chromatin immunoprecipitation (ChIP) assays with CTD phospho-specific antibodies, we confirm that RNAP II displays a dynamic association with specific genes during the cell cycle, preferentially associating with transcribed genes in S phase, while disassociating in M phase in a matter that correlates with changes in CTD phosphorylation. Using inducible Pin1 cell lines, we show that Pin1 overexpression is sufficient to release RNAP II from chromatin, which then accumulates in a hyperphosphorylated form in nuclear speckle-associated structures. In vitro transcription assays show that Pin1 inhibits transcription in nuclear extract, while an inactive Pin1 mutant in fact stimulates it. Several assays indicate that the inhibition largely reflects Pin1 activity during transcription initiation and not elongation, suggesting that Pin1 modulates CTD phosphorylation, and RNAP II activity, during an early stage of the transcription cycle. [Abstract]

Delmas V, Beermann F, Martinozzi S, Carreira S, Ackermann J, Kumasaka M, Denat L, Goodall J, Luciani F, Viros A, Demirkan N, Bastian BC, Goding CR, Larue L
Beta-catenin induces immortalization of melanocytes by suppressing p16INK4a expression and cooperates with N-Ras in melanoma development.
Genes Dev. 2007 Nov 15;21(22):2923-35.
Tumor progression is a multistep process in which proproliferation mutations must be accompanied by suppression of senescence. In melanoma, proproliferative signals are provided by activating mutations in NRAS and BRAF, whereas senescence is bypassed by inactivation of the p16(Ink4a) gene. Melanomas also frequently exhibit constitutive activation of the Wnt/beta-catenin pathway that is presumed to induce proliferation, as it does in carcinomas. We show here that, contrary to expectations, stabilized beta-catenin reduces the number of melanoblasts in vivo and immortalizes primary skin melanocytes by silencing the p16(Ink4a) promoter. Significantly, in a novel mouse model for melanoma, stabilized beta-catenin bypasses the requirement for p16(Ink4a) mutations and, together with an activated N-Ras oncogene, leads to melanoma with high penetrance and short latency. The results reveal that synergy between the Wnt and mitogen-activated protein (MAP) kinase pathways may represent an important mechanism underpinning the genesis of melanoma, a highly aggressive and increasingly common disease. [Abstract]

Aggarwal P, Lessie MD, Lin DI, Pontano L, Gladden AB, Nuskey B, Goradia A, Wasik MA, Klein-Szanto AJ, Rustgi AK, Bassing CH, Diehl JA
Nuclear accumulation of cyclin D1 during S phase inhibits Cul4-dependent Cdt1 proteolysis and triggers p53-dependent DNA rereplication.
Genes Dev. 2007 Nov 15;21(22):2908-22.
Deregulation of cyclin D1 occurs in numerous human cancers through mutations, alternative splicing, and gene amplification. Although cancer-derived cyclin D1 mutants are potent oncogenes in vitro and in vivo, the mechanisms whereby they contribute to neoplasia are poorly understood. We now provide evidence derived from both mouse models and human cancer-derived cells revealing that nuclear accumulation of catalytically active mutant cyclin D1/CDK4 complexes triggers DNA rereplication, resulting from Cdt1 stabilization, which in turn triggers the DNA damage checkpoint and p53-dependent apoptosis. Loss of p53 through mutations or targeted deletion results in increased genomic instability and neoplastic growth. Collectively, the data presented reveal mechanistic insights into how uncoupling of critical cell cycle regulatory events will perturb DNA replication fidelity, thereby contributing to neoplastic transformation. [Abstract]

Chen S, de Vries MA, Bell SP
Orc6 is required for dynamic recruitment of Cdt1 during repeated Mcm2 7 loading.
Genes Dev. 2007 Nov 15;21(22):2897-907.
The origin recognition complex (ORC) nucleates DNA replication initiation in eukaryotic cells. This six-protein complex binds replication origin DNA, recruits other initiation factors, and facilitates loading of the DNA helicase. Studying the function of individual ORC subunits during pre-RC formation has been hampered by the requirement of most subunits for DNA binding. In this study, we investigate the function of the Saccharomyces cerevisiae Orc6, the only ORC subunit not required for DNA binding. In vivo, depletion of Orc6 inhibits prereplicative complex (pre-RC) assembly and maintenance. In vitro, ORC lacking Orc6 fails to interact with Cdt1 and to load the Mcm2-7 helicase onto origin DNA. We demonstrate that two regions of Orc6 bind Cdt1 directly, and that the extreme C terminus of Orc6 (Orc6-CTD) interacts tightly with the remaining five ORC subunits. Replacing Orc6 with a fusion protein linking Cdt1 to the Orc6-CTD results in an ORC complex that loads Mcm2-7 onto DNA. Interestingly, this complex can only perform a single round of Mcm2-7 loading, suggesting that a dynamic association of Cdt1 with ORC is required for multiple rounds of Mcm2-7 loading. [Abstract]

Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A
Riboswitch-dependent gene regulation and its evolution in the plant kingdom.
Genes Dev. 2007 Nov 15;21(22):2874-9.
Riboswitches are natural RNA sensors that affect gene control via their capacity to bind small molecules. Their prevalence in higher eukaryotes is unclear. We discovered a post-transcriptional mechanism in plants that uses a riboswitch to control a metabolic feedback loop through differential processing of the precursor RNA 3' terminus. When cellular thiamin pyrophosphate (TPP) levels rise, metabolite sensing by the riboswitch located in TPP biosynthesis genes directs formation of an unstable splicing product, and consequently TPP levels drop. When transformed in plants, engineered TPP riboswitches can act autonomously to modulate gene expression. In an evolutionary perspective, a TPP riboswitch is also present in ancient plant taxa, suggesting that this mechanism is active since vascular plants emerged 400 million years ago. [Abstra