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- Volume 24, 2008
Annual Review of Cell and Developmental Biology - Volume 24, 2008
Volume 24, 2008
- Preface
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Microtubule Dynamics in Cell Division: Exploring Living Cells with Polarized Light Microscopy
Vol. 24 (2008), pp. 1–28More LessThis Perspective is an account of my early experience while I studied the dynamic organization and behavior of the mitotic spindle and its submicroscopic filaments using polarized light microscopy. The birefringence of spindle filaments in normally dividing plant and animal cells, and those treated by various agents, revealed (a) the reality of spindle fibers and fibrils in healthy living cells; (b) the labile, dynamic nature of the molecular filaments making up the spindle fibers; (c) the mode of fibrogenesis and action of orienting centers; and (d) force-generating properties based on the disassembly and assembly of the fibrils. These studies, which were carried out directly on living cells using improved polarizing microscopes, in fact predicted the reversible assembly properties of microtubules.
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Replicative Aging in Yeast: The Means to the End
Vol. 24 (2008), pp. 29–54More LessProgress in aging research is now rapid, and surprisingly, studies in a single-celled eukaryote are a driving force. The genetic modulators of replicative life span in yeast are being identified, the molecular events that accompany aging are being discovered, and the extent to which longevity pathways are conserved between yeast and multicellular eukaryotes is being tested. In this review, we provide a brief retrospective view on the development of yeast as a model for aging and then turn to recent discoveries that have pushed aging research into novel directions and also linked aging in yeast to well-developed hypotheses in mammals. Although the question of what causes aging still cannot be answered definitively, that day may be rapidly approaching.
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Auxin Receptors and Plant Development: A New Signaling Paradigm
Vol. 24 (2008), pp. 55–80More LessThe plant hormone auxin, in particular indole-3-acetic acid (IAA), is a key regulator of virtually every aspect of plant growth and development. Auxin regulates transcription by rapidly modulating levels of Aux/IAA proteins throughout development. Recent studies demonstrate that auxin perception occurs through a novel mechanism. Auxin binds to TIR1, the F-box subunit of the ubiquitin ligase complex SCFTIR1, and stabilizes the interaction between TIR1 and Aux/IAA substrates. This interaction results in Aux/IAA ubiquitination and subsequent degradation. Regulation of the Aux/IAA protein family by TIR1 and TIR1-like auxin receptors (AFBs) links auxin action to transcriptional regulation and provides a model by which the vast array of auxin influences on development may be understood. Moreover, auxin receptor function is the first example of small-molecule regulation of an SCF ubiquitin ligase and may have important implications for studies of regulated protein degradation in other species, including animals.
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Systems Approaches to Identifying Gene Regulatory Networks in Plants
Vol. 24 (2008), pp. 81–103More LessComplex gene regulatory networks are composed of genes, noncoding RNAs, proteins, metabolites, and signaling components. The availability of genome-wide mutagenesis libraries; large-scale transcriptome, proteome, and metabalome data sets; and new high-throughput methods that uncover protein interactions underscores the need for mathematical modeling techniques that better enable scientists to synthesize these large amounts of information and to understand the properties of these biological systems. Systems biology approaches can allow researchers to move beyond a reductionist approach and to both integrate and comprehend the interactions of multiple components within these systems. Descriptive and mathematical models for gene regulatory networks can reveal emergent properties of these plant systems. This review highlights methods that researchers are using to obtain large-scale data sets, and examples of gene regulatory networks modeled with these data. Emergent properties revealed by the use of these network models and perspectives on the future of systems biology are discussed.
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Sister Chromatid Cohesion: A Simple Concept with a Complex Reality
Vol. 24 (2008), pp. 105–129More LessIn eukaryotes, the process of sister chromatid cohesion holds the two sister chromatids (the replicated chromosomes) together from DNA replication to the onset of chromosome segregation. Cohesion is mediated by cohesin, a four-subunit SMC (structural maintenance of chromosome) complex. Cohesin and cohesion are required for proper chromosome segregation, DNA repair, and gene expression. To carry out these functions, cohesion is regulated by elaborate mechanisms involving a growing list of cohesin auxiliary factors. These factors control the timing and position of cohesin binding to chromatin, activate chromatin-bound cohesin to become cohesive, and orchestrate the orderly dissolution of cohesion. The 45-nm ringlike architecture of soluble cohesin is compatible with dramatically different mechanisms for both chromatin binding and cohesion generation. Solving the mechanism of cohesion and its complex regulation presents significant challenges but offers the potential to provide important insights into higher-order chromosome organization and chromosome biology.
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The Epigenetics of rRNA Genes: From Molecular to Chromosome Biology
Vol. 24 (2008), pp. 131–157More LessIn eukaryotes, the genes encoding ribosomal RNAs (rDNA) exist in two distinct epigenetic states that can be distinguished by a specific chromatin structure that is maintained throughout the cell cycle and is inherited from one cell to another. The fact that even in proliferating cells with a high demand of protein synthesis a fraction of rDNA is silenced provides a unique possibility to decipher the mechanism underlying epigenetic regulation of rDNA. This chapter summarizes our knowledge of the molecular mechanisms that establish and propagate the epigenetic state of rRNA genes, unraveling a complex interplay of DNA methyltransferases and histone-modifying enzymes that act in concert with chromatin remodeling complexes and RNA-guided mechanisms to define the transcriptional state of rDNA. We also review the critical role of the RNA polymerase I transcription factor UBF in the formation of active nucleolar organizer regions (NORs) and maintenance of the euchromatic state of rRNA genes.
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The Evolution, Regulation, and Function of Placenta-Specific Genes
Vol. 24 (2008), pp. 159–181More LessA number of placenta-specific genes (e.g., Tpbp, Plac1, Syncytin, and retrotransposon-associated genes such as Peg10, Rtl1, Endothelin B receptor, Insl4, Leptin, Midline1, and Pleiotrophin), enhancer elements (e.g., glycoprotein hormone α-subunit) and gene isoforms (e.g., 3βHSD, Cyp19), as well as placenta-specific members of gene families (e.g., Gcm1, Mash2, Rhox, Esx1, Cathepsin, PAG, TKDP, Psg, Siglec) have been identified. This review summarizes their evolution, regulation, and biochemical functions and discusses their significance for placental development and function. Strikingly, the number of unique, truly placenta-specific genes that have been discovered to date is very small. The vast majority of placenta-specific gene products have resulted from one of three mechanisms: evolution of placenta-specific promoters, evolution of large gene families with several placenta-specific members, or adoption of functions associated with endogenous retroviruses and retroelements. Interestingly, nearly all the examples of placenta-specific genes that have been discovered to date are not present in all placental mammals.
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Communication Between the Synapse and the Nucleus in Neuronal Development, Plasticity, and Disease
Vol. 24 (2008), pp. 183–209More LessSensory experience is critical for the proper development and plasticity of the brain throughout life. Successful adaptation to the environment is necessary for the survival of an organism, and this process requires the translation of specific sensory stimuli into changes in the structure and function of relevant neural circuits. Sensory-evoked activity drives synaptic input onto neurons within these behavioral circuits, initiating membrane depolarization and calcium influx into the cytoplasm. Calcium signaling triggers the molecular mechanisms underlying neuronal adaptation, including the activity-dependent transcriptional programs that drive the synthesis of the effector molecules required for long-term changes in neuronal function. Insight into the signaling pathways between the synapse and the nucleus that translate specific stimuli into altered patterns of connectivity within a circuit provides clues as to how activity-dependent programs of gene expression are coordinated and how disruptions in this process may contribute to disorders of cognitive function.
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Disulfide-Linked Protein Folding Pathways
Vol. 24 (2008), pp. 211–235More LessDetermining the mechanism by which proteins attain their native structure is an important but difficult problem in basic biology. The study of protein folding is difficult because it involves the identification and characterization of folding intermediates that are only very transiently present. Disulfide bond formation is thermodynamically linked to protein folding. The availability of thiol trapping reagents and the relatively slow kinetics of disulfide bond formation have facilitated the isolation, purification, and characterization of disulfide-linked folding intermediates. As a result, the folding pathways of several disulfide-rich proteins are among the best known of any protein. This review discusses disulfide bond formation and its relationship to protein folding in vitro and in vivo.
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Molecular Mechanisms of Presynaptic Differentiation
Yishi Jin, and Craig C. GarnerVol. 24 (2008), pp. 237–262More LessInformation processing in the nervous system relies on properly localized and organized synaptic structures at the correct locations. The formation of synapses is a long and intricate process involving multiple interrelated steps. Decades of research have identified a large number of molecular components of the presynaptic compartment. In addition to neurotransmitter-containing synaptic vesicles, presynaptic terminals are defined by cytoskeletal and membrane specializations that allow highly regulated exo- and endocytosis of synaptic vesicles and that maintain precise registration with postsynaptic targets. Functional studies at multiple levels have revealed complex interactions between the transport of vesicular intermediates, the presynaptic cytoskeleton, growth cone navigation, and synaptic targets. With the advent of finer anatomical, physiological, and molecular tools, great insights have been gained toward the mechanistic dissection of functionally redundant processes controlling the specificity and dynamics of synapses. This review highlights the recent findings pertaining to the cellular and molecular regulation of presynaptic differentiation.
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Regulation of Spermatogonial Stem Cell Self-Renewal in Mammals
Vol. 24 (2008), pp. 263–286More LessMammalian spermatogenesis is a classic adult stem cell–dependent process, supported by self-renewal and differentiation of spermatogonial stem cells (SSCs). Studying SSCs provides a model to better understand adult stem cell biology, and deciphering the mechanisms that control SSC functions may lead to treatment of male infertility and an understanding of the etiology of testicular germ cell tumor formation. Self-renewal of rodent SSCs is greatly influenced by the niche factor glial cell line–derived neurotrophic factor (GDNF). In mouse SSCs, GDNF activation upregulates expression of the transcription factor–encoding genes bcl6b, etv5, and lhx1, which influence SSC self-renewal. Additionally, the non-GDNF-stimulated transcription factors Plzf and Taf4b have been implicated in regulating SSC functions. Together, these molecules are part of a robust gene network controlling SSC fate decisions that may parallel the regulatory networks in other adult stem cell populations.
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Unconventional Mechanisms of Protein Transport to the Cell Surface of Eukaryotic Cells
Vol. 24 (2008), pp. 287–308More LessThe classical secretion of soluble proteins and transport of integral membrane proteins to the cell surface require transit into and through the endoplasmic reticulum and the Golgi apparatus. Signal peptides or transmembrane domains target proteins for translocation into the lumen or insertion into the membrane of the endoplasmic reticulum, respectively. Here we discuss two mechanisms of unconventional protein targeting to plasma membranes, i.e., transport processes that are active in the absence of a functional Golgi system. We first focus on integral membrane proteins that are inserted into the endoplasmic reticulum but that, however, are transported to plasma membranes in a Golgi-independent manner. We then discuss soluble secretory proteins that are secreted from cells without any involvement of the endoplasmic reticulum and the Golgi apparatus.
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The Immunoglobulin-Like Cell Adhesion Molecule Nectin and Its Associated Protein Afadin
Vol. 24 (2008), pp. 309–342More LessNectins are immunoglobulin-like cell adhesion molecules (CAMs) that compose a family of four members. Nectins homophilically and heterophilically interact in trans with each other to form cell-cell adhesions. In addition, they heterophilically interact in trans with other immunoglobulin-like CAMs. Nectins bind afadin, an actin filament (F-actin)-binding protein, at its cytoplasmic tail and associate with the actin cytoskeleton. Afadin additionally serves as an adaptor protein by further binding many scaffolding proteins and F-actin-binding proteins and contributes to the association of nectins with other cell-cell adhesion and intracellular signaling systems. Nectins and afadin play roles in the formation of a variety of cell-cell junctions cooperatively with, or independently of, cadherins. Cooperation between nectins and cadherins is required for the formation of cell-cell junctions; cadherins alone are not sufficient. Additionally, nectins regulate many other cellular activities (such as movement, proliferation, survival, differentiation, polarization, and the entry of viruses) in cooperation with other CAMs and cell surface membrane receptors.
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Regulation of MHC Class I Assembly and Peptide Binding
Vol. 24 (2008), pp. 343–368More LessPeptide binding to MHC class I molecules is a component of a folding and assembly process that occurs in the endoplasmic reticulum (ER) and uses both cellular chaperones and dedicated factors. The involvement of glycoprotein quality-control chaperones and cellular oxidoreductases in peptide binding has led to models that are gradually being refined. Some aspects of the peptide loading process (e.g., the biosynthesis and degradation of MHC class I complexes) conform to models of glycoprotein quality control, but other aspects (e.g., the formation of a stable disulfide-linked dimer between tapasin and ERp57) deviate from models of chaperone and oxidoreductase function. Here we review what is known about the intersection of glycoprotein folding, oxidative reactions, and MHC class I peptide loading, emphasizing events that occur in the ER and within the MHC class I peptide loading complex.
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Structural and Functional Aspects of Lipid Binding by CD1 Molecules
Vol. 24 (2008), pp. 369–395More LessOver the past ten years, investigators have shown that T lymphocytes can recognize not only peptides in the context of MHC class I and class II molecules but also foreign and self-lipids in association with the nonclassical MHC class I molecules the CD1 proteins. We describe the events that have led to the discovery of the role of CD1 molecules, their pattern of intracellular trafficking, and their ability to sample different intracellular compartments for self- and foreign lipids. Structural and functional aspects of lipid presentation by CD1 molecules are presented in the context of the function of CD1-restricted T cells in antimicrobial responses, antitumor immunity, and the regulation of the tolerance and autoimmunity immunoregulatory axis. Particular emphasis is on invariant NKT (iNKT) cells and their ability to modulate innate and adaptive immune responses.
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Prelude to a Division
Vol. 24 (2008), pp. 397–424More LessAccurate segregation of chromosomes during meiosis requires physical links between homologs. These links are usually established through chromosome pairing, synapsis, and recombination, which occur during meiotic prophase. How chromosomes pair with their homologous partners is one of the outstanding mysteries of meiosis. Surprisingly, experimental evidence indicates that different organisms have found more than one way to accomplish this feat. Whereas some species depend on recombination machinery to achieve homologous pairing, others are able to pair and synapse their homologs in the absence of recombination. To ensure specific pairing between homologous chromosomes, both recombination-dependent and recombination-independent mechanisms must strike the proper balance between forces that promote chromosome interactions and activities that temper the promiscuity of those interactions. The initiation of synapsis is likely to be a tightly regulated step in a process that must be mechanically coupled to homolog pairing.
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Evolution of Coloration Patterns
Vol. 24 (2008), pp. 425–446More LessThere is an amazing amount of diversity in coloration patterns in nature. The ease of observing this diversity and the recent application of genetic and molecular techniques to model and nonmodel animals are allowing us to investigate the genetic basis and evolution of coloration in an ever-increasing variety of animals. It is now possible to ask questions about how many genes are responsible for any given pattern, what types of genetic changes have occurred to generate the diversity, and if the same underlying genetic changes occur repeatedly when coloration phenotypes arise through convergent evolution or parallel evolution.
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Polar Targeting and Endocytic Recycling in Auxin-Dependent Plant Development
Vol. 24 (2008), pp. 447–473More LessPlant development is characterized by a profound phenotypic plasticity that often involves redefining of the developmental fate and polarity of cells within differentiated tissues. The plant hormone auxin and its directional intercellular transport play a major role in these processes because they provide positional information and link cell polarity with tissue patterning. This plant-specific mechanism of transport-dependent auxin gradients depends on subcellular dynamics of auxin transport components, in particular on endocytic recycling and polar targeting. Recent insights into these cellular processes in plants have revealed important parallels to yeast and animal systems, including clathrin-dependent endocytosis, retromer function, and transcytosis, but have also emphasized unique features of plant cells such as diversity of polar targeting pathways; integration of environmental signals into subcellular trafficking; and the link between endocytosis, cell polarity, and cell fate specification. We review these advances and focus on the translation of the subcellular dynamics to the regulation of whole-plant development.
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Regulation of APC/C Activators in Mitosis and Meiosis
Vol. 24 (2008), pp. 475–499More LessThe anaphase-promoting complex/cyclosome (APC/C) is a multisubunit E3 ubiquitin ligase that triggers the degradation of multiple substrates during mitosis. Cdc20/Fizzy and Cdh1/Fizzy-related activate the APC/C and confer substrate specificity through complex interactions with both the core APC/C and substrate proteins. The regulation of Cdc20 and Cdh1 is critical for proper APC/C activity and occurs in multiple ways: targeted protein degradation, phosphorylation, and direct binding of inhibitory proteins. During the specialized divisions of meiosis, the activity of the APC/C must be modified to achieve proper chromosome segregation. Recent studies show that one way in which APC/C activity is modified is through the use of meiosis-specific APC/C activators. Furthermore, regulation of the APC/C during meiosis is carried out by both mitotic regulators of the APC/C as well as meiosis-specific regulators. Here, we review the regulation of APC/C activators during mitosis and the role and regulation of the APC/C during female meiosis.
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Previous Volumes
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Volume 40 (2024)
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Volume 39 (2023)
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Volume 38 (2022)
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Volume 37 (2021)
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Volume 36 (2020)
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Volume 35 (2019)
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Volume 34 (2018)
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Volume 33 (2017)
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Volume 32 (2016)
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Volume 31 (2015)
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Volume 30 (2014)
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Volume 29 (2013)
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Volume 28 (2012)
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Volume 27 (2011)
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Volume 26 (2010)
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Volume 25 (2009)
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Volume 24 (2008)
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Volume 23 (2007)
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Volume 22 (2006)
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Volume 21 (2005)
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Volume 20 (2004)
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Volume 19 (2003)
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Volume 18 (2002)
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Volume 17 (2001)
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Volume 16 (2000)
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Volume 15 (1999)
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Volume 14 (1998)
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Volume 13 (1997)
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Volume 12 (1996)
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Volume 11 (1995)
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Volume 10 (1994)
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Volume 9 (1993)
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Volume 8 (1992)
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Volume 7 (1991)
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Volume 6 (1990)
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Volume 5 (1989)
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Volume 4 (1988)
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Volume 3 (1987)
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Volume 2 (1986)
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Volume 1 (1985)
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Volume 0 (1932)