Aug 07, 2009

In This Issue
PAGE 449

Evolutionary Biology Select
Life's ability to adapt to complex and changing environments is the subject of this issue's Evolutionary Biology Select. New findings suggest that microbes can prepare in advance for future changes in their environments and show that partial penetrance of a phenotype may be a stepping stone to dramatic evolutionary transitions. Other recent work links genetics and ecology, providing insight into the timing of flowering, disease susceptibility in nonhuman primates, and the impact of climate change on developmental plasticity in mammals.

Leading Edge

Analysis

Biotech's Perfect Storm
• Sascha Karberg
The global financial crisis has hit biotech companies hard both in the US and Europe as venture capital dries up. Finding new sources of long-term financing for translating research into new therapeutics will be essential for maintaining innovation and new drug development by biotech companies.

Essay

Learning Tolerance while Fighting Ignorance
• Philippe J. Sansonetti,
• Ruslan Medzhitov
Research on microbe-host interactions focuses principally on pathogens, yet our immune system must deal with the huge number of beneficial commensal bacteria in our gut. It is becoming clear that the host immune system must reach a delicate balance between destroying dangerous bacterial pathogens while preserving the beneficial gut microbiota.

Book Review

Developmental Biology Meets Ecology
• Antónia Monteiro
Outside a controlled lab environment, organisms confront a multitude of challenges in the natural world, such as temperature fluctuations, food shortages, pesticides, and predators. A new textbook, Ecological Developmental Biology, by the developmental biologists Scott Gilbert of Swarthmore College and David Epel of Stanford University focuses on how these ecological factors impact and guide normal organismal development. This new view of developmental biology highlights the relationship of organisms to one another and to their physical surroundings.

Previews

MicroRNAs and Parallel Stem Cell Lives
• Peter B. Dirks
A new study by Shimono et al. (2009) demonstrates that certain microRNAs that regulate the self-renewal factor BMI1 are downregulated in purified populations of normal mammary epithelial stem cells and breast tumor-initiating cells. These findings have important implications for the regulation of self-renewal and differentiation by microRNAs and suggest new ways of targeting cancer stem cells.

Alpha Cells Beget Beta Cells
• Zhengyu Liu,
• Joel F. Habener
Understanding the origins of insulin-producing beta cells of the pancreas could lead to new treatments for diabetes. Collombat et al. (2009) now show that in response to injury, a population of pancreatic progenitor cells can give rise to glucagon-expressing alpha cells that then transdifferentiate into beta cells.

Data Harvesting from Fields of Spindles
• Jesse C. Gatlin,
• E.D. Salmon
The mitotic spindle is essential for chromosome segregation and must be large enough to accommodate all of the chromatin in the dividing cell. In this issue, Dinarina et al. (2009) grow “fields” of spindles on coverslips to investigate the relationship between chromatin and spindle size as well as intrinsic mechanisms of spindle assembly.

DNA Makes RNA Makes Innate Immunity
• Luke A.J. O'Neill
Microbial DNA in the cytosol induces production of interferon-β (IFN-β) and an innate immune response. Chiu et al. (2009) now implicate cytosolic DNA-dependent RNA polymerase III as the DNA sensor linking DNA release by pathogenic bacteria and viruses in the host cell cytosol to IFN-β production and innate immunity.

Time's up: Bursting out of Transcription
• Ethan Ford,
• Dimitris Thanos
Many inducible genes are transcribed in bursts. In this issue, Degenhardt et al. (2009) report computational models that predict and validate patterns of stochastic gene expression.

Human Telomerase Caught in the Act
• Peng Wu,
• Titia de Lange
Based on prior work, it was expected that telomerase would preferentially elongate the shortest telomeres in a cell, extending the telomeric G-rich strand through a process that is coupled to the synthesis of the complementary strand. Contrary to this view, Zhao et al. (2009) now show that telomerase in human cancer cells extends most telomeres during every S phase and that complementary strand synthesis does not immediately follow telomerase action.

Review

Chromatin Architecture and the Generation of Antigen Receptor Diversity
• Suchit Jhunjhunwala,
• Menno C. van Zelm,
• Mandy M. Peak,
• Cornelis Murre
The adaptive immune system generates a specific response to a vast spectrum of antigens. This remarkable property is achieved by lymphocytes that each express single and unique antigen receptors. During lymphocyte development, antigen receptor coding elements are assembled from widely dispersed gene segments. The assembly of antigen receptors is controlled at multiple levels, including epigenetic marking, nuclear location, and chromatin topology. Here, we review recently uncovered mechanisms that underpin long-range genomic interactions and the generation of antigen receptor diversity.

Articles

The Ectopic Expression of Pax4 in the Mouse Pancreas Converts Progenitor Cells into α and Subsequently β Cells
• Patrick Collombat,
• Xiaobo Xu,
• Philippe Ravassard,
• Beatriz Sosa-Pineda,
• Sébastien Dussaud,
• Nils Billestrup,
• Ole D. Madsen,
• Palle Serup,
• Harry Heimberg,
• Ahmed Mansouri
We have previously reported that the loss of Arx and/or Pax4 gene activity leads to a shift in the fate of the different endocrine cell subtypes in the mouse pancreas, without affecting the total endocrine cell numbers. Here, we conditionally and ectopically express Pax4 using different cell-specific promoters and demonstrate that Pax4 forces endocrine precursor cells, as well as mature α cells, to adopt a β cell destiny. This results in a glucagon deficiency that provokes a compensatory and continuous glucagon⁺ cell neogenesis requiring the re-expression of the proendocrine gene Ngn3.

Telomere Extension Occurs at Most Chromosome Ends and Is Uncoupled from Fill-In in Human Cancer Cells
• Yong Zhao,
• Agnel J. Sfeir,
• Ying Zou,
• Christen M. Buseman,
• Tracy T. Chow,
• Jerry W. Shay,
• Woodring E. Wright
Telomeres are thought to be maintained by the preferential recruitment of telomerase to the shortest telomeres. The extension of the G-rich telomeric strand by telomerase is also believed to be coordinated with the complementary synthesis of the C strand by the conventional replication machinery. However, we show that under telomere length-maintenance conditions in cancer cells, human telomerase extends most chromosome ends during each S phase and is not preferentially recruited to the shortest telomeres.

Identification of a Physiologically Relevant Endogenous Ligand for PPARα in Liver
• Manu V. Chakravarthy,
• Irfan J. Lodhi,
• Li Yin,
• Raghu R.V. Malapaka,
• H. Eric Xu,
• John Turk,
• Clay F. Semenkovich
The nuclear receptor PPARα is activated by drugs to treat human disorders of lipid metabolism. Its endogenous ligand is unknown. PPARα-dependent gene expression is impaired with inactivation of fatty acid synthase (FAS), suggesting that FAS is involved in generation of a PPARα ligand. Here we demonstrate the FAS-dependent presence of a phospholipid bound to PPARα isolated from mouse liver. Binding was increased under conditions that induce FAS activity and displaced by systemic injection of a PPARα agonist.
RETRACTED: Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription
• Tatjana Degenhardt,
• Katja N. Rybakova,
• Aleksandra Tomaszewska,
• Martijn J. Moné,
• Hans V. Westerhoff,
• Frank J. Bruggeman,
• Carsten Carlberg
This article has been retracted: please see Elsevier Policy on Article Withdrawal ( http://www.elsevier.com/locate/withdrawalpolicy ). This article has been retracted at the request of the authors. In this paper we used computational approaches to show that transcriptional cycling, i.e., periodic assembly of transcription factors and their cofactors and the resulting cyclical accumulation of mRNA, may stem from stochastic timing and sequential activation of transcription in individual cells. We also presented experimental results in support of the model.

Chromatin Shapes the Mitotic Spindle
• Ana Dinarina,
• Céline Pugieux,
• Maria Mora Corral,
• Martin Loose,
• Joachim Spatz,
• Eric Karsenti,
• François Nédélec
In animal and plant cells, mitotic chromatin locally generates microtubules that self-organize into a mitotic spindle, and its dimensions and bipolar symmetry are essential for accurate chromosome segregation. By immobilizing microscopic chromatin-coated beads on slide surfaces using a microprinting technique, we have examined the effect of chromatin on the dimensions and symmetry of spindles in Xenopus laevis cytoplasmic extracts. While circular spots with diameters around 14–18 μm trigger bipolar spindle formation, larger spots generate an incorrect number of poles.

The Selectivity of Receptor Tyrosine Kinase Signaling Is Controlled by a Secondary SH2 Domain Binding Site
• Jae Hyun Bae,
• Erin Denise Lew,
• Satoru Yuzawa,
• Francisco Tomé,
• Irit Lax,
• Joseph Schlessinger
SH2 domain-mediated interactions represent a crucial step in transmembrane signaling by receptor tyrosine kinases. SH2 domains recognize phosphotyrosine (pY) in the context of particular sequence motifs in receptor phosphorylation sites. However, the modest binding affinity of SH2 domains to pY containing peptides may not account for and likely represents an oversimplified mechanism for regulation of selectivity of signaling pathways in living cells. Here we describe the crystal structure of the activated tyrosine kinase domain of FGFR1 in complex with a phospholipase Cγ fragment.

Sites of Regulated Phosphorylation that Control K-Cl Cotransporter Activity
• Jesse Rinehart,
• Yelena D. Maksimova,
• Jessica E. Tanis,
• Kathryn L. Stone,
• Caleb A. Hodson,
• Junhui Zhang,
• Mary Risinger,
• Weijun Pan,
• Dianqing Wu,
• Christopher M. Colangelo,
• Biff Forbush,
• Clinton H. Joiner,
• Erol E. Gulcicek,
• Patrick G. Gallagher,
• Richard P. Lifton
Modulation of intracellular chloride concentration ([Cl⁻]_i) plays a fundamental role in cell volume regulation and neuronal response to GABA. Cl⁻ exit via K-Cl cotransporters (KCCs) is a major determinant of [Cl⁻]_I; however, mechanisms governing KCC activities are poorly understood. We identified two sites in KCC3 that are rapidly dephosphorylated in hypotonic conditions in cultured cells and human red blood cells in parallel with increased transport activity. Alanine substitutions at these sites result in constitutively active cotransport.

Myosin VI Undergoes Cargo-Mediated Dimerization
• Cong Yu,
• Wei Feng,
• Zhiyi Wei,
• Yohei Miyanoiri,
• Wenyu Wen,
• Yanxiang Zhao,
• Mingjie Zhang
Myosin VI is the only known molecular motor that moves toward the minus ends of actin filaments; thus, it plays unique roles in diverse cellular processes. The processive walking of myosin VI on actin filaments requires dimerization of the motor, but the protein can also function as a nonprocessive monomer. The molecular mechanism governing the monomer-dimer conversion is not clear. We report the high-resolution NMR structure of the cargo-free myosin VI cargo-binding domain (CBD) and show that it is a stable monomer in solution.

A Class of Dynamin-like GTPases Involved in the Generation of the Tubular ER Network
• Junjie Hu,
• Yoko Shibata,
• Peng-Peng Zhu,
• Christiane Voss,
• Neggy Rismanchi,
• William A. Prinz,
• Tom A. Rapoport,
• Craig Blackstone
The endoplasmic reticulum (ER) consists of tubules that are shaped by the reticulons and DP1/Yop1p, but how the tubules form an interconnected network is unknown. Here, we show that mammalian atlastins, which are dynamin-like, integral membrane GTPases, interact with the tubule-shaping proteins. The atlastins localize to the tubular ER and are required for proper network formation in vivo and in vitro. Depletion of the atlastins or overexpression of dominant-negative forms inhibits tubule interconnections.

IRE1α Kinase Activation Modes Control Alternate Endoribonuclease Outputs to Determine Divergent Cell Fates
• Dan Han,
• Alana G. Lerner,
• Lieselotte Vande Walle,
• John-Paul Upton,
• Weihong Xu,
• Andrew Hagen,
• Bradley J. Backes,
• Scott A. Oakes,
• Feroz R. Papa
During endoplasmic reticulum (ER) stress, homeostatic signaling through the unfolded protein response (UPR) augments ER protein-folding capacity. If homeostasis is not restored, the UPR triggers apoptosis. We found that the ER transmembrane kinase/endoribonuclease (RNase) IRE1α is a key component of this apoptotic switch. ER stress induces IRE1α kinase autophosphorylation, activating the RNase to splice XBP1 mRNA and produce the homeostatic transcription factor XBP1s. Under ER stress—or forced autophosphorylation—IRE1α's RNase also causes endonucleolytic decay of many ER-localized mRNAs, including those encoding chaperones, as early events culminating in apoptosis.

RNA Polymerase III Detects Cytosolic DNA and Induces Type I Interferons through the RIG-I Pathway
• Yu-Hsin Chiu,
• John B. MacMillan,
• Zhijian J. Chen
Type I interferons (IFNs) are important for antiviral and autoimmune responses. Retinoic acid-induced gene I (RIG-I) and mitochondrial antiviral signaling (MAVS) proteins mediate IFN production in response to cytosolic double-stranded RNA or single-stranded RNA containing 5′-triphosphate (5′-ppp). Cytosolic B form double-stranded DNA, such as poly(dA-dT)•poly(dA-dT) [poly(dA-dT)], can also induce IFN-β, but the underlying mechanism is unknown. Here, we show that the cytosolic poly(dA-dT) DNA is converted into 5′-ppp RNA to induce IFN-β through the RIG-I pathway.

Downregulation of miRNA-200c Links Breast Cancer Stem Cells with Normal Stem Cells
• Yohei Shimono,
• Maider Zabala,
• Robert W. Cho,
• Neethan Lobo,
• Piero Dalerba,
• Dalong Qian,
• Maximilian Diehn,
• Huiping Liu,
• Sarita P. Panula,
• Eric Chiao,
• Frederick M. Dirbas,
• George Somlo,
• Renee A. Reijo Pera,
• Kaiqin Lao,
• Michael F. Clarke
Human breast tumors contain a breast cancer stem cell (BCSC) population with properties reminiscent of normal stem cells. We found 37 microRNAs that were differentially expressed between human BCSCs and nontumorigenic cancer cells. Three clusters, miR-200c-141, miR-200b-200a-429, and miR-183-96-182 were downregulated in human BCSCs, normal human and murine mammary stem/progenitor cells, and embryonal carcinoma cells. Expression of BMI1, a known regulator of stem cell self-renewal, was modulated by miR-200c.

Erratum

Mechanism for Activation of the EGF Receptor Catalytic Domain by the Juxtamembrane Segment
• Natalia Jura,
• Nicholas F. Endres,
• Kate Engel,
• Sebastian Deindl,
• Rahul Das,
• Meindert H. Lamers,
• David E. Wemmer,
• Xuewu Zhang,
• John Kuriyan
(Cell 137, 1293–1307; June 26, 2009)

SnapShot

SnapShot: Effector and Memory T Cell Differentiation
• Matthew E. Pipkin,
• Anjana Rao