6月29日Cell杂志文章要览（部分免费全文浏览）

　　

生物通编者按：6月29日，新一期的Cell杂志出炉。本期Cell封面图片文章的题目为《分子捕鼠器决定大肠杆菌DNA复制终止的极性》。值得一提的是，本期Cell上刊登了中国农业大学发表的一篇文章，题目为“A Protein Kinase, Interacting with Two Calcineurin B-like Proteins, Regulates K⁺ Transporter AKT1 in Arabidopsis”。另外，还有两篇文章可以免费全文阅览。

 

Article

Identification and Validation of Oncogenes in Liver Cancer Using an Integrative Oncogenomic Approach

Lars Zender,¹ Mona S. Spector,¹ Wen Xue,¹ Peer Flemming,^2,7 Carlos Cordon-Cardo,³ John Silke,^4,8 Sheung-Tat Fan,⁵ John M. Luk,⁵ Michael Wigler,¹ Gregory J. Hannon,^1,6 David Mu,¹ Robert Lucito,¹ Scott Powers,¹ and Scott W. Lowe^1,6,

¹ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
² Department of Pathology, Hannover Medical School, 30625 Hannover, Germany
³ Division of Molecular Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
⁴ The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
⁵ Department of Surgery, University of Hong Kong, Hong Kong, China
⁶ Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA

Summary

The heterogeneity and instability of human tumors hamper straightforward identification of cancer-causing mutations through genomic approaches alone. Herein we describe a mouse model of liver cancer initiated from progenitor cells harboring defined cancer-predisposing lesions. Genome-wide analyses of tumors in this mouse model and in human hepatocellular carcinomas revealed a recurrent amplification at mouse chromosome 9qA1, the syntenic region of human chromosome 11q22. Gene-expression analyses delineated cIAP1, a known inhibitor of apoptosis, and Yap, a transcription factor, as candidate oncogenes in the amplicon. In the genetic context of their amplification, both cIAP1 and Yap accelerated tumorigenesis and were required to sustain rapid growth of amplicon-containing tumors. Furthermore, cIAP1 and Yap cooperated to promote tumorigenesis. Our results establish a tractable model of liver cancer, identify two oncogenes that cooperate by virtue of their coamplification in the same genomic locus, and suggest an efficient strategy for the annotation of human cancer genes.

Article

Comparative Oncogenomics Identifies NEDD9 as a Melanoma Metastasis Gene

Minjung Kim,¹ Joseph D. Gans,¹ Cristina Nogueira,^1,2 Audrey Wang,¹ Ji-Hye Paik,¹ Bin Feng,³ Cameron Brennan,⁴ William C. Hahn,^1,5 Carlos Cordon-Cardo,⁶ Stephan N. Wagner,⁷ Thomas J. Flotte,⁸ Lyn M. Duncan,⁸ Scott R. Granter,⁹ and Lynda Chin^1,3,10,

¹ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
² Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Medical Faculty, University of Porto, Porto, Portugal
³ Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA
⁴ Department of Surgery, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
⁵ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
⁶ Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
⁷ DIAID, Department of Dermatology, Medical University of Vienna and Center of Molecular Medicine, Austrian Academy of Sciences, Wahringer Gurtel 18-20, A-1090 Vienna, Austria
⁸ Dermatopathology Unit, Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
⁹ Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
¹⁰ Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA

Summary

Genomes of human cancer cells are characterized by numerous chromosomal aberrations of uncertain pathogenetic significance. Here, in an inducible mouse model of melanoma, we characterized metastatic variants with an acquired focal chromosomal amplification that corresponds to a much larger amplification in human metastatic melanomas. Further analyses identified Nedd9, an adaptor protein related to p130CAS, as the only gene within the minimal common region that exhibited amplification-associated overexpression. A series of functional, biochemical, and clinical studies established NEDD9 as a bona fide melanoma metastasis gene. NEDD9 enhanced invasion in vitro and metastasis in vivo of both normal and transformed melanocytes, functionally interacted with focal adhesion kinase and modulated focal contact formation, and exhibited frequent robust overexpression in human metastatic melanoma relative to primary melanoma. Thus, comparative oncogenomics has enabled the identification and facilitated the validation of a highly relevant cancer gene governing metastatic potential in human melanoma.

 

The Pattern of Gene Amplification Is Determined by the Chromosomal Location of Hairpin-Capped Breaks

Vidhya Narayanan,¹ Piotr A. Mieczkowski,² Hyun-Min Kim,¹ Thomas D. Petes,² and Kirill S. Lobachev^1,

¹ School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
² Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA

Summary

DNA palindromes often colocalize in cancer cells with chromosomal regions that are predisposed to gene amplification. The molecular mechanisms by which palindromes can cause gene amplification are largely unknown. Using yeast as a model system, we found that hairpin-capped double-strand breaks (DSBs) occurring at the location of human Alu-quasipalindromes lead to the formation of intrachromosomal amplicons with large inverted repeats (equivalent to homogeneously staining regions in mammalian chromosomes) or extrachromosomal palindromic molecules (equivalent to double minutes [DM] in mammalian cells). We demonstrate that the specific outcomes of gene amplification depend on the applied selection, the nature of the break, and the chromosomal location of the amplified gene relative to the site of the hairpin-capped DSB. The rules for the palindrome-dependent pathway of gene amplification defined in yeast may operate during the formation of amplicons in human tumors.

Article

Live-Cell Imaging Reveals Replication of Individual Replicons in Eukaryotic Replication Factories

Etsushi Kitamura,¹ J. Julian Blow,¹ and Tomoyuki U. Tanaka^1,

¹ School of Life Sciences, University of Dundee, Wellcome Trust Biocentre, Dow Street, Dundee, UK

Summary

Faithful DNA replication ensures genetic integrity in eukaryotic cells, but it is still obscure how replication is organized in space and time within the nucleus. Using timelapse microscopy, we have developed a new assay to analyze the dynamics of DNA replication both spatially and temporally in individual Saccharomyces cerevisiae cells. This allowed us to visualize replication factories, nuclear foci consisting of replication proteins where the bulk of DNA synthesis occurs. We show that the formation of replication factories is a consequence of DNA replication itself. Our analyses of replication at specific DNA sequences support a long-standing hypothesis that sister replication forks generated from the same origin stay associated with each other within a replication factory while the entire replicon is replicated. This assay system allows replication to be studied at extremely high temporal resolution in individual cells, thereby opening a window into how replication dynamics vary from cell to cell.

全文免费阅览：http://www.cell.com/content/article/fulltext?uid=PIIS0092867406006520

 

Article （Cover Story）

A Molecular Mousetrap Determines Polarity of Termination of DNA Replication in E. coli

Mark D. Mulcair,¹ Patrick M. Schaeffer,¹ Aaron J. Oakley,¹ Hannah F. Cross,² Cameron Neylon,² Thomas M. Hill,³ and Nicholas E. Dixon^1,

¹ Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
² School of Chemistry, University of Southampton, SO17 1BJ, UK
³ Department of Microbiology and Immunology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA

Summary

During chromosome synthesis in Escherichia coli, replication forks are blocked by Tus bound Ter sites on approach from one direction but not the other. To study the basis of this polarity, we measured the rates of dissociation of Tus from forked TerB oligonucleotides, such as would be produced by the replicative DnaB helicase at both the fork-blocking (nonpermissive) and permissive ends of the Ter site. Strand separation of a few nucleotides at the permissive end was sufficient to force rapid dissociation of Tus to allow fork progression. In contrast, strand separation extending to and including the strictly conserved G-C(6) base pair at the nonpermissive end led to formation of a stable locked complex. Lock formation specifically requires the cytosine residue, C(6). The crystal structure of the locked complex showed that C(6) moves 14 Å from its normal position to bind in a cytosine-specific pocket on the surface of Tus.

Article

Cyclin-Dependent Kinase Directly Regulates Initiation of Meiotic Recombination

Kiersten A. Henderson,^1,2 Kehkooi Kee,^1,2,3 Shohreh Maleki,¹ Paul A. Santini,^1,2 and Scott Keeney^1,2,

¹ Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
² Weill Graduate School of Medical Sciences, Cornell University, New York, NY, 10021 USA

Summary

Meiosis is a specialized cell division that halves the genome complement, producing haploid gametes/spores from diploid cells. Proper separation of homologous chromosomes at the first meiotic division requires the production of physical connections (chiasmata) between homologs through recombinational exchange of chromosome arms after sister-chromatid cohesion is established but before chromosome segregation takes place. The events of meiotic prophase must thus occur in a strictly temporal order, but the molecular controls coordinating these events have not been well elucidated. Here, we demonstrate that the budding yeast cyclin-dependent kinase Cdc28 directly regulates the formation of the DNA double-strand breaks that initiate recombination by phosphorylating the Mer2/Rec107 protein and thereby modulating interactions of Mer2 with other proteins required for break formation. We propose that this function of Cdc28 helps to coordinate the events of meiotic prophase with each other and with progression through prophase.

Article

Intracellular Nucleotides Act as Critical Prosurvival Factors by Binding to Cytochrome C and Inhibiting Apoptosome

Dhyan Chandra,^1, Shawn B. Bratton,² Maria D. Person,² Yanan Tian,³ Angel G. Martin,⁴ Mary Ayres,⁵ Howard O. Fearnhead,⁴ Varsha Gandhi,⁵ and Dean G. Tang^1,6,

¹ Department of Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park-Research Division, Smithville, TX 78957, USA
² Division of Pharmacology/Toxicology, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
³ Department of Veterinary Physiology and Pharmacology, MS 4466, Texas A&M University, College Station, TX 77843, USA
⁴ Apoptosis Section, Laboratory of Protein Dynamics and Signaling, NCI-Frederick, Frederick, MD 21702, USA
⁵ Department of Experimental Therapeutics, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
⁶ Program in Molecular Carcinogenesis of Graduate School for Biomedical Science, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA

Summary

Cytochrome c (CC)-initiated Apaf-1 apoptosome formation represents a key initiating event in apoptosis. This process can be reconstituted in vitro with the addition of CC and ATP or dATP to cell lysates. How physiological levels of nucleotides, normally at high mM concentrations, affect apoptosome activation remains unclear. Here we show that physiological levels of nucleotides inhibit the CC-initiated apoptosome formation and caspase-9 activation by directly binding to CC on several key lysine residues and thus preventing CC interaction with Apaf-1. We show that in various apoptotic systems caspase activation is preceded or accompanied by decreases in overall intracellular NTP pools. Microinjection of nucleotides inhibits whereas experimentally reducing NTP pools enhances both CC and apoptotic stimuli-induced cell death. Our results thus suggest that the intracellular nucleotides represent critical prosurvival factors by functioning as natural inhibitors of apoptosome formation and a barrier that cells must overcome the nucleotide barrier to undergo apoptosis cell death.

 

Article

A Protein Kinase, Interacting with Two Calcineurin B-like Proteins, Regulates K⁺ Transporter AKT1 in Arabidopsis

Jiang Xu,^1,2 Hao-Dong Li,^1,2 Li-Qing Chen,^1,2 Yi Wang,^1,2 Li-Li Liu,^1,2 Liu He,¹ and Wei-Hua Wu^1,

¹ State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, National Plant Gene Research Centre (Beijing), Beijing 100094, China

Summary

Potassium is an essential mineral element for plant growth and development. Although it is known that plants absorb and transport K⁺ through membrane transporters, it remains unclear how these transporters are regulated. Here we show that the protein kinase CIPK23, encoded by the LKS1 gene, regulates K⁺ uptake under low-K⁺ conditions. Lesion of LKS1 significantly reduced K⁺ uptake and caused leaf chlorosis and growth inhibition, whereas overexpression of LKS1 significantly enhanced K⁺ uptake and tolerance to low K⁺. We demonstrate that CIPK23 directly phosphorylates the K⁺ transporter AKT1 and further find that CIPK23 is activated by the binding of two calcineurin B-like proteins, CBL1 and CBL9. We propose a model in which the CBL1/9–CIPK23 pathway ensures activation of AKT1 and enhanced K⁺ uptake under low-K⁺ conditions.

Article

Spatiotemporal Feedback between Actomyosin and Focal-Adhesion Systems Optimizes Rapid Cell Migration

Stephanie L. Gupton¹ and Clare M. Waterman-Storer^1,

¹ Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA

Summary

Cells exhibit a biphasic migration-velocity response to increasing adhesion strength, with fast migration occurring at intermediate extracellular matrix (ECM) concentration and slow migration occurring at low and high ECM concentration. A simple mechanical model has been proposed to explain this observation, in which too little adhesion does not provide sufficient traction whereas too much adhesion renders cells immobile. Here we characterize a phenotype for rapid cell migration, which in contrast to the previous model reveals a complex interdependence of subcellular systems that mediates optimal cell migration in response to increasing adhesion strength. The organization and activity of actin, myosin II, and focal adhesions (FAs) are spatially and temporally highly variable and do not exhibit a simple correlation with optimal motility rates. Furthermore, we can recapitulate rapid migration at a nonoptimal ECM concentration by manipulating myosin II activity. Thus, the interplay between actomyosin and FA dynamics results in a specific balance between adhesion and contraction, which induces maximal migration velocity.

全文免费浏览：http://www.cell.com/content/article/fulltext?uid=PIIS0092867406007197

 

Article

Flies without Centrioles

Renata Basto,¹ Joyce Lau,¹ Tatiana Vinogradova,^2,3 Alejandra Gardiol,¹ C. Geoffrey Woods,⁴ Alexey Khodjakov,^2,3 and Jordan W. Raff^1,

¹ The Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK
² Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
³ Department of Biomedical Sciences, State University of New York, Albany, NY 12222, USA
⁴ Department of Medical Genetics, Cambridge Institute of Medical Research, Cambridge CB2 2XY, UK

Summary

Centrioles and centrosomes have an important role in animal cell organization, but it is uncertain to what extent they are essential for animal development. The Drosophila protein DSas-4 is related to the human microcephaly protein CenpJ and the C. elegans centriolar protein Sas-4. We show that DSas-4 is essential for centriole replication in flies. DSas-4 mutants start to lose centrioles during embryonic development, and, by third-instar larval stages, no centrioles or centrosomes are detectable. Mitotic spindle assembly is slow in mutant cells, and ∼30% of the asymmetric divisions of larval neuroblasts are abnormal. Nevertheless, mutant flies develop with near normal timing into morphologically normal adults. These flies, however, have no cilia or flagella and die shortly after birth because their sensory neurons lack cilia. Thus, centrioles are essential for the formation of centrosomes, cilia, and flagella, but, remarkably, they are not essential for most aspects of Drosophila development.

Article

Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution

Sangyun Jeong,¹ Antonis Rokas,² and Sean B. Carroll^1,

¹ Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, 1525 Linden Drive, Madison, WI 53706, USA
² Microbial Genome Analysis and Annotation, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02141, USA

Summary

Hox genes have been implicated in the evolution of many animal body patterns, but the molecular events underlying trait modification have not been elucidated. Pigmentation of the posterior male abdomen is a recently acquired trait in the Drosophila melanogaster lineage. Here, we show that the Abdominal-B (ABD-B) Hox protein directly activates expression of the yellow pigmentation gene in posterior segments. ABD-B regulation of pigmentation evolved through the gain of ABD-B binding sites in a specific cis-regulatory element of the yellow gene of a common ancestor of sexually dimorphic species. Within the melanogaster species group, male-specific pigmentation has subsequently been lost by at least three different mechanisms, including the mutational inactivation of a key ABD-B binding site in one lineage. These results demonstrate how Hox regulation of traits and target genes is gained and lost at the species level and have general implications for the evolution of body form at higher taxonomic levels.