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Uncovering Ubiquitin and Ubiquitin-Like Signaling Networks Alfred C
REVIEW pubs.acs.org/CR Uncovering Ubiquitin and Ubiquitin-like Signaling Networks Alfred C. O. Vertegaal* Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands CONTENTS 8. Crosstalk between Post-Translational Modifications 7934 1. Introduction 7923 8.1. Crosstalk between Phosphorylation and 1.1. Ubiquitin and Ubiquitin-like Proteins 7924 Ubiquitylation 7934 1.2. Quantitative Proteomics 7924 8.2. Phosphorylation-Dependent SUMOylation 7935 8.3. Competition between Different Lysine 1.3. Setting the Scenery: Mass Spectrometry Modifications 7935 Based Investigation of Phosphorylation 8.4. Crosstalk between SUMOylation and the and Acetylation 7925 UbiquitinÀProteasome System 7935 2. Ubiquitin and Ubiquitin-like Protein Purification 9. Conclusions and Future Perspectives 7935 Approaches 7925 Author Information 7935 2.1. Epitope-Tagged Ubiquitin and Ubiquitin-like Biography 7935 Proteins 7925 Acknowledgment 7936 2.2. Traps Based on Ubiquitin- and Ubiquitin-like References 7936 Binding Domains 7926 2.3. Antibody-Based Purification of Ubiquitin and Ubiquitin-like Proteins 7926 1. INTRODUCTION 2.4. Challenges and Pitfalls 7926 Proteomes are significantly more complex than genomes 2.5. Summary 7926 and transcriptomes due to protein processing and extensive 3. Ubiquitin Proteomics 7927 post-translational modification (PTM) of proteins. Hundreds ff fi 3.1. Proteomic Studies Employing Tagged of di erent modi cations exist. Release 66 of the RESID database1 (http://www.ebi.ac.uk/RESID/) contains 559 dif- Ubiquitin 7927 ferent modifications, including small chemical modifications 3.2. Ubiquitin Binding Domains 7927 such as phosphorylation, acetylation, and methylation and mod- 3.3. Anti-Ubiquitin Antibodies 7927 ification by small proteins, including ubiquitin and ubiquitin- 3.4. -
Dissecting Genome Reduction and Trait Loss in Insect Endosymbionts
Ann. N.Y. Acad. Sci. ISSN 0077-8923 ANNALS OF THE NEW YORK ACADEMY OF SCIENCES Issue: The Year in Evolutionary Biology REVIEW ARTICLE Dissecting genome reduction and trait loss in insect endosymbionts Amparo Latorre1,2 and Alejandro Manzano-Mar´ın1 1Institut Cavanilles de Biodiversitat I Biologia Evolutiva, Universitat de Valencia, C/Catedratico´ JoseBeltr´ an,´ Paterna, Valencia, Spain. 2Area´ de Genomica´ y Salud de la Fundacion´ para el fomento de la Investigacion´ Sanitaria y Biomedicadela´ Comunitat Valenciana (FISABIO)-Salud Publica,´ Valencia,` Spain Address for correspondence: Amparo Latorre, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, C/Catedratico´ JoseBeltr´ an´ 2, 46071 Paterna, Valencia, Spain. [email protected] Symbiosis has played a major role in eukaryotic evolution beyond the origin of the eukaryotic cell. Thus, organisms across the tree of life are associated with diverse microbial partners, conferring to the host new adaptive traits that enable it to explore new niches. This is the case for insects thriving on unbalanced diets, which harbor mutualistic intracellular microorganisms, mostly bacteria that supply them with the required nutrients. As a consequence of the lifestyle change, from free-living to host-associated mutualist, a bacterium undergoes many structural and metabolic changes, of which genome shrinkage is the most dramatic. The trend toward genome size reduction in endosymbiotic bacteria is associated with large-scale gene loss, reflecting the lack of an effective selection mechanism to maintain genes that are rendered superfluous by the constant and rich environment provided by the host. This genome- reduction syndrome is so strong that it has generated the smallest bacterial genomes found to date, whose gene contents are so limited that their status as cellular entities is questionable. -
Omics Technologies: Insights Into the Transmission of Insect Vector-Borne Plant Viruses
Looking Through the Lens of ‘Omics Technologies: Insights into the Transmission of Insect Vector-borne Plant Viruses Jennifer R. Wilson1,2, Stacy L. DeBlasio1,2,3, Mariko M. Alexander1,2 and Michelle Heck1,2,3* 1Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA. 2Boyce Tompson Institute, Ithaca, NY, USA. 3Emerging Pests and Pathogens Research Unit, United States Department of Agriculture – Agricultural Research Service, Ithaca, NY, USA. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.034.113 Abstract interactions, and the development of novel control Insects in the orders Hemiptera and Tysanoptera strategies. transmit viruses and other pathogens associated with the most serious diseases of plants. Plant viruses transmited by these insects target similar Advances in whole genome tissues, genes, and proteins within the insect to sequencing of insect vectors of facilitate plant-to-plant transmission with some plant viruses fuels discovery degree of specifcity at the molecular level. ‘Omics Major advances in next generation sequencing tech- experiments are becoming increasingly important nologies and their increased afordability has led to and practical for vector biologists to use towards an explosion in the availability of whole-genome beter understanding the molecular mechanisms sequence data for each biological player in the and biochemistry underlying transmission of virus–vector–host relationship: virus, vector and these insect-borne diseases. -
Coordination Between Autophagy and the Heat Shock Response: Evidence from Exercise in Animals and Humans Nathan H
University of New Mexico UNM Digital Repository Health, Exercise, and Sports Sciences ETDs Education ETDs 9-1-2015 Coordination Between Autophagy and the Heat Shock Response: Evidence From Exercise in Animals and Humans Nathan H. Cole Follow this and additional works at: https://digitalrepository.unm.edu/educ_hess_etds Part of the Health and Physical Education Commons Recommended Citation Cole, Nathan H.. "Coordination Between Autophagy and the Heat Shock Response: Evidence From Exercise in Animals and Humans." (2015). https://digitalrepository.unm.edu/educ_hess_etds/52 This Thesis is brought to you for free and open access by the Education ETDs at UNM Digital Repository. It has been accepted for inclusion in Health, Exercise, and Sports Sciences ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Nathan H. Cole Candidate Health, Exercise, & Sports Sciences Department This thesis is approved, and it is acceptable in quality and form for publication: Approved by the Thesis Committee: Christine M. Mermier, Chairperson Karol Dokladny Orrin B. Myers i COORDINATION BETWEEN AUTOPHAGY AND THE HEAT SHOCK RESPONSE: EVIDENCE FROM EXERCISE IN ANIMALS AND HUMANS by NATHAN H. COLE B.S. University Studies, University of New Mexico, 2013 THESIS Submitted in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE PHYSICAL EDUCATION CONCENTRATION: EXERCISE SCIENCE The University of New Mexico Albuquerque, New Mexico July, 2015 ii Acknowledgments I would like to thank Dr. Christine Mermier for her unwavering guidance, support, generosity, and patience (throughout this project, and many that came before it); Dr. Orrin Myers for all his assistance in moving from the numbers to the meaning (not to mention putting up with my parabolic model); Dr. -
Unique Integrated Stress Response Sensors Regulate Cancer Cell
RESEARCH ARTICLE Unique integrated stress response sensors regulate cancer cell susceptibility when Hsp70 activity is compromised Sara Sannino1*, Megan E Yates2,3,4, Mark E Schurdak5,6, Steffi Oesterreich2,3,7, Adrian V Lee2,3,7, Peter Wipf8, Jeffrey L Brodsky1* 1Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States; 2Women’s Cancer Research Center, UPMC Hillman Cancer Center, Magee- Women Research Institute, Pittsburgh, United States; 3Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, United States; 4Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, United States; 5Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States; 6University of Pittsburgh Drug Discovery Institute, Pittsburgh, United States; 7Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, United States; 8Department of Chemistry, University of Pittsburgh, Pittsburgh, United States Abstract Molecular chaperones, such as Hsp70, prevent proteotoxicity and maintain homeostasis. This is perhaps most evident in cancer cells, which overexpress Hsp70 and thrive even when harboring high levels of misfolded proteins. To define the response to proteotoxic challenges, we examined adaptive responses in breast cancer cells in the presence of an Hsp70 inhibitor. We discovered that the cells bin into distinct classes based on inhibitor sensitivity. Strikingly, the most resistant cells have higher autophagy levels, and autophagy was maximally activated only in resistant cells upon Hsp70 inhibition. In turn, resistance to compromised Hsp70 *For correspondence: function required the integrated stress response transducer, GCN2, which is commonly associated [email protected] (SS); with amino acid starvation. In contrast, sensitive cells succumbed to Hsp70 inhibition by activating [email protected] (JLB) PERK. -
Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution
GBE Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution John P. McCutcheon*, 1,2, and Nancy A. Moranà,2 1Center for Insect Science, University of Arizona 2Department of Ecology and Evolutionary Biology, University of Arizona Present address: Division of Biological Sciences, University of Montana, Missoula, Montana 59812 àPresent address: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 *Corresponding author: E-mail: [email protected]. Data deposition: The Candidatus Sulcia muelleri and Candidatus Zinderia insecticola genomes have been deposited in GenBank with the Downloaded from accession numbers CP002163 and CP002161. Accepted: 6 September 2010 Abstract gbe.oxfordjournals.org The main genomic changes in the evolution of host-restricted microbial symbionts are ongoing inactivation and loss of genes combined with rapid sequence evolution and extreme structural stability; these changes reflect high levels of genetic drift due to small population sizes and strict clonality. This genomic erosion includes irreversible loss of genes in many functional categories and can include genes that underlie the nutritional contributions to hosts that are the basis of the symbiotic association. Candidatus Sulcia muelleri is an ancient symbiont of sap-feeding insects and is typically coresident with another bacterial symbiont that varies among host subclades. Previously sequenced Sulcia genomes retain pathways for the same at The University of Montana on October 6, 2010 eight essential amino acids, whereas coresident symbionts synthesize the remaining two. Here, we describe a dual symbiotic system consisting of Sulcia and a novel species of Betaproteobacteria, Candidatus Zinderia insecticola, both living in the spittlebug Clastoptera arizonana. -
Insecta: Hemiptera: Fulgoroidea) Julie M Urban1* and Jason R Cryan2
Urban and Cryan BMC Evolutionary Biology 2012, 12:87 http://www.biomedcentral.com/1471-2148/12/87 RESEARCH ARTICLE Open Access Two ancient bacterial endosymbionts have coevolved with the planthoppers (Insecta: Hemiptera: Fulgoroidea) Julie M Urban1* and Jason R Cryan2 Abstract Background: Members of the hemipteran suborder Auchenorrhyncha (commonly known as planthoppers, tree- and leafhoppers, spittlebugs, and cicadas) are unusual among insects known to harbor endosymbiotic bacteria in that they are associated with diverse assemblages of bacterial endosymbionts. Early light microscopic surveys of species representing the two major lineages of Auchenorrhyncha (the planthopper superfamily Fulgoroidea; and Cicadomorpha, comprising Membracoidea [tree- and leafhoppers], Cercopoidea [spittlebugs], and Cicadoidea [cicadas]), found that most examined species harbored at least two morphologically distinct bacterial endosymbionts, and some harbored as many as six. Recent investigations using molecular techniques have identified multiple obligate bacterial endosymbionts in Cicadomorpha; however, much less is known about endosymbionts of Fulgoroidea. In this study, we present the initial findings of an ongoing PCR-based survey (sequencing 16S rDNA) of planthopper-associated bacteria to document endosymbionts with a long-term history of codiversification with their fulgoroid hosts. Results: Results of PCR surveys and phylogenetic analyses of 16S rDNA recovered a monophyletic clade of Betaproteobacteria associated with planthoppers; this clade included Vidania fulgoroideae, a recently described bacterium identified in exemplars of the planthopper family Cixiidae. We surveyed 77 planthopper species representing 18 fulgoroid families, and detected Vidania in 40 species (representing 13 families). Further, we detected the Sulcia endosymbiont (identified as an obligate endosymbiont of Auchenorrhyncha in previous studies) in 30 of the 40 species harboring Vidania. -
Comparative Genomics of Ceriporiopsis Subvermispora and Phanerochaete Chrysosporium Provide Insight Into Selective Ligninolysis Elena Fernandez-Fueyoa, Francisco J
Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis Elena Fernandez-Fueyoa, Francisco J. Ruiz-Dueñasa, Patricia Ferreirab, Dimitrios Floudasc, David S. Hibbettc, Paulo Canessad, Luis F. Larrondod, Tim Y. Jamese, Daniela Seelenfreundf, Sergio Lobosf, Rubén Polancog, Mario Telloh, Yoichi Hondai, Takahito Watanabei, Takashi Watanabei, Ryu Jae Sanj, Christian P. Kubicekk,l, Monika Schmollk, Jill Gaskellm, Kenneth E. Hammelm, Franz J. St. Johnm, Amber Vanden Wymelenbergn, Grzegorz Sabato, Sandra Splinter BonDuranto, Khajamohiddin Syedp, Jagjit S. Yadavp, Harshavardhan Doddapaneniq, Venkataramanan Subramanianr, José L. Lavíns, José A. Oguizas, Gumer Perezs, Antonio G. Pisabarros, Lucia Ramirezs, Francisco Santoyos, Emma Mastert, Pedro M. Coutinhou, Bernard Henrissatu, Vincent Lombardu, Jon Karl Magnusonv, Ursula Küesw, Chiaki Horix, Kiyohiko Igarashix, Masahiro Samejimax, Benjamin W. Held y, Kerrie W. Barryz, Kurt M. LaButtiz, Alla Lapidusz, Erika A. Lindquistz, Susan M. Lucas z, Robert Rileyz, Asaf A. Salamovz, Dirk Hoffmeisteraa, Daniel Schwenkaa, Yitzhak Hadarbb, Oded Yardenbb, Ronald P. de Vriescc, Ad Wiebengacc, Jan Stenliddd, Daniel Eastwood ee, Igor V. Grigoriev z, Randy M. Berkaff, Robert A. Blanchettey, Phil Kerstenm, Angel T. Martineza, Rafael Vicunad, and Dan Cullenm,1 aCentro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, E-28040 Madrid, Spain; bDepartment of Biochemistry and Molecular and Cellular Biology and Institute of -
Edinburgh Research Explorer
Edinburgh Research Explorer A new lineage of segmented RNA viruses infecting animals Citation for published version: Obbard, D, Shi, M, Roberts, KE, Longdon, B & Dennis, AB 2020, 'A new lineage of segmented RNA viruses infecting animals', Virus Evolution, vol. 6, no. 1, vez061. https://doi.org/10.1093/ve/vez061 Digital Object Identifier (DOI): 10.1093/ve/vez061 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Virus Evolution General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 30. Sep. 2021 Virus Evolution, 2020, 6(1): vez061 doi: 10.1093/ve/vez061 Research article Downloaded from https://academic.oup.com/ve/article-abstract/6/1/vez061/5708932 by Edinburgh University user on 22 January 2020 A new lineage of segmented RNA viruses infecting animals Darren J. Obbard,1,*,‡ Mang Shi,2,†,§ Katherine E. Roberts,3,†,** Ben Longdon,3,†,†† -
The Incredible Journey of Begomoviruses in Their Whitefly Vector
Review The Incredible Journey of Begomoviruses in Their Whitefly Vector Henryk Czosnek 1,*, Aliza Hariton-Shalev 1, Iris Sobol 1, Rena Gorovits 1 and Murad Ghanim 2 1 Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel; [email protected] (A.H.-S.); [email protected] (I.S.); [email protected] (R.G.) 2 Department of Entomology, Agricultural Research Organization, Volcani Center, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel; [email protected] * Correspondence: [email protected]; Tel.: +972-54-8820-627 Received: 28 August 2017; Accepted: 18 September 2017; Published: 24 September 2017 Abstract: Begomoviruses are vectored in a circulative persistent manner by the whitefly Bemisia tabaci. The insect ingests viral particles with its stylets. Virions pass along the food canal and reach the esophagus and the midgut. They cross the filter chamber and the midgut into the haemolymph, translocate into the primary salivary glands and are egested with the saliva into the plant phloem. Begomoviruses have to cross several barriers and checkpoints successfully, while interacting with would-be receptors and other whitefly proteins. The bulk of the virus remains associated with the midgut and the filter chamber. In these tissues, viral genomes, mainly from the tomato yellow leaf curl virus (TYLCV) family, may be transcribed and may replicate. However, at the same time, virus amounts peak, and the insect autophagic response is activated, which in turn inhibits replication and induces the destruction of the virus. -
Protein Quality Control in the Endoplasmic Reticulum and Cancer
Review Protein Quality Control in the Endoplasmic Reticulum and Cancer Hye Won Moon 1,2,†, Hye Gyeong Han 1,2,† and Young Joo Jeon 1,2,* 1 Department of Biochemistry, Chungnam National University College of Medicine, Daejeon 35015, Korea; [email protected] (H.W.M.); [email protected] (H.G.H.) 2 Department of Medical Science, Chungnam National University College of Medicine, Daejeon 35015, Korea * Correspondence: [email protected]; Tel.: +82-42-280-6766; Fax: +82-42-280-6769 † These authors contributed equally to this work. Received: 8 September 2018; Accepted: 1 October 2018; Published: 3 October 2018 Abstract: The endoplasmic reticulum (ER) is an essential compartment of the biosynthesis, folding, assembly, and trafficking of secretory and transmembrane proteins, and consequently, eukaryotic cells possess specialized machineries to ensure that the ER enables the proteins to acquire adequate folding and maturation for maintaining protein homeostasis, a process which is termed proteostasis. However, a large variety of physiological and pathological perturbations lead to the accumulation of misfolded proteins in the ER, which is referred to as ER stress. To resolve ER stress and restore proteostasis, cells have evolutionary conserved protein quality-control machineries of the ER, consisting of the unfolded protein response (UPR) of the ER, ER-associated degradation (ERAD), and autophagy. Furthermore, protein quality-control machineries of the ER play pivotal roles in the control of differentiation, progression of cell cycle, inflammation, immunity, and aging. Therefore, severe and non-resolvable ER stress is closely associated with tumor development, aggressiveness, and response to therapies for cancer. In this review, we highlight current knowledge in the molecular understanding and physiological relevance of protein quality control of the ER and discuss new insights into how protein quality control of the ER is implicated in the pathogenesis of cancer, which could contribute to therapeutic intervention in cancer. -
Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution
GBE Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution John P. McCutcheon*, 1,2, and Nancy A. Moranà,2 1Center for Insect Science, University of Arizona 2Department of Ecology and Evolutionary Biology, University of Arizona Present address: Division of Biological Sciences, University of Montana, Missoula, Montana 59812 àPresent address: Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 *Corresponding author: E-mail: [email protected]. Data deposition: The Candidatus Sulcia muelleri and Candidatus Zinderia insecticola genomes have been deposited in GenBank with the accession numbers CP002163 and CP002161. Accepted: 6 September 2010 Abstract The main genomic changes in the evolution of host-restricted microbial symbionts are ongoing inactivation and loss of genes combined with rapid sequence evolution and extreme structural stability; these changes reflect high levels of genetic drift due to small population sizes and strict clonality. This genomic erosion includes irreversible loss of genes in many functional categories and can include genes that underlie the nutritional contributions to hosts that are the basis of the symbiotic association. Candidatus Sulcia muelleri is an ancient symbiont of sap-feeding insects and is typically coresident with another bacterial symbiont that varies among host subclades. Previously sequenced Sulcia genomes retain pathways for the same eight essential amino acids, whereas coresident symbionts synthesize the remaining two. Here, we describe a dual symbiotic system consisting of Sulcia and a novel species of Betaproteobacteria, Candidatus Zinderia insecticola, both living in the spittlebug Clastoptera arizonana. This Sulcia has completely lost the pathway for the biosynthesis of tryptophan and, therefore, retains the ability to make only 7 of the 10 essential amino acids.