Recombination in Viruses: Mechanisms, Methods of Study, and Evolutionary Consequences
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Direct Agroinoculation of Maize Seedlings by Injection with Recombinant Foxtail Mosaic Virus and Sugarcane Mosaic Virus Infectious Clones
Direct Agroinoculation of Maize Seedlings by Injection with Recombinant Foxtail Mosaic Virus and Sugarcane Mosaic Virus Infectious Clones Bliss M. Beernink*,1, Katerina L. Holan*,1, Ryan R. Lappe1, Steven A. Whitham1 1 Department of Plant Pathology and Microbiology, Iowa State University * These authors contributed equally Corresponding Author Abstract Steven A. Whitham [email protected] Agrobacterium-based inoculation approaches are widely used for introducing viral vectors into plant tissues. This study details a protocol for the injection of maize Citation seedlings near meristematic tissue with Agrobacterium carrying a viral vector. Beernink, B.M., Holan, K.L., Lappe, R.R., Recombinant foxtail mosaic virus (FoMV) clones engineered for gene silencing and Whitham, S.A. Direct Agroinoculation of Maize Seedlings by Injection with gene expression were used to optimize this method, and its use was expanded Recombinant Foxtail Mosaic Virus and to include a recombinant sugarcane mosaic virus (SCMV) engineered for gene Sugarcane Mosaic Virus Infectious Clones. J. Vis. Exp. (168), e62277, expression. Gene fragments or coding sequences of interest are inserted into a doi:10.3791/62277 (2021). modified, infectious viral genome that has been cloned into the binary T-DNA plasmid vector pCAMBIA1380. The resulting plasmid constructs are transformed into Date Published Agrobacterium tumefaciens strain GV3101. Maize seedlings as young as 4 days February 27, 2021 old can be injected near the coleoptilar node with bacteria resuspended in MgSO4 DOI -
Mobile Genetic Elements in Streptococci
Curr. Issues Mol. Biol. (2019) 32: 123-166. DOI: https://dx.doi.org/10.21775/cimb.032.123 Mobile Genetic Elements in Streptococci Miao Lu#, Tao Gong#, Anqi Zhang, Boyu Tang, Jiamin Chen, Zhong Zhang, Yuqing Li*, Xuedong Zhou* State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China. #Miao Lu and Tao Gong contributed equally to this work. *Address correspondence to: [email protected], [email protected] Abstract Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance. caister.com/cimb 123 Curr. Issues Mol. Biol. (2019) Vol. 32 Mobile Genetic Elements Lu et al Introduction Streptococci are a group of Gram-positive bacteria widely distributed across human and animals. Unlike the Staphylococcus species, streptococci are catalase negative and are subclassified into the three subspecies alpha, beta and gamma according to the partial, complete or absent hemolysis induced, respectively. The beta hemolytic streptococci species are further classified by the cell wall carbohydrate composition (Lancefield, 1933) and according to human diseases in Lancefield groups A, B, C and G. -
Homologous Recombination Between a Defective Virus and a Chromosomal Sequence in Mammalian Cells (DNA Integation/Simian Virus 40) YOSEF SHAUL*, ORGAD Laubt, MICHAEL D
Proc. Nad. Acad. Sci. USA Vol. 82, pp. 3781-3784, June 1985 Genetics Homologous recombination between a defective virus and a chromosomal sequence in mammalian cells (DNA integation/simian virus 40) YOSEF SHAUL*, ORGAD LAUBt, MICHAEL D. WALKERt, AND WILLIAM J. RUTTER* Departments of *Virology and tGenetics, The Weizmann Institute of Science, Rehovot, Israel; and *Hormone Research Laboratory, University of California, San Francisco, CA 94143 Contributed by William J. Rutter, February 14, 1985 ABSTRACT Replacement of the early region of simian vi- M 2 3 4 5 6 7 8 9 10 11 12 M rus 40 results in virus that cannot replicate in a normal host, kb 231 - CV-1 cells, but can replicate in COS cells, a derivative of CV-1 9.4 - cells that constitutively express simian virus 40 tumor antigen 6.6 - (T antigen). However, passage of such an early replacement 44 --I _ simian virus 40 mutant in COS cells results in the emergence of _ _ virus that can propagate in CV-1 cells. Analysis of this virus 2.3- revealed that the mutant rescued the integrated T-antigen gene 2.0 - from the COS cell genome. Comparison of the sequence of the recovered virus with that of the viral DNA resident in COS 135- cells (strain 776) and the mutant used in our studies (derived 108 -- from strain 777) proves that the mutant virus acquired the T- .87- _ antigen gene from the COS cell chromosome via homologous ,_ . 1 recombination. Most probably this process was mediated by a .60- direct genetic exchange. -
Bacterial Superinfection of Influenza Protein-2 Expression Drives Illness in Dysregulated Macrophage-Inflammatory
Dysregulated Macrophage-Inflammatory Protein-2 Expression Drives Illness in Bacterial Superinfection of Influenza This information is current as Caleb C. J. Zavitz, Carla M. T. Bauer, Gordon J. Gaschler, of October 3, 2021. Katie M. Fraser, Robert M. Strieter, Cory M. Hogaboam and Martin R. Stampfli J Immunol published online 11 January 2010 http://www.jimmunol.org/content/early/2010/01/11/jimmun ol.0903304 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2010/01/11/jimmunol.090330 Material 4.DC1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on October 3, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published January 11, 2010, doi:10.4049/jimmunol.0903304 The Journal of Immunology Dysregulated Macrophage-Inflammatory Protein-2 Expression Drives Illness in Bacterial Superinfection of Influenza Caleb C. J. Zavitz,* Carla M. T. Bauer,* Gordon J. Gaschler,* Katie M. Fraser,† Robert M. Strieter,‡ Cory M. Hogaboam,x and Martin R. Stampfli†,{ Influenza virus infection is a leading cause of death and disability throughout the world. -
Treating Opportunistic Infections Among HIV-Infected Adults and Adolescents
Morbidity and Mortality Weekly Report Recommendations and Reports December 17, 2004 / Vol. 53 / No. RR-15 Treating Opportunistic Infections Among HIV-Infected Adults and Adolescents Recommendations from CDC, the National Institutes of Health, and the HIV Medicine Association/ Infectious Diseases Society of America INSIDE: Continuing Education Examination department of health and human services Centers for Disease Control and Prevention MMWR CONTENTS The MMWR series of publications is published by the Epidemiology Program Office, Centers for Disease Introduction......................................................................... 1 Control and Prevention (CDC), U.S. Department of How To Use the Information in This Report .......................... 2 Health and Human Services, Atlanta, GA 30333. Effect of Antiretroviral Therapy on the Incidence and Management of OIs .................................................... 2 SUGGESTED CITATION Initiation of ART in the Setting of an Acute OI Centers for Disease Control and Prevention. Treating (Treatment-Naïve Patients) ................................................. 3 Management of Acute OIs in the Setting of ART .................. 4 opportunistic infections among HIV-infected adults and When To Initiate ART in the Setting of an OI ........................ 4 adolescents: recommendations from CDC, the National Special Considerations During Pregnancy ........................... 4 Institutes of Health, and the HIV Medicine Association/ Disease Specific Recommendations .................................... -
Helicase Mechanisms During Homologous Recombination in Saccharomyces Cerevisiae
BB48CH11_Greene ARjats.cls April 18, 2019 12:24 Annual Review of Biophysics Helicase Mechanisms During Homologous Recombination in Saccharomyces cerevisiae J. Brooks Crickard and Eric C. Greene Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; email: [email protected], [email protected] Annu. Rev. Biophys. 2019. 48:255–73 Keywords First published as a Review in Advance on homologous recombination, helicase, Srs2, Sgs1, Rad54 March 11, 2019 Access provided by 68.175.70.229 on 06/02/20. For personal use only. The Annual Review of Biophysics is online at Abstract Annu. Rev. Biophys. 2019.48:255-273. Downloaded from www.annualreviews.org biophys.annualreviews.org Helicases are enzymes that move, manage, and manipulate nucleic acids. https://doi.org/10.1146/annurev-biophys-052118- They can be subdivided into six super families and are required for all aspects 115418 of nucleic acid metabolism. In general, all helicases function by converting Copyright © 2019 by Annual Reviews. the chemical energy stored in the bond between the gamma and beta phos- All rights reserved phates of adenosine triphosphate into mechanical work, which results in the unidirectional movement of the helicase protein along one strand of a nu- cleic acid. The results of this translocation activity can range from separation of strands within duplex nucleic acids to the physical remodeling or removal of nucleoprotein complexes. In this review, we focus on describing key heli- cases from the model organism Saccharomyces cerevisiae that contribute to the regulation of homologous recombination, which is an essential DNA repair pathway for fxing damaged chromosomes. -
Recombinant and Chimeric Viruses
Recombinant and chimeric viruses: Evaluation of risks associated with changes in tropism Ben P.H. Peeters Animal Sciences Group, Wageningen University and Research Centre, Division of Infectious Diseases, P.O. Box 65, 8200 AB Lelystad, The Netherlands. May 2005 This report represents the personal opinion of the author. The interpretation of the data presented in this report is the sole responsibility of the author and does not necessarily represent the opinion of COGEM or the Animal Sciences Group. Dit rapport is op persoonlijke titel door de auteur samengesteld. De interpretatie van de gepresenteerde gegevens komt geheel voor rekening van de auteur en representeert niet de mening van de COGEM, noch die van de Animal Sciences Group. Advisory Committee Prof. dr. R.C. Hoeben (Chairman) Leiden University Medical Centre Dr. D. van Zaane Wageningen University and Research Centre Dr. C. van Maanen Animal Health Service Drs. D. Louz Bureau Genetically Modified Organisms Ing. A.M.P van Beurden Commission on Genetic Modification Recombinant and chimeric viruses 2 INHOUDSOPGAVE RECOMBINANT AND CHIMERIC VIRUSES: EVALUATION OF RISKS ASSOCIATED WITH CHANGES IN TROPISM Executive summary............................................................................................................................... 5 Introduction............................................................................................................................................ 7 1. Genetic modification of viruses .................................................................................................9 -
Evolution with Recombination Affects the Stability of Mobile Genetic Element Insertions Within Gene Families of Salmonella
Molecular Microbiology (2018) 108(6), 697–710 doi:10.1111/mmi.13959 First published online 25 April 2018 Co-evolution with recombination affects the stability of mobile genetic element insertions within gene families of Salmonella Gerrit Brandis ,† Sha Cao† and Introduction Diarmaid Hughes * Department of Medical Biochemistry and Gene families with multiple copies of the same gene Microbiology, Box 582 Biomedical Center, Uppsala separately located on the chromosome are a frequent University, Uppsala, Sweden. feature in prokaryotic and eukaryotic genomes. One common gene family in bacteria are the genes for trans- lation elongation factor EF-Tu, tufA and tufB. The dupli- cation of the tuf gene, that led to the creation of this gene family, most likely occurred early in the evolution Summary of the eubacterial taxon (Sela et al., 1989; Lathe and Bork, 2001). Despite the ancient origin of the duplica- Bacteria can have multiple copies of a gene at sepa- tion, the tuf genes of Salmonella enterica serovar Typhi- rate locations on the same chromosome. Some of murium strain LT2 differ at only 13 of 1185 nucleotides these gene families, including tuf (translation elonga- (Abdulkarim and Hughes, 1996). This high degree of tion factor EF-Tu) and rrl (ribosomal RNA), encode nucleotide identity indicates that the tuf genes evolve in functions critically important for bacterial fitness. concert. It has been shown that homologous recombina- Genes within these families are known to evolve in tion between the genes leads to the exchange of concert using homologous recombination to transfer genetic information, which facilitates this co-evolution genetic information from one gene to another. -
Homology Requirements for Targeting Heterologous Sequences During P-Induced Gap Repair in Drosophila Melanogastd
Copyright 0 1997 by the Genetics Society of America Homology Requirements for Targeting Heterologous Sequences During P-Induced Gap Repair in Drosophila melanogastd Tammy Dray and Gregory B. Gloor Department of Biochemistry, University of Western Ontario, London, Ontario, Canada Manuscript received January 23, 1997 Accepted for publication June 26, 1997 ABSTRACT The effect of homology on gene targeting was studied in the context of P-element-induced double- strand breaks at the white locus of Lkosophila melanogaster. Double-strand breaks were made by excision of F'-Whd, a P-element insertion in the white gene. A nested set of repair templates was generated that contained the 8 kilobase (kb) yellow gene embedded within varying amounts of white gene sequence. Repair with unlimited homology was also analyzed. Flies were scored phenotypically for conversion of the yellow gene to thewhite locus. Targeting of the yellow gene was abolished when all of the 3' homology was removed. Increases in template homology up to 51 base pairs (bp) did not significantly promote targeting. Maximum conversion was observed with a construct containing493 bp of homology, without a significant increase in frequency when homology extended to the tips of the chromosome. These results demonstrate that the homology requirements for targeting a large heterologous insertion are quite different than those for a point mutation. Furthermore, heterologous insertions strongly affect the homology requirements for the conversion of distal point mutations. Several aberrant conversion tracts, which arose from templates that contained reducedhomology, also were examined andcharacter- ized. OUBLE-STRAND breaks arise in the genome as or noncrossover event depends upon the resolution of D a direct result of ionizing radiation, transposon the Holidayjunctions on eitherside of the newly synthe- excision or site-specific nucleases, and indirectly sized DNA (SZOST~et al. -
Analysis of HIV-1 Intersubtype Recombination Breakpoints
Jia et al. Virology Journal (2016) 13:156 DOI 10.1186/s12985-016-0616-1 RESEARCH Open Access Analysis of HIV-1 intersubtype recombination breakpoints suggests region with high pairing probability may be a more fundamental factor than sequence similarity affecting HIV-1 recombination Lei Jia, Lin Li, Tao Gui, Siyang Liu, Hanping Li, Jingwan Han, Wei Guo, Yongjian Liu* and Jingyun Li* Abstract Background: With increasing data on HIV-1, a more relevant molecular model describing mechanism details of HIV-1 genetic recombination usually requires upgrades. Currently an incomplete structural understanding of the copy choice mechanism along with several other issues in the field that lack elucidation led us to perform an analysis of the correlation between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarity to further explore structural mechanisms. Methods: Near full length sequences of URFs from Asia, Europe, and Africa (one sequence/patient), and representative sequences of worldwide CRFs were retrieved from the Los Alamos HIV database. Their recombination patterns were analyzed by jpHMM in detail. Then the relationships between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarities were investigated. Results: Pearson correlation test showed that all URF groups and the CRF group exhibit the same breakpoint distribution pattern. Additionally, the Wilcoxon two-sample test indicated a significant and inexplicable limitation of recombination in regions with high pairing probability. These regions have been found to be strongly conserved across distinct biological states (i.e., strong intersubtype similarity), and genetic similarity has been determined to be a very important factor promoting recombination. -
Approaches to Maximize Sgrna-Barcode Coupling in Perturb-Seq Screens
bioRxiv preprint doi: https://doi.org/10.1101/298349; this version posted April 11, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Approaches to maximize sgRNA-barcode coupling in Perturb-seq screens Britt Adamson1-4, Thomas M. Norman1-4, Marco Jost1-5, Jonathan S. Weissman1-4, † 1 Department of Cellular & Molecular Pharmacology, 2 Howard Hughes Medical Institute, 3 California Institute for Quantitative Biomedical Research, 4 Center for RNA Systems Biology, 5 Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA † Lead contact; Correspondence should be addressed to [email protected] ABSTRACT Perturb-seq is a platform for single-cell gene expression profiling of pooled CRISPR screens. Like many functional genomics platforms, Perturb-seq relies on lentiviral transduction to introduce perturbation libraries to cells. On this platform, these are barcoded sgRNA libraries. A critical consideration for performing Perturb-seq experiments is uncoupling of barcodes from linked sgRNA expression cassettes, which can occur during lentiviral transduction of co-packaged libraries due to reverse transcriptase-mediated template switching. This problem is common to lentiviral libraries designed with linked variable regions. Here, we demonstrate that recombination between Perturb-seq vectors scrambles linked variable regions separated by 2 kb. This predicts information loss in Perturb-seq screens performed with co-packaged libraries. We also demonstrate ways to address this problem and discuss best practices for single-cell screens with transcriptional readouts. -
Western Equine Encephalitis Virus Is a Recombinant Virus (RNA Recombination/Alphavirus/Evolution of RNA Viruses) CHANG S
Proc. Natl. Acad. Sci. USA Vol. 85, pp. 5997-6001, August 1988 Evolution Western equine encephalitis virus is a recombinant virus (RNA recombination/Alphavirus/evolution of RNA viruses) CHANG S. HAHN, SHLOMO LUSTIG*, ELLEN G. STRAUSS, AND JAMES H. STRAUSSt Division of Biology, 156-29, California Institute of Technology, Pasadena, CA 91125 Communicated by James Bonner, April 14, 1988 ABSTRACT The alphaviruses are a group of 26 mosquito- virus; O'Nyong-nyong virus; and Ross River virus. Sindbis borne viruses that cause a variety of human diseases. Many of and Semliki Forest viruses have been intensively studied as the New World alphaviruses cause encephalitis, whereas the models for alphavirus replication (7). Sindbis virus is widely Old World viruses more typically cause fever, rash, and distributed, being found in Europe, India, southeast Asia, arthralgia. The genome is a single-stranded nonsegmented Australia, and Africa. Close relatives of this virus, such as RNA molecule of + polarity; it is about 11,700 nucleotides in Ockelbo virus in Europe (8) and Babanki virus in Africa, length. Several alphavirus genomes have been sequenced in cause disease in humans characterized by fever, rash, and whole or in part, and these sequences demonstrate that alpha- arthritis. Chikungunya and O'Nyong-nyong viruses have viruses have descended from a common ancestor by divergent caused large epidemics in Africa of a dengue-like disease also evolution. We have now obtained the sequence of the 3'- characterized by fever, rash, and arthralgia. Ross River virus terminal 4288 nucleotides of the RNA of the New World is the causative agent of epidemic polyarthritis in Australia Alphavirus western equine encephalitis virus (WEEV).