Inducibility of Lambda Phage Development in Escherichia
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The Genetic Material: DNA the Central Dogma of Genetics
The Genetic material: DNA The Central Dogma of Genetics DNA transcription Reverse tititranscriptio RNA n translation Protein • A, T, G, C in DNA • A, U, G, C in RNA • DNA is double stranded • DNA has po lar ity 5’ to 3’ • A T base pair, G C base pair • RNA is single stranded, also has polarity , generally referred as upstream and downstream. In RNA: A U base pair G C base pair. This type of base pa iri ng i n RNA causes secon dary st ruct ure. 1. 5’ vs 3’ 2. Purines vs. Pyrimidines 3. A vs. G 4. C vs. T 5. Transitions vs. transversions AT/GC ratios and their applications • Genome composition and chtitiharacterization • Implications in sequencing • Primer design • PCR yields • … The Polarity of DNA Higher order organization of genomes Most chromosomal DNA does not code for proteins or RNAs: e.g., Human genome 3 billion base pairs 25,000 genes x 2,000 bp per gene =5x10= 5 x 107 bp 5 x 107/3 x 109 = 1.67% MlMolecu lar P rob es: The tools of molecular genetics Concept of probes • “For diagnostic tests, the agent that is used to detect the presence of a molecule in the sample”. • “A DNA sequence that is used to detect the presence o f a comp lement ary sequence by hybridization with a nucleic acid sample”. Need for probes • Screen for the gene of interest • Southern blot to understand genomic structure and gene copy numbers • Northern blot for analysis of RNA expression • Verification of allelic amplification in PCR • .. -
1 Mechanistic Studies of DNA Replication, Lesion Bypass, And
Mechanistic Studies of DNA Replication, Lesion Bypass, and Editing Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Austin Tyler Raper, B.S. The Ohio State University Biochemistry Graduate Program The Ohio State University 2018 Dissertation Committee Dr. Zucai Suo, Advisor Dr. Ross Dalbey Dr. Michael Poirier Dr. Richard Swenson 1 Copyrighted by Austin Tyler Raper 2018 2 Abstract DNA acts as a molecular blueprint for life. Adenosine, cytidine, guanosine, and thymidine nucleotides serve as the building blocks of DNA and can be arranged in near- endless combinations. These unique sequences of DNA may encode genes that when expressed produce RNA, proteins, and enzymes responsible for executing diverse tasks necessary for biological existence. Accordingly, careful maintenance of the molecular integrity of DNA is paramount for the growth, development, and functioning of organisms. However, DNA is damaged upon reaction with pervasive chemicals generated by normal cellular metabolism or encountered through the environment. The resulting DNA lesions act as roadblocks to high-fidelity A- and B-family DNA polymerases responsible for replicating DNA in preparation for cell division which may lead to programmed cell death. Additionally, these lesions may fool the polymerase into making errors during DNA replication, leading to genetic mutations and cancer. Fortunately, the cell has evolved DNA damage tolerance as an emergency response to such lesions. During DNA damage tolerance, a damage-stalled high-fidelity polymerase is substituted for a specialized Y-family polymerase, capable of bypassing the offending DNA lesion, for replication to continue. -
A MUTYH Germline Mutation Is Associated with Small Intestinal
248 J P Dumanski et al. MUTYH substitution 24:8 427–443 Research Gly396Asp in SI-NETs Open Access A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors Jan P Dumanski1,*, Chiara Rasi1,*, Peyman Björklund2, Hanna Davies1, Abir S Ali3, Malin Grönberg3, Staffan Welin3, Halfdan Sorbye4,5, Henning Grønbæk6, Janet L Cunningham7, Lars A Forsberg1, Lars Lind8, Erik Ingelsson9, Peter Stålberg10, Per Hellman10 and Eva Tiensuu Janson3 1Department of Immunology, Genetics and Pathology and SciLifeLab, Uppsala University, Uppsala, Sweden 2Department of Surgical Sciences, Experimental Surgery, Uppsala University, Uppsala, Sweden 3Department of Medical Sciences, Endocrine Oncology, Uppsala University, Uppsala, Sweden 4Department of Oncology, Haukeland University Hospital, Bergen, Norway 5Department of Clinical Science, University of Bergen, Bergen, Norway 6Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark 7 Department of Neuroscience, Uppsala University, Uppsala, Sweden Correspondence 8 Department of Medical Sciences, Uppsala University, Uppsala, Sweden should be addressed 9 Division of Cardiovascular Medicine, Department of Medicine, Stanford University, San Francisco, California, USA to E Tiensuu Janson 10 Department of Surgical Sciences, Endocrine Surgery, Uppsala University, Uppsala, Sweden Email *(J P Dumanski and C Rasi shared first co-authorship) eva.tiensuu_janson@medsci. uu.se Abstract The genetics behind predisposition to small intestinal neuroendocrine tumors (SI-NETs) Key Words Endocrine-Related Cancer Endocrine-Related is largely unknown, but there is growing awareness of a familial form of the disease. f familial cancer We aimed to identify germline mutations involved in the carcinogenesis of SI-NETs. f cancer predisposition The strategy included next-generation sequencing of exome- and/or whole-genome of f small intestinal carcinoid blood DNA, and in selected cases, tumor DNA, from 24 patients from 15 families with f oxidative stress the history of SI-NETs. -
Distinct Co-Evolution Patterns of Genes Associated to DNA Polymerase III Dnae and Polc Stefan Engelen1,2, David Vallenet2, Claudine Médigue2 and Antoine Danchin1,3*
Engelen et al. BMC Genomics 2012, 13:69 http://www.biomedcentral.com/1471-2164/13/69 RESEARCHARTICLE Open Access Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC Stefan Engelen1,2, David Vallenet2, Claudine Médigue2 and Antoine Danchin1,3* Abstract Background: Bacterial genomes displaying a strong bias between the leading and the lagging strand of DNA replication encode two DNA polymerases III, DnaE and PolC, rather than a single one. Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase. Results: Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with dnaE and polC. Clusters were highly informative. DnaE co-evolves with the ribosome, the transcription machinery, the core of intermediary metabolism enzymes. It is also connected to the energy-saving enzyme necessary for RNA degradation, polynucleotide phosphorylase. Most of the proteins of this co-evolving set belong to the persistent set in bacterial proteomes, that is fairly ubiquitously distributed. In contrast, PolC co- evolves with RNA degradation enzymes that are present only in the A+T-rich Firmicutes clade, suggesting at least two origins for the degradosome. Conclusion: DNA replication involves two machineries, DnaE and PolC. DnaE co-evolves with the core functions of bacterial life. In contrast PolC co-evolves with a set of RNA degradation enzymes that does not derive from the degradosome identified in gamma-Proteobacteria. This suggests that at least two independent RNA degradation pathways existed in the progenote community at the end of the RNA genome world. -
Conversion of OX174 and Fd Single-Stranded DNA to Replicative Forms in Extracts of Escherichia Coli (Dnac, Dnad, and Dnag Gene Products/DNA Polymerase III) REED B
Proc. Nat. Acad. Sci. USA Vol. 69, No. 11, pp. 3233-3237, November 1972 Conversion of OX174 and fd Single-Stranded DNA to Replicative Forms in Extracts of Escherichia coli (dnaC, dnaD, and dnaG gene products/DNA polymerase III) REED B. WICKNER, MICHEL WRIGHT, SUE WICKNER, AND JERARD HURWITZ Department of Developmental Biology and Cancer, Division of Biological Sciences, Albert Einstein College of Medicine, Bronx, New York 10461 Communicated by Harry Eagle, August 28, 1972 ABSTRACT 4X174 and M13 (fd) single-stranded cir- MATERIALS AND METHODS cular DNAs are converted to their replicative forms by ex- tracts of E. coli pol Al cells. We find that the qX174 DNA- [a-32P]dTTP was obtained from New England Nuclear Corp. dependent reaction requires Mg++, ATP, and all four de- OX174 DNA was prepared by the method of Sinsheimer (7) oxynucleoside triphosphates, but not CTP, UTP, or GTP. or Franke and Ray (8), while fd viral DNA was prepared as This reaction also involves the products of the dnaC, dnaD, dnaE (DNA polymerase III), and dnaG genes, described (9). Pancreatic RNase was the highest grade ob- but not that of dnaF (ribonucleotide reductase). The in tainable from Worthington Biochemical Corp. It was further vitro conversion of fd single-stranded DNA to the replica- freed of possible contaminating DNase by heating a solution tive form requires all four ribonucleoside triphosphates, (2 mg/ml in 15 mM sodium citrate, pH 5) at 800 for 10 min. Mg++, and all four deoxynucleoside triphosphates. The E. protein was purified from E. coli strain reaction involves the product of gene dnaE but not those coli unwinding of genes dnaC, dnaD, dnaF, or dnaG. -
Consequences and Resolution of Transcription–Replication Conflicts
life Review Consequences and Resolution of Transcription–Replication Conflicts Maxime Lalonde †, Manuel Trauner †, Marcel Werner † and Stephan Hamperl * Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, 81377 Munich, Germany; [email protected] (M.L.); [email protected] (M.T.); [email protected] (M.W.) * Correspondence: [email protected] † These authors contributed equally. Abstract: Transcription–replication conflicts occur when the two critical cellular machineries respon- sible for gene expression and genome duplication collide with each other on the same genomic location. Although both prokaryotic and eukaryotic cells have evolved multiple mechanisms to coordinate these processes on individual chromosomes, it is now clear that conflicts can arise due to aberrant transcription regulation and premature proliferation, leading to DNA replication stress and genomic instability. As both are considered hallmarks of aging and human diseases such as cancer, understanding the cellular consequences of conflicts is of paramount importance. In this article, we summarize our current knowledge on where and when collisions occur and how these en- counters affect the genome and chromatin landscape of cells. Finally, we conclude with the different cellular pathways and multiple mechanisms that cells have put in place at conflict sites to ensure the resolution of conflicts and accurate genome duplication. Citation: Lalonde, M.; Trauner, M.; Keywords: transcription–replication conflicts; genomic instability; R-loops; torsional stress; common Werner, M.; Hamperl, S. fragile sites; early replicating fragile sites; replication stress; chromatin; fork reversal; MIDAS; G-MiDS Consequences and Resolution of Transcription–Replication Conflicts. Life 2021, 11, 637. https://doi.org/ 10.3390/life11070637 1. -
The Functional Analysis of Yaba, Which Interacts with Dnaa and Regulates Initiation of Chromosome Replication in Bacillus Subtils
Genes Genet. Syst. (2008) 83, p. 111–125 The functional analysis of YabA, which interacts with DnaA and regulates initiation of chromosome replication in Bacillus subtils Eunha Cho, Naotake Ogasawara and Shu Ishikawa* Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan (Received 15 January 2008, accepted 1 February 2008) The initiation of bacterial chromosome DNA replication and its regulation are critical events. DnaA is essential for initiation of DNA replication and is con- served throughout bacteria. In Escherichia coli, hydrolysis of ATP-DnaA is pro- moted by Hda through formation of a ternary complex with DnaA and DnaN, ensuring the timely inactivation of DnaA during the replication cycle. In Bacillus subtilis, YabA also forms a ternary complex with DnaA and DnaN, and negatively regulates the initiation step of DNA replication. However, YabA shares no struc- tural homology with Hda and the regulatory mechanism itself has not been clarified. Here, in contrast to Hda, we observed that dnaA transcription was stable during under- and overexpression of YabA. ChAP-chip assays showed that the depletion of YabA did not affect DNA binding by DnaA. On the other hand, yeast two-hybrid analysis indicated that the DnaA ATP-binding domain interacts with YabA. Moreover, mutations in YabA interaction-deficient mutants, isolated by yeast two-hybrid analysis, are located at the back of the ATP-binding domain, whereas Hda is thought to interact with the ATP-binding pocket itself. The intro- duction into B. subtilis of a dnaAY144C mutation, which disabled the interaction with YabA but did not affect interactions either with DnaA itself or with DnaD, resulted in over-initiation and asynchronous initiation of replication and disabled the formation of YabA foci, further demonstrating that the amino acid on the oppo- site side to the ATP-binding pocket is important for YabA binding. -
Ordered Association of Helicase Loader Proteins with the Bacillus Subtilis Origin of Replication in Vivo
Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Smits, Wiep Klaas, Alexi I. Goranov, and Alan D. Grossman. “Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo.” Molecular Microbiology 75.2 (2010): 452–461. As Published http://dx.doi.org/10.1111/j.1365-2958.2009.06999.x Publisher Wiley Blackwell (Blackwell Publishing) Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/73616 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike 3.0 Detailed Terms http://creativecommons.org/licenses/by-nc-sa/3.0/ NIH Public Access Author Manuscript Mol Microbiol. Author manuscript; available in PMC 2011 January 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Mol Microbiol. 2010 January ; 75(2): 452±461. doi:10.1111/j.1365-2958.2009.06999.x. Ordered association of helicase loader proteins with the Bacillus subtilis origin of replication in vivo Wiep Klaas Smits, Alexi I. Goranov, and Alan D. Grossman* Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 Summary The essential proteins DnaB, DnaD, and DnaI of Bacillus subtilis are required for initiation, but not elongation, of DNA replication, and for replication restart at stalled forks. The interactions and functions of these proteins have largely been determined in vitro based on their roles in replication restart. During replication initiation in vivo, it is not known if these proteins, and the replication initiator DnaA, associate with oriC independently of each other by virtue of their DNA binding activities, as a (sub)complex like other loader proteins, or in a particular dependent order. -
Mechanism of Staphylococcal Multiresistance Plasmid Replication Origin Assembly by the Repa Protein
Mechanism of staphylococcal multiresistance plasmid replication origin assembly by the RepA protein Maria A. Schumachera,1, Nam K. Tonthata, Stephen M. Kwongb, Naga babu Chinnama, Michael A. Liub, Ronald A. Skurrayb, and Neville Firthb aDepartment of Biochemistry, Duke University Medical Center, Durham, NC 27710; and bSchool of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia Edited by James M. Berger, The Johns Hopkins University School of Medicine, Baltimore, MD, and approved May 15, 2014 (received for review April 1, 2014) The staphylococcal multiresistance plasmids are key contributors (16). In Gram-negative bacteria the primosome includes DnaG to the alarming rise in bacterial multidrug resistance. A conserved primase, the replicative helicase (DnaB), and DnaC (17). Rep- replication initiator, RepA, encoded on these plasmids is essential lication initiation in Gram-positive bacteria involves DnaG pri- for their propagation. RepA proteins consist of flexibly linked mase and helicase (DnaC) and the proteins DnaD, DnaI, and N-terminal (NTD) and C-terminal (CTD) domains. Despite their essen- DnaB (18–22). DnaD binds first to DnaA at the origin. This is tial role in replication, the molecular basis for RepA function is followed by binding of DnaI/DnaB and DnaG, which together unknown. Here we describe a complete structural and functional recruit the replicative helicase (23, 24). Instead of DnaA, plas- dissection of RepA proteins. Unexpectedly, both the RepA NTD and mids encode and use their own specific replication initiator CTD show similarity to the corresponding domains of the bacterial binding protein. Structures are only available for RepA proteins primosome protein, DnaD. Although the RepA and DnaD NTD both (F, R6K, and pPS10 Rep) harbored in Gram-negative bacteria. -
The Primosomal Protein Dnad Inhibits Cooperative DNA Binding by the Replication Initiator Dnaa in Bacillus Subtilis
The primosomal protein DnaD inhibits cooperative DNA binding by the replication initiator DnaA in Bacillus subtilis The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Bonilla, C. Y., and A. D. Grossman. “The Primosomal Protein DnaD Inhibits Cooperative DNA Binding by the Replication Initiator DnaA in Bacillus Subtilis.” Journal of Bacteriology 194.18 (2012): 5110–5117. As Published http://dx.doi.org/10.1128/jb.00958-12 Publisher American Society for Microbiology Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/74629 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike 3.0 Detailed Terms http://creativecommons.org/licenses/by-nc-sa/3.0/ Bonilla and Grossman 1 1 2 The primosomal protein DnaD inhibits cooperative DNA binding by the 3 replication initiator DnaA in Bacillus subtilis 4 5 6 Carla Y. Bonilla and Alan D. Grossman* 7 Department of Biology 8 Massachusetts Institute of Technology 9 Cambridge, MA 02139 10 11 Running title: Primosomal protein DnaD affects DNA binding by DnaA 12 13 14 15 *Corresponding author: 16 Department of Biology 17 Building 68-530 18 Massachusetts Institute of Technology 19 Cambridge, MA 02139 20 phone: 617-253-1515 21 fax: 617-253-2643 22 E-mail: [email protected] 23 24 25 26 Bonilla and Grossman 2 27 Abstract 28 DnaA is a AAA+ ATPase and the conserved replication initiator in bacteria. Bacteria control 29 the timing of replication initiation by regulating the activity of DnaA. DnaA binds to multiple 30 sites in the origin of replication (oriC) and is required for recruitment of proteins needed to load 31 the replicative helicase. -
Regulation of Netrin-1 by P53 Isoforms Yan Sun
Regulation of Netrin-1 by p53 isoforms Yan Sun To cite this version: Yan Sun. Regulation of Netrin-1 by p53 isoforms. Cellular Biology. Université de Lyon, 2020. English. NNT : 2020LYSE1058. tel-03310180 HAL Id: tel-03310180 https://tel.archives-ouvertes.fr/tel-03310180 Submitted on 30 Jul 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. N°d’ordre NNT : 2020LYSE1058 THESE de DOCTORAT DE L’UNIVERSITE DE LYON opérée au sein de l’Université Claude Bernard Lyon 1 Ecole Doctorale ED 340 (Biologie Moléculaire Intégrative et Cellulaire) Spécialité de doctorat : Biologie Moléculaire et Cellulaire Soutenue publiquement le 24/03/2020, par : Yan SUN Régulation de la Nétrine-1 par les isoformes de p53 Devant le jury composé de : BERNET Agnès Professeure des Université de Lyon UMR5286 - Présidente Universités CRCL GAIDDON Christian Directeur de Recherche Université de Strasbourg - Rapporteur U1113 THIBERT Chantal Chargée de Recherche Institute for Advanced Rapporteur Biosciences – Grenoble U1209 - UMR5309 MARCEL Virginie Chargée de Recherche Université de -
Phenotypic Characterization of Self-Assembling
PHENOTYPIC CHARACTERIZATION OF SELF-ASSEMBLING PROTEIN FRAGMENTS USING NEGATIVE DOMINANCE A Dissertation by ADRIENNE ELIZABETH ZWEIFEL Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2010 Major Subject: Biochemistry PHENOTYPIC CHARACTERIZATION OF SELF-ASSEMBLING PROTEIN FRAGMENTS USING NEGATIVE DOMINANCE A Dissertation by ADRIENNE ELIZABETH ZWEIFEL Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, James C. Hu Committee Members, Michael Polymenis Donald W. Pettigrew Michael Benedik Head of Department, Gregory D. Reinhart May 2010 Major Subject: Biochemistry iii ABSTRACT Phenotypic Characterization of Self-Assembling Protein Fragments Using Negative Dominance. (May 2010) Adrienne Elizabeth Zweifel, B.S., University of Missouri-Columbia Chair of Advisory Committee: Dr. James C. Hu Protein oligomerization provides a way for cells to modulate function in vivo. In this study, self-assembling protein fragments from ParC, DnaX, and proteins of unknown function were used to generate phenotypes in a dominant negative manner. These fragments were expressed as Thioredoxin (TRX) fusions under the control of the inducible araBAD promoter. Fragments chosen contain only the oligomerization domain of the protein, lacking the regions necessary for catalytic function. Fragments of ParC, a subunit of Topoisomerase (Topo) IV, generated fragment-specific phenotypes. Regions that expressed both the oligomerization domain and CTD of ParC (ParC206-752 and ParC332-752) yielded filamentous cells with several different nucleoid segregation phenotypes. Another ParC fragment containing only the oligomerization domain of ParC (ranging from 333-485) yields a recA-dependent septation defect in a subset of the population.