1
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Bocanegra R, Ortíz-Rodríguez M, Zumeta L, Plaza-G A I, Faro E, Ibarra B. DNA replication machineries: Structural insights from crystallography and electron microscopy. Enzymes 2023; 54:249-271. [PMID: 37945174 DOI: 10.1016/bs.enz.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Since the discovery of DNA as the genetic material, scientists have been investigating how the information contained in this biological polymer is transmitted from generation to generation. X-ray crystallography, and more recently, cryo-electron microscopy techniques have been instrumental in providing essential information about the structure, functions and interactions of the DNA and the protein machinery (replisome) responsible for its replication. In this chapter, we highlight several works that describe the structure and structure-function relationships of the core components of the prokaryotic and eukaryotic replisomes. We also discuss the most recent studies on the structural organization of full replisomes.
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Affiliation(s)
| | | | - Lyra Zumeta
- IMDEA Nanociencia, Campus Cantoblanco, Madrid, Spain
| | | | - Elías Faro
- IMDEA Nanociencia, Campus Cantoblanco, Madrid, Spain
| | - Borja Ibarra
- IMDEA Nanociencia, Campus Cantoblanco, Madrid, Spain.
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2
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Kinetics of DNA strand transfer between polymerase and proofreading exonuclease active sites regulates error correction during high-fidelity replication. J Biol Chem 2022; 299:102744. [PMID: 36436560 PMCID: PMC9800556 DOI: 10.1016/j.jbc.2022.102744] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
We show that T7 DNA polymerase (pol) and exonuclease (exo) domains contribute to selective error correction during DNA replication by regulating bidirectional strand transfer between the two active sites. To explore the kinetic basis for selective removal of mismatches, we used a fluorescent cytosine analog (1,3-diaza-2-oxophenoxazine) to monitor the kinetics of DNA transfer between the exo and pol sites. We globally fit stopped-flow fluorescence and base excision kinetic data and compared results obtained with ssDNA versus duplex DNA to resolve how DNA transfer governs exo specificity. We performed parallel studies using hydrolysis-resistant phosphorothioate oligonucleotides to monitor DNA transfer to the exo site without hydrolysis. ssDNA binds to the exo site at the diffusion limit (109 M-1 s-1, Kd = 40 nM) followed by fast hydrolysis of the 3'-terminal nucleotide (>5000 s-1). Analysis using duplex DNA with a 3'-terminal mismatch or a buried mismatch exposed a unique intermediate state between pol and exo active sites and revealed that transfer via the intermediate to the exo site is stimulated by free nucleoside triphosphates. Transfer from the exo site back to the pol site after cleavage is fast and efficient. We propose a model to explain why buried mismatches are removed faster than single 3'-terminal mismatches and thereby provide an additional opportunity for error correction. Our data provide the first comprehensive model to explain how DNA transfer from pol to exo active sites and back again after base excision allow efficient selective mismatch removal during DNA replication to improve fidelity by more than 1000-fold.
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3
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Measuring the Complex Effects of the Single-Stranded DNA-Binding Protein gp2.5 on Primer Synthesis and Extension by the Bacteriophage T7 Replisome. Methods Mol Biol 2021; 2281:323-332. [PMID: 33847969 DOI: 10.1007/978-1-0716-1290-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The single-stranded DNA-binding protein gp2.5 of bacteriophage T7 plays myriad functions in the replication of phage genomes. In addition to interacting with ssDNA, gp2.5 binds to the T7 DNA polymerase and primase/helicase proteins, regulating their enzymatic activities. Here we describe in vitro methods to examine the effects of gp2.5 on primer synthesis and extension by the T7 replisome.
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4
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Geronimo I, Vidossich P, Donati E, Vivo M. Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Inacrist Geronimo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Elisa Donati
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Marco Vivo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
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5
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Luzon-Hidalgo R, Risso VA, Delgado A, Andrés-León E, Ibarra-Molero B, Sanchez-Ruiz JM. Evidence for a role of phenotypic mutations in virus adaptation. iScience 2021; 24:102257. [PMID: 33817569 PMCID: PMC8010470 DOI: 10.1016/j.isci.2021.102257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/22/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
Viruses interact extensively with the host molecular machinery, but the underlying mechanisms are poorly understood. Bacteriophage T7 recruits the small protein thioredoxin of the Escherichia coli host as an essential processivity factor for the viral DNA polymerase. We challenged the phage to propagate in a host in which thioredoxin had been extensively modified to hamper its recruitment. The virus adapted to the engineered host without losing the capability to propagate in the original host, but no genetic mutations were fixed in the thioredoxin binding domain of the viral DNA polymerase. Virus adaptation correlated with mutations in the viral RNA polymerase, supporting that promiscuous thioredoxin recruitment was enabled by phenotypic mutations caused by transcription errors. These results point to a mechanism of virus adaptation that may play a role in cross-species transmission. We propose that phenotypic mutations may generally contribute to the capability of viruses to evade antiviral strategies. Phage adapts to a host modified to hinder the essential recruitment of a host protein No genetic mutations are fixed at the engineered virus-host interaction interface Adaptation is likely linked to phenotypic mutations caused by transcription errors Sub-genomic RNAs may enable this kind of adaptation mechanism in coronaviruses
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Affiliation(s)
- Raquel Luzon-Hidalgo
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Valeria A Risso
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Asuncion Delgado
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Eduardo Andrés-León
- Unidad de Bioinformática. Instituto de Parasitología y Biomedicina "López Neyra", CSIC, Armilla, Granada 18016, Spain
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
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6
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Tandon H, de Brevern AG, Srinivasan N. Transient association between proteins elicits alteration of dynamics at sites far away from interfaces. Structure 2020; 29:371-384.e3. [PMID: 33306961 DOI: 10.1016/j.str.2020.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
Proteins are known to undergo structural changes upon binding to partner proteins. However, the prevalence, extent, location, and function of change in protein dynamics due to transient protein-protein interactions is not well documented. Here, we have analyzed a dataset of 58 protein-protein complexes of known three-dimensional structure and structures of their corresponding unbound forms to evaluate dynamics changes induced by binding. Fifty-five percent of cases showed significant dynamics change away from the interfaces. This change is not always accompanied by an observed structural change. Binding of protein partner is found to alter inter-residue communication within the tertiary structure in about 90% of cases. Also, residue motions accessible to proteins in unbound form were not always maintained in the bound form. Further analyses revealed functional roles for the distant site where dynamics change was observed. Overall, the results presented here strongly suggest that alteration of protein dynamics due to binding of a partner protein commonly occurs.
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Affiliation(s)
- Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, 75739 Paris, France; Univ Paris, UMR_S 1134, 75739 Paris, France; Institut National de la Transfusion Sanguine (INTS), 75739 Paris, France; Laboratoire d'Excellence GR-Ex, 75739 Paris, France
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7
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Engineering Stem Cell Factor Ligands with Different c-Kit Agonistic Potencies. Molecules 2020; 25:molecules25204850. [PMID: 33096693 PMCID: PMC7588011 DOI: 10.3390/molecules25204850] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are major players in signal transduction, regulating cellular activities in both normal regeneration and malignancy. Thus, many RTKs, c-Kit among them, play key roles in the function of both normal and neoplastic cells, and as such constitute attractive targets for therapeutic intervention. We thus sought to manipulate the self-association of stem cell factor (SCF), the cognate ligand of c-Kit, and hence its suboptimal affinity and activation potency for c-Kit. To this end, we used directed evolution to engineer SCF variants having different c-Kit activation potencies. Our yeast-displayed SCF mutant (SCFM) library screens identified altered dimerization potential and increased affinity for c-Kit by specific SCF-variants. We demonstrated the delicate balance between SCF homo-dimerization, c-Kit binding, and agonistic potencies by structural studies, in vitro binding assays and a functional angiogenesis assay. Importantly, our findings showed that a monomeric SCF variant exhibited superior agonistic potency vs. the wild-type SCF protein and vs. other high-affinity dimeric SCF variants. Our data showed that action of the monomeric ligands in binding to the RTK monomers and inducing receptor dimerization and hence activation was superior to that of the wild-type dimeric ligand, which has a higher affinity to RTK dimers but a lower activation potential. The findings of this study on the binding and c-Kit activation of engineered SCF variants thus provides insights into the structure–function dynamics of ligands and RTKs.
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8
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Rosenfeld L, Sananes A, Zur Y, Cohen S, Dhara K, Gelkop S, Ben Zeev E, Shahar A, Lobel L, Akabayov B, Arbely E, Papo N. Nanobodies Targeting Prostate-Specific Membrane Antigen for the Imaging and Therapy of Prostate Cancer. J Med Chem 2020; 63:7601-7615. [PMID: 32442375 PMCID: PMC7383930 DOI: 10.1021/acs.jmedchem.0c00418] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
The repertoire of
methods for the detection and chemotherapeutic
treatment of prostate cancer (PCa) is currently limited. Prostate-specific
membrane antigen (PSMA) is overexpressed in PCa tumors and can be
exploited for both imaging and drug delivery. We developed and characterized
four nanobodies that present tight and specific binding and internalization
into PSMA+ cells and that accumulate specifically in PSMA+ tumors. We then conjugated one of these nanobodies to the
cytotoxic drug doxorubicin, and we show that the conjugate internalizes
specifically into PSMA+ cells, where the drug is released
and induces cytotoxic activity. In vivo studies show
that the extent of tumor growth inhibition is similar when mice are
treated with commercial doxorubicin and with a 42-fold lower amount
of the nanobody-conjugated doxorubicin, attesting to the efficacy
of the conjugated drug. These data highlight nanobodies as promising
agents for the imaging of PCa tumors and for the targeted delivery
of chemotherapeutic drugs.
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Affiliation(s)
- Lior Rosenfeld
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Amiram Sananes
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Yuval Zur
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Shira Cohen
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Kalyan Dhara
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Sigal Gelkop
- Department of Virology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Efrat Ben Zeev
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Shahar
- The National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Leslie Lobel
- Department of Virology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Barak Akabayov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Eyal Arbely
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Niv Papo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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9
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Onn L, Portillo M, Ilic S, Cleitman G, Stein D, Kaluski S, Shirat I, Slobodnik Z, Einav M, Erdel F, Akabayov B, Toiber D. SIRT6 is a DNA double-strand break sensor. eLife 2020; 9:51636. [PMID: 31995034 PMCID: PMC7051178 DOI: 10.7554/elife.51636] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/23/2020] [Indexed: 12/18/2022] Open
Abstract
DNA double-strand breaks (DSB) are the most deleterious type of DNA damage. In this work, we show that SIRT6 directly recognizes DNA damage through a tunnel-like structure that has high affinity for DSB. SIRT6 relocates to sites of damage independently of signaling and known sensors. It activates downstream signaling for DSB repair by triggering ATM recruitment, H2AX phosphorylation and the recruitment of proteins of the homologous recombination and non-homologous end joining pathways. Our findings indicate that SIRT6 plays a previously uncharacterized role as a DNA damage sensor, a critical factor in initiating the DNA damage response (DDR). Moreover, other Sirtuins share some DSB-binding capacity and DDR activation. SIRT6 activates the DDR before the repair pathway is chosen, and prevents genomic instability. Our findings place SIRT6 as a sensor of DSB, and pave the road to dissecting the contributions of distinct DSB sensors in downstream signaling. DNA is a double-stranded molecule in which the two strands run in opposite directions, like the lanes on a two-lane road. Also like a road, DNA can be damaged by use and adverse conditions. Double-strand breaks – where both strands of DNA snap at once – are the most dangerous type of DNA damage, so cells have systems in place to rapidly detect and repair this kind of damage. There are three confirmed sensors for double-strand break in human cells. A fourth protein, known as SIRT6, arrives within five seconds of DNA damage, and was known to make the DNA more accessible so that it can be repaired. However, it was unclear whether SIRT6 could detect the double-strand break itself, or whether it was recruited to the damage by another double-strand break sensor. To address this issue, Onn et al. blocked the three other sensors in human cells and watched the response to DNA damage. Even when all the other sensors were inactive, SIRT6 still arrived at damaged DNA and activated the DNA damage response. To find out how SIRT6 sensed DNA damage, Onn et al. examined how purified SIRT6 interacts with different kinds of DNA. This revealed that SIRT6 sticks to broken DNA ends, especially if the end of one strand slightly overhangs the other – a common feature of double-strand breaks. A closer look at the structure of the SIRT6 protein revealed that it contains a narrow tube, which fits over the end of one broken DNA strand. When both strands break at once, two SIRT6 molecules cap the broken ends, joining together to form a pair. This pair not only protects the open ends of the DNA from further damage, it also sends signals to initiating repairs. In this way, SIRT6 could be thought of acting like a paramedic who arrives first on the scene of an accident and works to treat the injured while waiting for more specialized help to arrive. Understanding the SIRT6 sensor could improve knowledge about how cells repair their DNA. SIRT6 arrives before the cell chooses how to fix its broken DNA, so studying it further could reveal how that critical decision happens. This is important for medical research because DNA damage builds up in age-related diseases like cancer and neurodegeneration. In the long term, these findings can help us develop new treatments that target different types of DNA damage sensors.
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Affiliation(s)
- Lior Onn
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Miguel Portillo
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stefan Ilic
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gal Cleitman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Stein
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shai Kaluski
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ido Shirat
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Zeev Slobodnik
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Monica Einav
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ), BioQuant, Heidelberg, Germany.,Centre de Biologie Intégrative, CNRS UPS, Toulouse, France
| | - Barak Akabayov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Debra Toiber
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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10
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Yang EJ, Yoo CY, Liu J, Wang H, Cao J, Li FW, Pryer KM, Sun TP, Weigel D, Zhou P, Chen M. NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches. Nat Commun 2019; 10:2630. [PMID: 31201314 PMCID: PMC6570768 DOI: 10.1038/s41467-019-10517-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/17/2019] [Indexed: 12/30/2022] Open
Abstract
Phytochromes initiate chloroplast biogenesis by activating genes encoding the photosynthetic apparatus, including photosynthesis-associated plastid-encoded genes (PhAPGs). PhAPGs are transcribed by a bacterial-type RNA polymerase (PEP), but how phytochromes in the nucleus activate chloroplast gene expression remains enigmatic. We report here a forward genetic screen in Arabidopsis that identified NUCLEAR CONTROL OF PEP ACTIVITY (NCP) as a necessary component of phytochrome signaling for PhAPG activation. NCP is dual-targeted to plastids and the nucleus. While nuclear NCP mediates the degradation of two repressors of chloroplast biogenesis, PIF1 and PIF3, NCP in plastids promotes the assembly of the PEP complex for PhAPG transcription. NCP and its paralog RCB are non-catalytic thioredoxin-like proteins that diverged in seed plants to adopt nonredundant functions in phytochrome signaling. These results support a model in which phytochromes control PhAPG expression through light-dependent double nuclear and plastidial switches that are linked by evolutionarily conserved and dual-localized regulatory proteins. Phytochrome signaling in the nucleus can activate expression of photosynthesis-associated genes in plastids. Here Yang et al. show that NCP is a dual-targeted protein that promotes phytochrome B localization to photobodies in the nucleus while facilitating PEP polymerase assembly in the plastids.
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Affiliation(s)
- Emily J Yang
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.,Department of Biology, Duke University, Durham, NC, 27708, USA.,Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Chan Yul Yoo
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Jiangxin Liu
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA.,State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China
| | - He Wang
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Jun Cao
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, NC, 27708, USA.,Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | | | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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11
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Lee SJ, Tran NQ, Lee J, Richardson CC. Hydrophobic Residue in Escherichia coli Thioredoxin Critical for the Processivity of T7 DNA Polymerase. Biochemistry 2018; 57:5807-5817. [DOI: 10.1021/acs.biochem.8b00341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seung-Joo Lee
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ngoc Q. Tran
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joseph Lee
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Charles C. Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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12
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Magill DJ, McGrath JW, O'Flaherty V, Quinn JP, Kulakov LA. Insights into the structural dynamics of the bacteriophage T7 DNA polymerase and its complexes. J Mol Model 2018; 24:144. [PMID: 29858666 PMCID: PMC5984650 DOI: 10.1007/s00894-018-3671-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 05/10/2018] [Indexed: 11/24/2022]
Abstract
The T7 DNA polymerase is dependent on the host protein thioredoxin (trx) for its processivity and fidelity. Using all-atom molecular dynamics, we demonstrate the specific interactions between trx and the T7 polymerase, and show that trx docking to its binding domain on the polymerase results in a significant level of stability and exposes a series of basic residues within the domain that interact with the phosphodiester backbone of the DNA template. We also characterize the nature of interactions between the T7 DNA polymerase and its DNA template. We show that the trx-binding domain acts as an intrinsic clamp, constraining the DNA via a two-step hinge motion, and characterize the interactions necessary for this to occur. Together, these insights provide a significantly improved understanding of the interactions responsible for highly processive DNA replication by T7 polymerase.
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Affiliation(s)
- Damian J Magill
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, H91 TK33, Ireland.
- School of Biological Sciences and Institute for Global Food Security, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland.
| | - John W McGrath
- School of Biological Sciences and Institute for Global Food Security, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences and Ryan Institute, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - John P Quinn
- School of Biological Sciences and Institute for Global Food Security, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
| | - Leonid A Kulakov
- School of Biological Sciences and Institute for Global Food Security, Medical Biology Centre, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
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13
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Afek A, Ilic S, Horton J, Lukatsky DB, Gordan R, Akabayov B. DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase. iScience 2018; 2:141-147. [PMID: 30428370 PMCID: PMC6136900 DOI: 10.1016/j.isci.2018.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 12/30/2017] [Accepted: 03/05/2018] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ariel Afek
- Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Stefan Ilic
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - John Horton
- Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - David B Lukatsky
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - Raluca Gordan
- Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA; Department of Computer Science, Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA.
| | - Barak Akabayov
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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14
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Increased Processivity, Misincorporation, and Nucleotide Incorporation Efficiency in Sulfolobus solfataricus Dpo4 Thumb Domain Mutants. Appl Environ Microbiol 2017; 83:AEM.01013-17. [PMID: 28710267 DOI: 10.1128/aem.01013-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/04/2017] [Indexed: 01/21/2023] Open
Abstract
The present study aimed to increase the processivity of Sulfolobus solfataricus DNA polymerase Dpo4. Protein engineering and bioinformatics were used to compile a library of potential Dpo4 mutation sites. Ten potential mutants were identified and constructed. A primer extension assay was used to evaluate the processivity of Dpo4 mutants. Thumb (A181D) and finger (E63K) domain mutants showed a processivity of 20 and 19 nucleotides (nt), respectively. A little finger domain mutant (I248Y) exhibited a processivity of 17 nt, only 1 nt more than wild-type Dpo4. Furthermore, the A181D mutant showed lower fidelity and higher nucleotide incorporation efficiency (4.74 × 10-4 s-1 μM-1) than E63K and I248Y mutants. When tasked with bypassing damage, the A181D mutant exhibited a 3.81-fold and 2.62-fold higher catalytic efficiency (kcat/Km ) at incorporating dCTP and dATP, respectively, than wild-type Dpo4. It also showed a 55% and 91.5% higher catalytic efficiency when moving beyond the damaged 8-oxoG:C and 8-oxoG:A base pairs, respectively, compared to wild-type Dpo4. Protein engineering and bioinformatics methods can effectively increase the processivity and translesion synthesis ability of Dpo4.IMPORTANCE DNA polymerases with poor fidelity can be exploited to store data and record changes in response to the intracellular environment. Sulfolobus solfataricus Dpo4 is such an enzyme, although its use is hindered by its low processivity. In this work, we used a bioinformatics and protein engineering approach to generate Dpo4 mutants with improved processivity. We identified the Dpo4 thumb domain as the most relevant in controlling processivity.
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15
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Engineering a monomeric variant of macrophage colony-stimulating factor (M-CSF) that antagonizes the c-FMS receptor. Biochem J 2017; 474:2601-2617. [PMID: 28655719 DOI: 10.1042/bcj20170276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 11/17/2022]
Abstract
Enhanced activation of the signaling pathways that mediate the differentiation of mononuclear monocytes into osteoclasts is an underlying cause of several bone diseases and bone metastasis. In particular, dysregulation and overexpression of macrophage colony-stimulating factor (M-CSF) and its c-FMS tyrosine kinase receptor, proteins that are essential for osteoclast differentiation, are known to promote bone metastasis and osteoporosis, making both the ligand and its receptor attractive targets for therapeutic intervention. With this aim in mind, our starting point was the previously held concept that the potential of the M-CSFC31S mutant as a therapeutic is derived from its inability to dimerize and hence to act as an agonist. The current study showed, however, that dimerization is not abolished in M-CSFC31S and that the protein retains agonistic activity toward osteoclasts. To design an M-CSF mutant with diminished dimerization capabilities, we solved the crystal structure of the M-CSFC31S dimer complex and used structure-based energy calculations to identify the residues responsible for its dimeric form. We then used that analysis to develop M-CSFC31S,M27R, a ligand-based, high-affinity antagonist for c-FMS that retained its binding ability but prevented the ligand dimerization that leads to receptor dimerization and activation. The monomeric properties of M-CSFC31S,M27R were validated using dynamic light scattering and small-angle X-ray scattering analyses. It was shown that this mutant is a functional inhibitor of M-CSF-dependent c-FMS activation and osteoclast differentiation in vitro Our study, therefore, provided insights into the sequence-structure-function relationships of the M-CSF/c-FMS interaction and of ligand/receptor tyrosine kinase interactions in general.
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16
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DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase. Sci Rep 2017; 7:4756. [PMID: 28684739 PMCID: PMC5500549 DOI: 10.1038/s41598-017-02578-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/12/2017] [Indexed: 11/09/2022] Open
Abstract
DNA polymerase (pol) processivity, i.e., the bases a polymerase extends before falling off the DNA, and activity are important for copying difficult DNA sequences, including simple repeats. Y-family pols would be appealing for copying difficult DNA and incorporating non-natural dNTPs, due to their low fidelity and loose active site, but are limited by poor processivity and activity. In this study, the binding between Dbh and DNA was investigated to better understand how to rationally design enhanced processivity in a Y-family pol. Guided by structural simulation, a fused pol Sdbh with non-specific dsDNA binding protein Sso7d in the N-terminus was designed. This modification increased in vitro processivity 4-fold as compared to the wild-type Dbh. Additionally, bioinformatics was used to identify amino acid mutations that would increase stabilization of Dbh bound to DNA. The variant SdbhM76I further improved the processivity of Dbh by 10 fold. The variant SdbhKSKIP241–245RVRKS showed higher activity than Dbh on the incorporation of dCTP (correct) and dATP (incorrect) opposite the G (normal) or 8-oxoG(damaged) template base. These results demonstrate the capability to rationally design increases in pol processivity and catalytic efficiency through computational DNA binding predictions and the addition of non-specific DNA binding domains.
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17
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Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance. Cell Rep 2017; 19:1247-1256. [DOI: 10.1016/j.celrep.2017.04.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 02/14/2017] [Accepted: 04/13/2017] [Indexed: 11/17/2022] Open
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18
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Cryo-EM structure of the replisome reveals multiple interactions coordinating DNA synthesis. Proc Natl Acad Sci U S A 2017; 114:E1848-E1856. [PMID: 28223502 DOI: 10.1073/pnas.1701252114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We present a structure of the ∼650-kDa functional replisome of bacteriophage T7 assembled on DNA resembling a replication fork. A structure of the complex consisting of six domains of DNA helicase, five domains of RNA primase, two DNA polymerases, and two thioredoxin (processivity factor) molecules was determined by single-particle cryo-electron microscopy. The two molecules of DNA polymerase adopt a different spatial arrangement at the replication fork, reflecting their roles in leading- and lagging-strand synthesis. The structure, in combination with biochemical data, reveals molecular mechanisms for coordination of leading- and lagging-strand synthesis. Because mechanisms of DNA replication are highly conserved, the observations are relevant to other replication systems.
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19
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Chang HW, Pandey M, Kulaeva OI, Patel SS, Studitsky VM. Overcoming a nucleosomal barrier to replication. SCIENCE ADVANCES 2016; 2:e1601865. [PMID: 27847876 PMCID: PMC5106197 DOI: 10.1126/sciadv.1601865] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/11/2016] [Indexed: 05/05/2023]
Abstract
Efficient overcoming and accurate maintenance of chromatin structure and associated histone marks during DNA replication are essential for normal functioning of the daughter cells. However, the molecular mechanisms of replication through chromatin are unknown. We have studied traversal of uniquely positioned mononucleosomes by T7 replisome in vitro. Nucleosomes present a strong, sequence-dependent barrier for replication, with particularly strong pausing of DNA polymerase at the +(31-40) and +(41-65) regions of the nucleosomal DNA. The exonuclease activity of T7 DNA polymerase increases the overall rate of progression of the replisome through a nucleosome, likely by resolving nonproductive complexes. The presence of nucleosome-free DNA upstream of the replication fork facilitates the progression of DNA polymerase through the nucleosome. After replication, at least 50% of the nucleosomes assume an alternative conformation, maintaining their original positions on the DNA. Our data suggest a previously unpublished mechanism for nucleosome maintenance during replication, likely involving transient formation of an intranucleosomal DNA loop.
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Affiliation(s)
- Han-Wen Chang
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Manjula Pandey
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | | | - Smita S. Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Corresponding author. (S.S.P.); (V.M.S.)
| | - Vasily M. Studitsky
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Corresponding author. (S.S.P.); (V.M.S.)
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20
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Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers. Sci Rep 2016; 6:33257. [PMID: 27641327 PMCID: PMC5027553 DOI: 10.1038/srep33257] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 01/24/2023] Open
Abstract
Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.
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21
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Ganji M, Docter M, Le Grice SFJ, Abbondanzieri EA. DNA binding proteins explore multiple local configurations during docking via rapid rebinding. Nucleic Acids Res 2016; 44:8376-84. [PMID: 27471033 PMCID: PMC5041478 DOI: 10.1093/nar/gkw666] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/12/2016] [Indexed: 12/15/2022] Open
Abstract
Finding the target site and associating in a specific orientation are essential tasks for DNA-binding proteins. In order to make the target search process as efficient as possible, proteins should not only rapidly diffuse to the target site but also dynamically explore multiple local configurations before diffusing away. Protein flipping is an example of this second process that has been observed previously, but the underlying mechanism of flipping remains unclear. Here, we probed the mechanism of protein flipping at the single molecule level, using HIV-1 reverse transcriptase (RT) as a model system. In order to test the effects of long-range attractive forces on flipping efficiency, we varied the salt concentration and macromolecular crowding conditions. As expected, increased salt concentrations weaken the binding of RT to DNA while increased crowding strengthens the binding. Moreover, when we analyzed the flipping kinetics, i.e. the rate and probability of flipping, at each condition we found that flipping was more efficient when RT bound more strongly. Our data are consistent with a view that DNA bound proteins undergo multiple rapid re-binding events, or short hops, that allow the protein to explore other configurations without completely dissociating from the DNA.
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Affiliation(s)
- Mahipal Ganji
- Kavli Institute of Nanoscience, Department of Bionanoscience, TU Delft, 2629HZ, Delft, The Netherlands
| | - Margreet Docter
- Kavli Institute of Nanoscience, Department of Bionanoscience, TU Delft, 2629HZ, Delft, The Netherlands
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Elio A Abbondanzieri
- Kavli Institute of Nanoscience, Department of Bionanoscience, TU Delft, 2629HZ, Delft, The Netherlands
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22
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Lerner E, Ploetz E, Hohlbein J, Cordes T, Weiss S. A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET). J Phys Chem B 2016; 120:6401-10. [PMID: 27184889 PMCID: PMC4939467 DOI: 10.1021/acs.jpcb.6b03692] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Single-molecule,
protein-induced fluorescence enhancement (PIFE)
serves as a molecular ruler at molecular distances inaccessible to
other spectroscopic rulers such as Förster-type resonance energy
transfer (FRET) or photoinduced electron transfer. In order to provide
two simultaneous measurements of two distances on different molecular
length scales for the analysis of macromolecular complexes, we and
others recently combined measurements of PIFE and FRET (PIFE-FRET)
on the single molecule level. PIFE relies on steric hindrance of the
fluorophore Cy3, which is covalently attached to a biomolecule of
interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate.
In this work, we provide a theoretical framework that accounts for
relevant photophysical and kinetic parameters of PIFE-FRET, show how
this framework allows the extraction of the fold-decrease in isomerization
mobility from experimental data, and show how these results provide
information on changes in the accessible volume of Cy3. The utility
of this model is then demonstrated for experimental results on PIFE-FRET
measurement of different protein–DNA interactions. The proposed
model and extracted parameters could serve as a benchmark to allow
quantitative comparison of PIFE effects in different biological systems.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Evelyn Ploetz
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research , Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.,Microspectroscopy Centre, Wageningen University and Research , Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California Los Angeles , 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
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23
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Timm AC, Shankles PG, Foster CM, Doktycz MJ, Retterer ST. Toward Microfluidic Reactors for Cell-Free Protein Synthesis at the Point-of-Care. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:810-7. [PMID: 26690885 DOI: 10.1002/smll.201502764] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/14/2015] [Indexed: 05/04/2023]
Abstract
Cell-free protein synthesis (CFPS) is a powerful technology that allows for optimization of protein production without maintenance of a living system. Integrated within micro and nanofluidic architectures, CFPS can be optimized for point-of-care use. Here, the development of a microfluidic bioreactor designed to facilitate the production of a single-dose of a therapeutic protein, in a small footprint device at the point-of-care, is described. This new design builds on the use of a long, serpentine channel bioreactor and is enhanced by integrating a nanofabricated membrane to allow exchange of materials between parallel "reactor" and "feeder" channels. This engineered membrane facilitates the exchange of metabolites, energy, and inhibitory species, and can be altered by plasma-enhanced chemical vapor deposition and atomic layer deposition to tune the exchange rate of small molecules. This allows for extended reaction times and improved yields. Further, the reaction product and higher molecular weight components of the transcription/translation machinery in the reactor channel can be retained. It has been shown that the microscale bioreactor design produces higher protein yields than conventional tube-based batch formats, and that product yields can be dramatically improved by facilitating small molecule exchange within the dual-channel bioreactor.
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Affiliation(s)
- Andrea C Timm
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Peter G Shankles
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
- The University of Tennessee, Knoxville, TN, 37996, USA
| | - Carmen M Foster
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Mitchel J Doktycz
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
- The University of Tennessee, Knoxville, TN, 37996, USA
| | - Scott T Retterer
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
- The University of Tennessee, Knoxville, TN, 37996, USA
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24
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Velazquez G, Sousa R, Brieba LG. The thumb subdomain of yeast mitochondrial RNA polymerase is involved in processivity, transcript fidelity and mitochondrial transcription factor binding. RNA Biol 2016; 12:514-24. [PMID: 25654332 DOI: 10.1080/15476286.2015.1014283] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Single subunit RNA polymerases have evolved 2 mechanisms to synthesize long transcripts without falling off a DNA template: binding of nascent RNA and interactions with an RNA:DNA hybrid. Mitochondrial RNA polymerases share a common ancestor with T-odd bacteriophage single subunit RNA polymerases. Herein we characterized the role of the thumb subdomain of the yeast mtRNA polymerase gene (RPO41) in complex stability, processivity, and fidelity. We found that deletion and point mutants of the thumb subdomain of yeast mtRNA polymerase increase the synthesis of abortive transcripts and the probability that the polymerase will disengage from the template during the formation of the late initial transcription and elongation complexes. Mutations in the thumb subdomain increase the amount of slippage products from a homopolymeric template and, unexpectedly, thumb subdomain deletions decrease the binding affinity for mitochondrial transcription factor (Mtf1). The latter suggests that the thumb subdomain is part of an extended binding surface area involved in binding Mtf1.
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Affiliation(s)
- Gilberto Velazquez
- a Laboratorio Nacional de Genómica para la Biodiversidad ; Centro de Investigación y de Estudios ; Irapuato , Guanajuato , México
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25
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26
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Abstract
I spent my childhood and adolescence in North and South Carolina, attended Duke University, and then entered Duke Medical School. One year in the laboratory of George Schwert in the biochemistry department kindled my interest in biochemistry. After one year of residency on the medical service of Duke Hospital, chaired by Eugene Stead, I joined the group of Arthur Kornberg at Stanford Medical School as a postdoctoral fellow. Two years later I accepted a faculty position at Harvard Medical School, where I remain today. During these 50 years, together with an outstanding group of students, postdoctoral fellows, and collaborators, I have pursued studies on DNA replication. I have experienced the excitement of discovering a number of important enzymes in DNA replication that, in turn, triggered an interest in the dynamics of a replisome. My associations with industry have been stimulating and fostered new friendships. I could not have chosen a better career.
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Affiliation(s)
- Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115;
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27
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Abstract
A cell can be thought of as a highly sophisticated micro factory: in a pool of billions of molecules - metabolites, structural proteins, enzymes, oligonucleotides - multi-subunit complexes assemble to perform a large number of basic cellular tasks, such as DNA replication, RNA/protein synthesis or intracellular transport. By purifying single components and using them to reconstitute molecular processes in a test tube, researchers have gathered crucial knowledge about mechanistic, dynamic and structural properties of biochemical pathways. However, to sort this information into an accurate cellular road map, we need to understand reactions in their relevant context within the cellular hierarchy, which is at the individual molecule level within a crowded, cellular environment. Reactions occur in a stochastic fashion, have short-lived and not necessarily well-defined intermediates, and dynamically form functional entities. With the use of single-molecule techniques these steps can be followed and detailed kinetic information that otherwise would be hidden in ensemble averaging can be obtained. One of the first complex cellular tasks that have been studied at the single-molecule level is the replication of DNA. The replisome, the multi-protein machinery responsible for copying DNA, is built from a large number of proteins that function together in an intricate and efficient fashion allowing the complex to tolerate DNA damage, roadblocks or fluctuations in subunit concentration. In this review, we summarize advances in single-molecule studies, both in vitro and in vivo, that have contributed to our current knowledge of the mechanistic principles underlying DNA replication.
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Affiliation(s)
- S A Stratmann
- Zernike Institute for Advanced Materials, Centre for Synthetic Biology, University of Groningen, The Netherlands.
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28
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Zhu B. Bacteriophage T7 DNA polymerase - sequenase. Front Microbiol 2014; 5:181. [PMID: 24795710 PMCID: PMC3997047 DOI: 10.3389/fmicb.2014.00181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/01/2014] [Indexed: 11/29/2022] Open
Abstract
An ideal DNA polymerase for chain-terminating DNA sequencing should possess the following features: (1) incorporate dideoxy- and other modified nucleotides at an efficiency similar to that of the cognate deoxynucleotides; (2) high processivity; (3) high fidelity in the absence of proofreading/exonuclease activity; and (4) production of clear and uniform signals for detection. The DNA polymerase encoded by bacteriophage T7 is naturally endowed with or can be engineered to have all these characteristics. The chemically or genetically modified enzyme (Sequenase) expedited significantly the development of DNA sequencing technology. This article reviews the history of studies on T7 DNA polymerase with emphasis on the serial key steps leading to its use in DNA sequencing. Lessons from the study and development of T7 DNA polymerase have and will continue to enlighten the characterization of novel DNA polymerases from newly discovered microbes and their modification for use in biotechnology.
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Affiliation(s)
- Bin Zhu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Boston, MA, USA
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29
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Akabayov B, Akabayov SR, Lee SJ, Wagner G, Richardson CC. Impact of macromolecular crowding on DNA replication. Nat Commun 2013; 4:1615. [PMID: 23511479 PMCID: PMC3666333 DOI: 10.1038/ncomms2620] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 02/20/2013] [Indexed: 11/23/2022] Open
Abstract
Enzymatic activities in vivo occur in a crowded environment composed of
many macromolecules. This environment influences DNA replication by increasing the concentration of
the constituents, desolvation, decreasing the degrees of freedom for diffusion and hopping of
proteins onto DNA, and enhancing binding equilibria and catalysis. However, the effect of
macromolecular crowding on protein structure is poorly understood. Here we examine macromolecular
crowding using the replication system of bacteriophage T7 and we show that it affects several
aspects of DNA replication; the activity of DNA helicase increases and the sensitivity of DNA
polymerase to salt is reduced. We also demonstrate, using SAXS analysis, that the complex between
DNA helicase and DNA polymerase/trx is far more compact in a crowded environment. The highest
enzymatic activity corresponds to the most compact structure. Better knowledge of the effect of
crowding on structure and activity will enhance mechanistic insight beyond information obtained from
NMR and X-ray structures.
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Affiliation(s)
- Barak Akabayov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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30
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Geertsema HJ, van Oijen AM. A single-molecule view of DNA replication: the dynamic nature of multi-protein complexes revealed. Curr Opin Struct Biol 2013; 23:788-93. [PMID: 23890728 DOI: 10.1016/j.sbi.2013.06.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 06/21/2013] [Indexed: 01/31/2023]
Abstract
Recent advances in the development of single-molecule approaches have made it possible to study the dynamics of biomolecular systems in great detail. More recently, such tools have been applied to study the dynamic nature of large multi-protein complexes that support multiple enzymatic activities. In this review, we will discuss single-molecule studies of the replisome, the protein complex responsible for the coordinated replication of double-stranded DNA. In particular, we will focus on new insights obtained into the dynamic nature of the composition of the DNA-replication machinery and how the dynamic replacement of components plays a role in the regulation of the DNA-replication process.
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Affiliation(s)
- Hylkje J Geertsema
- Zernike Institute for Advanced Materials, Centre for Synthetic Biology, University of Groningen, 9747 AG Groningen, The Netherlands
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31
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Akabayov SR, Akabayov B, Richardson CC, Wagner G. Molecular crowding enhanced ATPase activity of the RNA helicase eIF4A correlates with compaction of its quaternary structure and association with eIF4G. J Am Chem Soc 2013; 135:10040-7. [PMID: 23767688 DOI: 10.1021/ja404404h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymatic reactions occur in a crowded and confined environment in vivo, containing proteins, RNA and DNA. Previous reports have shown that interactions between macromolecules, and reactions rates differ significantly between crowded environments and dilute buffers. However, the direct effect of crowding on the level of high-resolution structures of macromolecules has not been extensively analyzed and is not well understood. Here we analyze the effect of macromolecular crowding on structure and function of the human translation initiation factors eIF4A, a two-domain DEAD-Box helicase, the HEAT-1 domain of eIF4G, and their complex. We find that crowding enhances the ATPase activity of eIF4A, which correlates with a shift to a more compact structure as revealed with small-angle X-ray scattering. However, the individual domains of eIF4A, or the eIF4G-HEAT-1 domain alone show little structural changes due to crowding except for flexible regions. Thus, the effect of macromolecular crowding on activity and structure need to be taken into account when evaluating enzyme activities and structures of multidomain proteins, proteins with flexible regions, or protein complexes obtained by X-ray crystallography, NMR, or other structural methods.
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Affiliation(s)
- Sabine R Akabayov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
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32
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Abstract
Moonlighting--the performance of more than one function by a single protein--is becoming recognized as a common phenomenon with important implications for systems biology and human health. The different functions of a moonlighting protein may use different regions of the protein structure, or alternative structures that occur due to post-translational modifications and/or differences in binding partners. Often the different functions of moonlighting proteins are used at different times or in different places. The existence of moonlighting functions complicates efforts to understand metabolic and regulatory networks, as well as physiological and pathological processes in organisms. Because moonlighting functions can play important roles in disease processes, an improved understanding of moonlighting proteins will provide new opportunities for pharmacological manipulations that specifically target a function involved in pathology while sparing physiologically important functions.
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Affiliation(s)
- Shelley D Copley
- Department of Molecular, Cellular and Developmental Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.
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Tran NQ, Lee SJ, Akabayov B, Johnson DE, Richardson CC. Thioredoxin, the processivity factor, sequesters an exposed cysteine in the thumb domain of bacteriophage T7 DNA polymerase. J Biol Chem 2012; 287:39732-41. [PMID: 23012374 DOI: 10.1074/jbc.m112.409235] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Gene 5 protein (gp5) of bacteriophage T7 is a non-processive DNA polymerase. It achieves processivity by binding to Escherichia coli thioredoxin (trx). gp5/trx complex binds tightly to a primer-DNA template enabling the polymerization of hundreds of nucleotides per binding event. gp5 contains 10 cysteines. Under non-reducing condition, exposed cysteines form intermolecular disulfide linkages resulting in the loss of polymerase activity. No disulfide linkage is detected when Cys-275 and Cys-313 are replaced with serines. Cys-275 and Cys-313 are located on loop A and loop B of the thioredoxin binding domain, respectively. Replacement of either cysteine with serine (gp5-C275S, gp5-C313S) drastically decreases polymerase activity of gp5 on dA(350)/dT(25). On this primer-template gp5/trx in which Cys-313 or Cys-275 is replaced with serine have 50 and 90%, respectively, of the polymerase activity observed with wild-type gp5/trx. With single-stranded M13 DNA as a template gp5-C275S/trx retains 60% of the polymerase activity of wild-type gp5/trx. In contrast, gp5-C313S/trx has only one-tenth of the polymerase activity of wild-type gp5/trx on M13 DNA. Both wild-type gp5/trx and gp5-C275S/trx catalyze the synthesis of the entire complementary strand of M13 DNA, whereas gp5-C313S/trx has difficulty in synthesizing DNA through sites of secondary structure. gp5-C313S fails to form a functional complex with trx as measured by the apparent binding affinity as well as by the lack of a physical interaction with thioredoxin during hydroxyapatite-phosphate chromatography. Small angle x-ray scattering reveals an elongated conformation of gp5-C313S in comparison to a compact and spherical conformation of wild-type gp5.
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Affiliation(s)
- Ngoc Q Tran
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Kulczyk AW, Akabayov B, Lee SJ, Bostina M, Berkowitz SA, Richardson CC. An interaction between DNA polymerase and helicase is essential for the high processivity of the bacteriophage T7 replisome. J Biol Chem 2012; 287:39050-60. [PMID: 22977246 DOI: 10.1074/jbc.m112.410647] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Synthesis of the leading DNA strand requires the coordinated activity of DNA polymerase and DNA helicase, whereas synthesis of the lagging strand involves interactions of these proteins with DNA primase. We present the first structural model of a bacteriophage T7 DNA helicase-DNA polymerase complex using a combination of small angle x-ray scattering, single-molecule, and biochemical methods. We propose that the protein-protein interface stabilizing the leading strand synthesis involves two distinct interactions: a stable binding of the helicase to the palm domain of the polymerase and an electrostatic binding of the carboxyl-terminal tail of the helicase to a basic patch on the polymerase. DNA primase facilitates binding of DNA helicase to ssDNA and contributes to formation of the DNA helicase-DNA polymerase complex by stabilizing DNA helicase.
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Affiliation(s)
- Arkadiusz W Kulczyk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard University Medical School, Boston, Massachusetts 02115, USA
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Zhang H, Lee SJ, Kulczyk AW, Zhu B, Richardson CC. Heterohexamer of 56- and 63-kDa Gene 4 Helicase-Primase of Bacteriophage T7 in DNA Replication. J Biol Chem 2012; 287:34273-87. [PMID: 22887996 DOI: 10.1074/jbc.m112.401158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteriophage T7 expresses two forms of gene 4 protein (gp4). The 63-kDa full-length gp4 contains both the helicase and primase domains. T7 phage also express a 56-kDa truncated gp4 lacking the zinc binding domain of the primase; the protein has helicase activity but no DNA-dependent primase activity. Although T7 phage grow better when both forms are present, the role of the 56-kDa gp4 is unknown. The two molecular weight forms oligomerize by virtue of the helicase domain to form heterohexamers. The 56-kDa gp4 and any mixture of 56- and 63-kDa gp4 show higher helicase activity in DNA unwinding and strand-displacement DNA synthesis than that observed for the 63-kDa gp4. However, single-molecule measurements show that heterohexamers have helicase activity similar to the 63-kDa gp4 hexamers. In oligomerization assays the 56-kDa gp4 and any mixture of the 56- and 63-kDa gp4 oligomerize to form more hexamers than does the 63-kDa gp4. The zinc binding domain of the 63-kDa gp4 interferes with hexamer formation, an inhibition that is relieved by the insertion of the 56-kDa species. Compared with the 63-kDa gp4, heterohexamers synthesize a reduced amount of oligoribonucleotides, mediated predominately by the 63-kDa subunits via a cis mode. During coordinated DNA synthesis 7% of the tetraribonucleotides synthesized are used as primers by both heterohexamers and hexamers of the 63-kDa gp4. Overall, an equimolar mixture of the two forms of gp4 shows the highest rate of DNA synthesis during coordinated DNA synthesis.
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Affiliation(s)
- Huidong Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Abstract
The lagging-strand DNA polymerase requires an oligoribonucleotide, synthesized by DNA primase, to initiate the synthesis of an Okazaki fragment. In the replication system of bacteriophage T7 both DNA primase and DNA helicase activities are contained within a single protein, the bifunctional gene 4 protein (gp4). Intermolecular interactions between gp4 and T7 DNA polymerase are crucial for the stabilization of the oligoribonucleotide, its transfer to the polymerase, and its extension by DNA polymerase. We have identified conditions necessary to assemble the T7 priming complex and characterized its biophysical properties using fluorescence anisotropy. In order to reveal molecular interactions that occur during delivery of the oligoribonucleotide to DNA polymerase, we have used four genetically altered gp4 to demonstrate that both the RNA polymerase and the zinc-finger domains of DNA primase are involved in the stabilization of the priming complex and in sequence recognition in the DNA template. We find that the helicase domain of gp4 contributes to the stability of the complex by binding to the ssDNA template. The C-terminal tail of gp4 is not required for complex formation.
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Choreography of bacteriophage T7 DNA replication. Curr Opin Chem Biol 2011; 15:580-6. [PMID: 21907611 DOI: 10.1016/j.cbpa.2011.07.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 07/25/2011] [Accepted: 07/27/2011] [Indexed: 11/21/2022]
Abstract
The replication system of phage T7 provides a model for DNA replication. Biochemical, structural, and single-molecule analyses together provide insight into replisome mechanics. A complex of polymerase, a processivity factor, and helicase mediates leading strand synthesis. Establishment of the complex requires an interaction of the C-terminal tail of the helicase with the polymerase. During synthesis the complex is stabilized by other interactions to provide for a processivity of 5 kilobase (kb). The C-terminal tail also interacts with a distinct region of the polymerase to captures dissociating polymerase to increase the processivity to >17kb. The lagging strand is synthesized discontinuously within a loop that forms and resolves during each cycle of Okazaki fragment synthesis. The synthesis of a primer as well as the termination of a fragment signal loop resolution.
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Akabayov B, Kulczyk AW, Akabayov SR, Theile C, McLaughlin LW, Beauchamp B, van Oijen AM, Richardson CC. Pyrovanadolysis, a pyrophosphorolysis-like reaction mediated by pyrovanadate, Mn2+, and DNA polymerase of bacteriophage T7. J Biol Chem 2011; 286:29146-29157. [PMID: 21697085 DOI: 10.1074/jbc.m111.250944] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerases catalyze the 3'-5'-pyrophosphorolysis of a DNA primer annealed to a DNA template in the presence of pyrophosphate (PP(i)). In this reversal of the polymerization reaction, deoxynucleotides in DNA are converted to deoxynucleoside 5'-triphosphates. Based on the charge, size, and geometry of the oxygen connecting the two phosphorus atoms of PP(i), a variety of compounds was examined for their ability to carry out a reaction similar to pyrophosphorolysis. We describe a manganese-mediated pyrophosphorolysis-like activity using pyrovanadate (VV) catalyzed by the DNA polymerase of bacteriophage T7. We designate this reaction pyrovanadolysis. X-ray absorption spectroscopy reveals a shorter Mn-V distance of the polymerase-VV complex than the Mn-P distance of the polymerase-PP(i) complex. This structural arrangement at the active site accounts for the enzymatic activation by Mn-VV. We propose that the Mn(2+), larger than Mg(2+), fits the polymerase active site to mediate binding of VV into the active site of the polymerase. Our results may be the first documentation that vanadium can substitute for phosphorus in biological processes.
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Affiliation(s)
- Barak Akabayov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Arkadiusz W Kulczyk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Sabine R Akabayov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Christopher Theile
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Larry W McLaughlin
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, and
| | - Benjamin Beauchamp
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Antoine M van Oijen
- Zernike Institute for Advanced Materials Centre for Synthetic Biology, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115,.
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Söte S, Kleine S, Schlicke M, Brakmann S. Directed Evolution of an Error-Prone T7 DNA Polymerase that Attenuates Viral Replication. Chembiochem 2011; 12:1551-8. [DOI: 10.1002/cbic.201000799] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Indexed: 11/07/2022]
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