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Zhu HX, Wright BW, Logel DY, Needham P, Yehl K, Molloy MP, Jaschke PR. IbpAB small heat shock proteins are not host factors for bacteriophage ϕX174 replication. Virology 2024; 597:110169. [PMID: 38996611 DOI: 10.1016/j.virol.2024.110169] [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] [Received: 02/01/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024]
Abstract
Bacteriophage ϕX174 is a small icosahedral virus of the Microviridae with a rapid replication cycle. Previously, we found that in ϕX174 infections of Escherichia coli, the most highly upregulated host proteins are two small heat shock proteins, IbpA and IbpB, belonging to the HSP20 family, which is a universally conserved group of stress-induced molecular chaperones that prevent irreversible aggregation of proteins. Heat shock proteins were found to protect against ϕX174 lysis, but IbpA/B have not been studied. In this work, we disrupted the ibpA and ibpB genes and measured the effects on ϕX174 replication. We found that in contrast to other E. coli heat shock proteins, they are not necessary for ϕX174 replication; moreover, their absence has no discernible effect on ϕX174 fecundity. These results suggest IbpA/B upregulation is a response to ϕX174 protein expression but does not play a role in phage replication, and they are not Microviridae host factors.
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Affiliation(s)
- Hannah X Zhu
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Bradley W Wright
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Patrick Needham
- Miami University, Department of Chemistry and Biochemistry, Oxford, 45056, USA
| | - Kevin Yehl
- Miami University, Department of Chemistry and Biochemistry, Oxford, 45056, USA
| | - Mark P Molloy
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; Kolling Institute, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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2
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Xu L, Halma MTJ, Wuite GJL. Mapping fast DNA polymerase exchange during replication. Nat Commun 2024; 15:5328. [PMID: 38909023 PMCID: PMC11193749 DOI: 10.1038/s41467-024-49612-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
Despite extensive studies on DNA replication, the exchange mechanisms of DNA polymerase during replication remain unclear. Existing models propose that this exchange is facilitated by protein partners like helicase. Here we present data, employing a combination of mechanical DNA manipulation and single fluorescent protein observation, that reveal DNA polymerase undergoing rapid and autonomous exchange during replication not coordinated by other proteins. The DNA polymerase shows fast unbinding and rebinding dynamics, displaying a preference for either exonuclease or polymerase activity, or pausing events, during each brief binding event. We also observed a 'memory effect' in DNA polymerase rebinding, i.e., the enzyme tends to preserve its prior activity upon reassociation. This effect, potentially linked to the ssDNA/dsDNA junction's conformation, might play a role in regulating binding preference enabling high processivity amidst rapid protein exchange. Taken together, our findings support an autonomous replication model that includes rapid protein exchange, burst of activity, and a 'memory effect' while moving processively forward.
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Affiliation(s)
- Longfu Xu
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Matthew T J Halma
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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3
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Kamagata K. Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates. Front Mol Biosci 2021; 8:795367. [PMID: 34869607 PMCID: PMC8639857 DOI: 10.3389/fmolb.2021.795367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
DNA-binding proteins trigger various cellular functions and determine cellular fate. Before performing functions such as transcription, DNA repair, and DNA recombination, DNA-binding proteins need to search for and bind to their target sites in genomic DNA. Under evolutionary pressure, DNA-binding proteins have gained accurate and rapid target search and binding strategies that combine three-dimensional search in solution, one-dimensional sliding along DNA, hopping and jumping on DNA, and intersegmental transfer between two DNA molecules. These mechanisms can be achieved by the unique structural and dynamic properties of these proteins. Single-molecule fluorescence microscopy and molecular dynamics simulations have characterized the molecular actions of DNA-binding proteins in detail. Furthermore, these methodologies have begun to characterize liquid condensates induced by liquid-liquid phase separation, e.g., molecular principles of uptake and dynamics in droplets. This review discusses the molecular action of DNA-binding proteins on DNA and in liquid condensate based on the latest studies that mainly focused on the model protein p53.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
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4
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Luzon-Hidalgo R, Risso VA, Delgado A, Ibarra-Molero B, Sanchez-Ruiz JM. A protocol to study bacteriophage adaptation to new hosts. STAR Protoc 2021; 2:100784. [PMID: 34485945 PMCID: PMC8403759 DOI: 10.1016/j.xpro.2021.100784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A general protocol for the experimental assessment of bacteriophage adaptation to new hosts is described. We use as a model system the lytic phage T7 and an engineered E. coli strain modified to hamper the recruitment of a known proviral factor. Our protocol includes steps of phage amplification, plaque and liquid lysis assays, and DNA extraction for next-generation sequencing of the viral genome over several rounds of laboratory evolution thus allowing the investigation of the sequence determinants of viral adaptation. For complete information on the generation and use of this protocol, please refer to Luzon-Hidalgo et al. (2021). Protocol for experimental characterization of phage adaptation to new hosts DNA extraction for NGS of viral genome to unwind the molecular basis of adaptation Potential application in the development of anti-microbial phage therapies
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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, 18071 Granada, 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, 18071 Granada, Spain
| | - Asuncion Delgado
- Departamento de Quimica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, 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, 18071 Granada, 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, 18071 Granada, Spain
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5
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Šimoliūnienė M, Kazlauskas D, Zajančkauskaitė A, Meškys R, Truncaitė L. Escherichia coli trxAgene as a molecular marker for genome engineering of felixounoviruses. Biochim Biophys Acta Gen Subj 2021; 1865:129967. [PMID: 34324954 DOI: 10.1016/j.bbagen.2021.129967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/02/2021] [Accepted: 07/24/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Bacterial viruses (bacteriophages or phages) have a lot of uncharacterized genes, which hinders the progress of their applied research. Functional characterization of these genes is often hampered by a lack of suitable methods for engineering of phage genomes. METHODS Phages vB_EcoM_Alf5 (Alf5) and VB_EcoM_VpaE1 (VpaE1) were used as the model phages of Felixounovirus genus. The phage-coded properties were predicted by bioinformatics analysis. The 'pull-down' assay was used for detection of protein-protein interactions. Primer extension analysis was used for the DNA polymerase (DNAP) activity testing. Bacteriophage lambda Redγβα-assisted homologous recombination was used for construction of phage mutants. RESULTS Bioinformatics analysis showed that felixounoviruses encode DNA polymerase, which is homologous to the T7 DNAP. We found that the Escherichia coli thioredoxin A (TrxA) in vitro interacts with the predicted DNAP of Alf5 phage (gp096) and enhances its activity. Phages Alf5 and VpaE1 do not grow on E. coli strains lacking trxA gene unless it is provided in trans. This feature was used for construction of the deletion/insertion mutants of non-essential genes of felixounoviruses. CONCLUSION DNA replication of phages from Felixonuvirus genus depends on the host trxA, which therefore may be used as a molecular marker for their genome engineering. GENERAL SIGNIFICANCE We present a proof-of-principle of a strategy for targeted engineering of bacteriophages of Felixounovirus genus. The method developed here will facilitate the basic and applied research of this unexplored phage group. Furthermore, detected functional interactions between the phage and host proteins will be significant for basic research of DNA replication.
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Affiliation(s)
- Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
| | - Darius Kazlauskas
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
| | - Aurelija Zajančkauskaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 7 Saulėtekio av., LT-10257 Vilnius, Lithuania.
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6
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Ahmadi A, Till K, Backe PH, Blicher P, Diekmann R, Schüttpelz M, Glette K, Tørresen J, Bjørås M, Rowe AD, Dalhus B. Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex. Commun Biol 2021; 4:876. [PMID: 34267321 PMCID: PMC8282808 DOI: 10.1038/s42003-021-02400-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/25/2021] [Indexed: 11/09/2022] Open
Abstract
The multi-step base excision repair (BER) pathway is initiated by a set of enzymes, known as DNA glycosylases, able to scan DNA and detect modified bases among a vast number of normal bases. While DNA glycosylases in the BER pathway generally bend the DNA and flip damaged bases into lesion specific pockets, the HEAT-like repeat DNA glycosylase AlkD detects and excises bases without sequestering the base from the DNA helix. We show by single-molecule tracking experiments that AlkD scans DNA without forming a stable interrogation complex. This contrasts with previously studied repair enzymes that need to flip bases into lesion-recognition pockets and form stable interrogation complexes. Moreover, we show by design of a loss-of-function mutant that the bimodality in scanning observed for the structural homologue AlkF is due to a key structural differentiator between AlkD and AlkF; a positively charged β-hairpin able to protrude into the major groove of DNA.
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Affiliation(s)
- Arash Ahmadi
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Katharina Till
- FOM Institute AMOLF, Science Park 104, Amsterdam, The Netherlands.,Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Paul Hoff Backe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway
| | - Pernille Blicher
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Robin Diekmann
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Kyrre Glette
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Jim Tørresen
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Newborn Screening, Division of Child and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. .,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.
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7
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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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8
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Jana T, Brodsky S, Barkai N. Speed-Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites. Trends Genet 2021; 37:421-432. [PMID: 33414013 DOI: 10.1016/j.tig.2020.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022]
Abstract
Transcription factors (TFs) regulate gene expression by binding DNA sequences recognized by their DNA-binding domains (DBDs). DBD-recognized motifs are short and highly abundant in genomes. The ability of TFs to bind a specific subset of motif-containing sites, and to do so rapidly upon activation, is fundamental for gene expression in all eukaryotes. Despite extensive interest, our understanding of the TF-target search process is fragmented; although binding specificity and detection speed are two facets of this same process, trade-offs between them are rarely addressed. In this opinion article, we discuss potential speed-specificity trade-offs in the context of existing models. We further discuss the recently described 'distributed specificity' paradigm, suggesting that intrinsically disordered regions (IDRs) promote specificity while reducing the TF-target search time.
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Affiliation(s)
- Tamar Jana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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9
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Hernandez AJ, Lee SJ, Chang S, Lee JA, Loparo JJ, Richardson CC. Catalytically inactive T7 DNA polymerase imposes a lethal replication roadblock. J Biol Chem 2020; 295:9542-9550. [PMID: 32430399 DOI: 10.1074/jbc.ra120.013738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/18/2020] [Indexed: 11/06/2022] Open
Abstract
Bacteriophage T7 encodes its own DNA polymerase, the product of gene 5 (gp5). In isolation, gp5 is a DNA polymerase of low processivity. However, gp5 becomes highly processive upon formation of a complex with Escherichia coli thioredoxin, the product of the trxA gene. Expression of a gp5 variant in which aspartate residues in the metal-binding site of the polymerase domain were replaced by alanine is highly toxic to E. coli cells. This toxicity depends on the presence of a functional E. coli trxA allele and T7 RNA polymerase-driven expression but is independent of the exonuclease activity of gp5. In vitro, the purified gp5 variant is devoid of any detectable polymerase activity and inhibited DNA synthesis by the replisomes of E. coli and T7 in the presence of thioredoxin by forming a stable complex with DNA that prevents replication. On the other hand, the highly homologous Klenow fragment of DNA polymerase I containing an engineered gp5 thioredoxin-binding domain did not exhibit toxicity. We conclude that gp5 alleles encoding inactive polymerases, in combination with thioredoxin, could be useful as a shutoff mechanism in the design of a bacterial cell-growth system.
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Affiliation(s)
- Alfredo J Hernandez
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Seung-Joo Lee
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Seungwoo Chang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jaehun A Lee
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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10
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Mi C, Zhang S, Huang W, Dai M, Chai Z, Yang W, Deng S, Ao L, Zhang H. Strand displacement DNA synthesis by DNA polymerase gp90 exo - of Pseudomonas aeruginosa phage 1. Biochimie 2020; 170:73-87. [PMID: 31911177 DOI: 10.1016/j.biochi.2019.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/31/2019] [Indexed: 12/27/2022]
Abstract
Strand displacement DNA synthesis is essential for DNA replication. Gp90, the sole DNA polymerase of Pseudomonas aeruginosa phage 1, can bypass multiply DNA lesions. However, whether it can perform strand displacement synthesis is still unknown. In this work, we found that gp90 exo- could perform strand displacement synthesis, albeit its activity and processivity were lower than those of primer extension. Gp90 exo- itself could not unwind Y-shaped or fork DNA. Tail and gap at DNA fork were necessary for efficient synthesis. High GC content obviously inhibited strand displacement synthesis. Consecutive GC sequence at the entrance of fork showed more inhibition effect on DNA synthesis than that in the downstream DNA fork. The fraction of productive polymerase and DNA complex (A values) was higher for fork than gap; while their average extension rates (kp values) were similar. However, both A and kp values were lower than those for the primer/template (P/T) substrate. The binding of gp90 exo- to fork was tighter than P/T or gap in the absence of dATP. In the presence of dATP to form ternary complex, the binding affinity of gp90 exo- to P/T or gap was increased compared with that in the binary complex. Abasic site, 8-oxoG, and O6-MeG inhibited and even blocked strand displacement synthesis. This work shows that gp90 exo- could perform strand displacement DNA synthesis at DNA fork, discovering the presence of new functions of PaP1 DNA polymerase in DNA replication and propagation of PaP1.
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Affiliation(s)
- Chenyang Mi
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Wenxin Huang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengyuan Dai
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Zili Chai
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Wang Yang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Shanshan Deng
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500, China
| | - Lin Ao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China.
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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11
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Epigenetic DNA modification N6-methyladenine inhibits DNA replication by Sulfolobus solfataricus Y-family DNA polymerase Dpo4. Arch Biochem Biophys 2019; 675:108120. [DOI: 10.1016/j.abb.2019.108120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 12/18/2022]
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12
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Li B, Du K, Gu S, Xie J, Liang T, Xu Z, Gao H, Ling Y, Lu S, Sun Z, Zhang H. Epigenetic DNA Modification N 6-Methyladenine Inhibits DNA Replication by DNA Polymerase of Pseudomonas aeruginosa Phage PaP1. Chem Res Toxicol 2019; 32:840-849. [PMID: 30938985 DOI: 10.1021/acs.chemrestox.8b00348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
N6-methyladenine (6mA), a newly identified epigenetic modification, plays important roles in regulation of various biological processes. However, the effect of 6mA on DNA replication has been little addressed. In this work, we investigated how 6mA affected DNA replication by DNA polymerase of Pseudomonas aeruginosa Phage PaP1 (gp90 exo-). The presence of 6mA, as well as its intermediate hypoxanthine (Hyp), inhibited DNA replication by gp90 exo-. The 6mA reduced dTTP incorporation efficiency by 10-fold and inhibited next-base extension efficiency by 100-fold. Differently, dCTP was preferentially incorporated opposite Hyp among four dNTPs. Gp90 exo- reduced the extension priority beyond the 6mA:T pair rather than the 6mA:C mispair and preferred to extend beyond Hyp:C rather than the Hyp:T pair. Incorporation of dTTP opposite 6mA and dCTP opposite Hyp showed fast burst phases. The burst rate and burst amplitude were both reduced for 6mA compared with unmodified A. Moreover, the total incorporation efficiency ( kpol/ Kd,dNTP) was decreased for dTTP incorporation opposite 6mA and dCTP incorporation opposite Hyp compared with dTTP incorporation opposite A. 6mA reduced the incorporation rate ( kpol), and Hyp increased the dissociation constant ( Kd,dNTP). However, 6mA or Hyp on template did not affect the binding of DNA polymerase to DNA in binary or ternary complexes. This work provides new insight into the inhibited effects of epigenetic modification of 6mA on DNA replication in PaP1.
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Affiliation(s)
- Bianbian Li
- School of Biological Engineering , Dalian Polytechnic University , Dalian , 116034 , China.,Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Ke Du
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Shiling Gu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Jiayu Xie
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Tingting Liang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Zhongyan Xu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Hui Gao
- School of Biological Engineering , Dalian Polytechnic University , Dalian , 116034 , China
| | - Yihui Ling
- Institute for Chemical Carcinogenesis , Guangzhou Medical University , Xinzao, Panyu District, Guangzhou , China
| | - Shuguang Lu
- Department of Microbiology, College of Basic Medical Science , Third Military Medical University , Chongqing , China
| | - Zhen Sun
- School of Biological Engineering , Dalian Polytechnic University , Dalian , 116034 , China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
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13
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Du K, Zhang X, Zou Z, Li B, Gu S, Zhang S, Qu X, Ling Y, Zhang H. Epigenetically modified N 6-methyladenine inhibits DNA replication by human DNA polymerase η. DNA Repair (Amst) 2019; 78:81-90. [PMID: 30991231 DOI: 10.1016/j.dnarep.2019.03.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 01/06/2023]
Abstract
N6-methyladenine (6mA), as a newly reported epigenetic marker, plays significant roles in regulation of various biological processes in eukaryotes. However, the effect of 6mA on human DNA replication remain elusive. In this work, we used Y-family human DNA polymerase η as a model to investigate the kinetics of bypass of 6mA by hPol η. We found 6mA and its intermediate hypoxanthine (I) on template partially inhibited DNA replication by hPol η. dTMP incorporation opposite 6mA and dCMP incorporation opposite I can be considered as correct incorporation. However, both 6mA and I reduced correct incorporation efficiency, next-base extension efficiency, and the priority in extension beyond correct base pair. Both dTMP incorporation opposite 6mA and dCTP opposite I showed fast burst phases. However, 6mA and I reduced the burst incorporation rates (kpol) and increased the dissociation constant (Kd,dNTP), compared with that of dTMP incorporation opposite unmodified A. Biophysical binding assays revealed that both 6mA and I on template reduced the binding affinity of hPol η to DNA in binary or ternary complex compared with unmodified A. All the results explain the inhibition effects of 6mA and I on DNA replication by hPol η, providing new insight in the effects of epigenetically modified 6mA on human DNA replication.
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Affiliation(s)
- Ke Du
- College of Life Science, Yan´an University, Yan'an, Shaanxi, China; Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiangqian Zhang
- College of Life Science, Yan´an University, Yan'an, Shaanxi, China
| | - Zhenyu Zou
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Bianbian Li
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shiling Gu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaoyi Qu
- College of Life Science, Yan´an University, Yan'an, Shaanxi, China
| | - Yihui Ling
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao Panyu District, Guangzhou, China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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14
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Breaking the speed limit with multimode fast scanning of DNA by Endonuclease V. Nat Commun 2018; 9:5381. [PMID: 30568191 PMCID: PMC6300609 DOI: 10.1038/s41467-018-07797-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 11/27/2018] [Indexed: 01/04/2023] Open
Abstract
In order to preserve genomic stability, cells rely on various repair pathways for removing DNA damage. The mechanisms how enzymes scan DNA and recognize their target sites are incompletely understood. Here, by using high-localization precision microscopy along with 133 Hz high sampling rate, we have recorded EndoV and OGG1 interacting with 12-kbp elongated λ-DNA in an optical trap. EndoV switches between three distinct scanning modes, each with a clear range of activation energy barriers. These results concur with average diffusion rate and occupancy of states determined by a hidden Markov model, allowing us to infer that EndoV confinement occurs when the intercalating wedge motif is involved in rigorous probing of the DNA, while highly mobile EndoV may disengage from a strictly 1D helical diffusion mode and hop along the DNA. This makes EndoV the first example of a monomeric, single-conformation and single-binding-site protein demonstrating the ability to switch between three scanning modes. How DNA repair proteins locate their target sites on DNA is still a matter of debate. Here the authors characterize by single-molecule fluorescence imaging the modes of scanning adopted by bacterial endonuclease V as it moves along linear DNA tracks.
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15
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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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16
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Liu X, Zou X, Li H, Zou Z, Yang J, Wang C, Wu S, Zhang H. Bypass of an Abasic Site via the A-Rule by DNA Polymerase of Pseudomonas aeruginosa Phage PaP1. Chem Res Toxicol 2017; 31:58-65. [PMID: 29183115 DOI: 10.1021/acs.chemrestox.7b00287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xiaoying Liu
- School
of Public Health, Xinjiang Medical University, Urumqi 830011, China
- Public
Health Laboratory Sciences and Toxicology, West China School of Public
Health, Sichuan University, Chengdu 610041, China
| | - Xiaoli Zou
- Public
Health Laboratory Sciences and Toxicology, West China School of Public
Health, Sichuan University, Chengdu 610041, China
| | - Huangyuan Li
- Key
Laboratory of Environment and Health among Universities and Colleges
in Fujian, School of Public Health, Fujian Medical University, Minhou
County, Fuzhou 350108, China
| | - Zhenyu Zou
- Public
Health Laboratory Sciences and Toxicology, West China School of Public
Health, Sichuan University, Chengdu 610041, China
| | - Jie Yang
- Public
Health Laboratory Sciences and Toxicology, West China School of Public
Health, Sichuan University, Chengdu 610041, China
| | - Chenlu Wang
- School
of Public Health, Xinjiang Medical University, Urumqi 830011, China
| | - Shunhua Wu
- School
of Public Health, Xinjiang Medical University, Urumqi 830011, China
| | - Huidong Zhang
- Public
Health Laboratory Sciences and Toxicology, West China School of Public
Health, Sichuan University, Chengdu 610041, China
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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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Kamagata K, Murata A, Itoh Y, Takahashi S. Characterization of facilitated diffusion of tumor suppressor p53 along DNA using single-molecule fluorescence imaging. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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19
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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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20
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TALE proteins search DNA using a rotationally decoupled mechanism. Nat Chem Biol 2016; 12:831-7. [DOI: 10.1038/nchembio.2152] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/27/2016] [Indexed: 12/27/2022]
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21
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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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22
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Xiong K, Blainey PC. Molecular sled sequences are common in mammalian proteins. Nucleic Acids Res 2016; 44:2266-73. [PMID: 26857546 PMCID: PMC4797294 DOI: 10.1093/nar/gkw035] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/07/2016] [Indexed: 12/13/2022] Open
Abstract
Recent work revealed a new class of molecular machines called molecular sleds, which are small basic molecules that bind and slide along DNA with the ability to carry cargo along DNA. Here, we performed biochemical and single-molecule flow stretching assays to investigate the basis of sliding activity in molecular sleds. In particular, we identified the functional core of pVIc, the first molecular sled characterized; peptide functional groups that control sliding activity; and propose a model for the sliding activity of molecular sleds. We also observed widespread DNA binding and sliding activity among basic polypeptide sequences that implicate mammalian nuclear localization sequences and many cell penetrating peptides as molecular sleds. These basic protein motifs exhibit weak but physiologically relevant sequence-nonspecific DNA affinity. Our findings indicate that many mammalian proteins contain molecular sled sequences and suggest the possibility that substantial undiscovered sliding activity exists among nuclear mammalian proteins.
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Affiliation(s)
- Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA Department of Biological Engineering, MIT, Cambridge, MA 02142, USA
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23
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Brown MW, Kim Y, Williams GM, Huck JD, Surtees JA, Finkelstein IJ. Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions. Nat Commun 2016; 7:10607. [PMID: 26837705 PMCID: PMC4742970 DOI: 10.1038/ncomms10607] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/04/2016] [Indexed: 12/17/2022] Open
Abstract
DNA-binding proteins search for specific targets via facilitated diffusion along a crowded genome. However, little is known about how crowded DNA modulates facilitated diffusion and target recognition. Here we use DNA curtains and single-molecule fluorescence imaging to investigate how Msh2-Msh3, a eukaryotic mismatch repair complex, navigates on crowded DNA. Msh2-Msh3 hops over nucleosomes and other protein roadblocks, but maintains sufficient contact with DNA to recognize a single lesion. In contrast, Msh2-Msh6 slides without hopping and is largely blocked by protein roadblocks. Remarkably, the Msh3-specific mispair-binding domain (MBD) licences a chimeric Msh2-Msh6(3MBD) to bypass nucleosomes. Our studies contrast how Msh2-Msh3 and Msh2-Msh6 navigate on a crowded genome and suggest how Msh2-Msh3 locates DNA lesions outside of replication-coupled repair. These results also provide insights into how DNA repair factors search for DNA lesions in the context of chromatin.
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Affiliation(s)
- Maxwell W Brown
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yoori Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Gregory M Williams
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | - John D Huck
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | - Jennifer A Surtees
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York 14214, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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24
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Zhang H, Tang Y, Lee SJ, Wei Z, Cao J, Richardson CC. Binding Affinities among DNA Helicase-Primase, DNA Polymerase, and Replication Intermediates in the Replisome of Bacteriophage T7. J Biol Chem 2015; 291:1472-80. [PMID: 26620561 DOI: 10.1074/jbc.m115.698233] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Indexed: 11/06/2022] Open
Abstract
The formation of a replication loop on the lagging strand facilitates coordinated synthesis of the leading- and lagging-DNA strands and provides a mechanism for recycling of the lagging-strand DNA polymerase. As an Okazaki fragment is completed, the loop is released, and a new loop is formed as the synthesis of a new Okazaki fragment is initiated. Loop release requires the dissociation of the complex formed by the interactions among helicase, DNA polymerase, and DNA. The completion of the Okazaki fragment may result in either a nick or a single-stranded DNA region. In the replication system of bacteriophage T7, the dissociation of the polymerase from either DNA region is faster than that observed for the dissociation of the helicase from DNA polymerase, implying that the replication loop is released more likely through the dissociation of the lagging-strand DNA from polymerase, retaining the polymerase at replication fork. Both dissociation of DNA polymerase from DNA and that of helicase from a DNA polymerase · DNA complex are much faster at a nick DNA region than the release from a ssDNA region. These results suggest that the replication loop is released as a result of the nick formed when the lagging-strand DNA polymerase encounters the previously synthesized Okazaki fragment, releasing lagging-strand DNA and retaining DNA polymerase at the replication fork for the synthesis of next Okazaki fragment.
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Affiliation(s)
- Huidong Zhang
- From the Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China and the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boson, Massachusetts 02115
| | - Yong Tang
- From the Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China and
| | - Seung-Joo Lee
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boson, Massachusetts 02115
| | - Zeliang Wei
- From the Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China and
| | - Jia Cao
- From the Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, China and
| | - Charles C Richardson
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boson, Massachusetts 02115
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25
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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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26
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Schmidt HG, Sewitz S, Andrews SS, Lipkow K. An integrated model of transcription factor diffusion shows the importance of intersegmental transfer and quaternary protein structure for target site finding. PLoS One 2014; 9:e108575. [PMID: 25333780 PMCID: PMC4204827 DOI: 10.1371/journal.pone.0108575] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 08/30/2014] [Indexed: 11/30/2022] Open
Abstract
We present a computational model of transcription factor motion that explains both the observed rapid target finding of transcription factors, and how this motion influences protein and genome structure. Using the Smoldyn software, we modelled transcription factor motion arising from a combination of unrestricted 3D diffusion in the nucleoplasm, sliding along the DNA filament, and transferring directly between filament sections by intersegmental transfer. This presents a fine-grain picture of the way in which transcription factors find their targets two orders of magnitude faster than 3D diffusion alone allows. Eukaryotic genomes contain sections of nucleosome free regions (NFRs) around the promoters; our model shows that the presence and size of these NFRs can be explained as their acting as antennas on which transcription factors slide to reach their targets. Additionally, our model shows that intersegmental transfer may have shaped the quaternary structure of transcription factors: sequence specific DNA binding proteins are unusually enriched in dimers and tetramers, perhaps because these allow intersegmental transfer, which accelerates target site finding. Finally, our model shows that a ‘hopping’ motion can emerge from 3D diffusion on small scales. This explains the apparently long sliding lengths that have been observed for some DNA binding proteins observed in vitro. Together, these results suggest that transcription factor diffusion dynamics help drive the evolution of protein and genome structure.
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Affiliation(s)
- Hugo G. Schmidt
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (HS); (KL)
| | - Sven Sewitz
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Steven S. Andrews
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Karen Lipkow
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, United Kingdom
- * E-mail: (HS); (KL)
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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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Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery. Proc Natl Acad Sci U S A 2014; 111:4073-8. [PMID: 24591606 DOI: 10.1073/pnas.1402010111] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Replication of DNA plays a central role in transmitting hereditary information from cell to cell. To achieve reliable DNA replication, multiple proteins form a stable complex, known as the replisome, enabling them to act together in a highly coordinated fashion. Over the past decade, the roles of the various proteins within the replisome have been determined. Although many of their interactions have been characterized, it remains poorly understood how replication proteins enter and leave the replisome. In this study, we visualize fluorescently labeled bacteriophage T7 DNA polymerases within the replisome while we simultaneously observe the kinetics of the replication process. This combination of observables allows us to monitor both the activity and dynamics of individual polymerases during coordinated leading- and lagging-strand synthesis. Our data suggest that lagging-strand polymerases are exchanged at a frequency similar to that of Okazaki fragment synthesis and that two or more polymerases are present in the replisome during DNA replication. Our studies imply a highly dynamic picture of the replisome with lagging-strand DNA polymerases residing at the fork for the synthesis of only a few Okazaki fragments. Further, new lagging-strand polymerases are readily recruited from a pool of polymerases that are proximally bound to the replisome and continuously replenished from solution.
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Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies. Nat Rev Microbiol 2013; 11:303-15. [DOI: 10.1038/nrmicro2994] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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31
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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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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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Normanno D, Dahan M, Darzacq X. Intra-nuclear mobility and target search mechanisms of transcription factors: a single-molecule perspective on gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:482-93. [PMID: 22342464 DOI: 10.1016/j.bbagrm.2012.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/26/2012] [Accepted: 02/03/2012] [Indexed: 12/26/2022]
Abstract
Precise expression of specific genes in time and space is at the basis of cellular viability as well as correct development of organisms. Understanding the mechanisms of gene regulation is fundamental and still one of the great challenges for biology. Gene expression is regulated also by specific transcription factors that recognize and bind to specific DNA sequences. Transcription factors dynamics, and especially the way they sample the nucleoplasmic space during the search for their specific target in the genome, are a key aspect for regulation and it has been puzzling researchers for forty years. The scope of this review is to give a state-of-the-art perspective over the intra-nuclear mobility and the target search mechanisms of specific transcription factors at the molecular level. Going through the seminal biochemical experiments that have raised the first questions about target localization and the theoretical grounds concerning target search processes, we describe the most recent experimental achievements and current challenges in understanding transcription factors dynamics and interactions with DNA using in vitro assays as well as in live prokaryotic and eukaryotic cells. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Davide Normanno
- Institut de Biologie de l'Ecole normale supérieure (IBENS), CNRS UMR 8197, Ecole normale supérieure, 46, Rue d'Ulm, 75005 Paris, France.
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Dynamics of lesion processing by bacterial nucleotide excision repair proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:1-24. [PMID: 22749140 DOI: 10.1016/b978-0-12-387665-2.00001-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Single-molecule approaches permit an unrivalled view of how complex systems operate and have recently been used to understand DNA-protein interactions. These tools have enabled advances in a particularly challenging problem, the search for damaged sites on DNA. DNA repair proteins are present at the level of just a few hundred copies in bacterial cells to just a few thousand in human cells, and they scan the entire genome in search of their specific substrates. How do these proteins achieve this herculean task when their targets may differ from undamaged DNA by only a single hydrogen bond? Here we examine, using single-molecule approaches, how the prokaryotic nucleotide excision repair system balances the necessity for speed against specificity. We discuss issues at a theoretical, biological, and technical level and finally pose questions for future research.
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Sobhy MA, Elshenawy MM, Takahashi M, Whitman BH, Walter NG, Hamdan SM. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:113702. [PMID: 22128979 DOI: 10.1063/1.3657153] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy transfer (FRET) and a technically challenging four-color FRET experiments on doubly labeled duplex DNA and quadruple-labeled Holliday junction, respectively.
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Affiliation(s)
- M A Sobhy
- Laboratory of DNA Replication and Recombination, Division of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
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36
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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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Candelli A, Wuite GJL, Peterman EJG. Combining optical trapping, fluorescence microscopy and micro-fluidics for single molecule studies of DNA-protein interactions. Phys Chem Chem Phys 2011; 13:7263-72. [PMID: 21416086 DOI: 10.1039/c0cp02844d] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Complexity and heterogeneity are common denominators of the many molecular events taking place inside the cell. Single-molecule techniques are important tools to quantify the actions of biomolecules. Heterogeneous interactions between multiple proteins, however, are difficult to study with these technologies. One solution is to integrate optical trapping with micro-fluidics and single-molecule fluorescence microscopy. This combination opens the possibility to study heterogeneous/complex protein interactions with unprecedented levels of precision and control. It is particularly powerful for the study of DNA-protein interactions as it allows manipulating the DNA while at the same time, individual proteins binding to it can be visualized. In this work, we aim to illustrate several published and unpublished key results employing the combination of fluorescence microscopy and optical tweezers. Examples are recent studies of the structural properties of DNA and DNA-protein complexes, the molecular mechanisms of nucleo-protein filament assembly on DNA and the motion of DNA-bound proteins. In addition, we present new results demonstrating that single, fluorescently labeled proteins bound to individual, optically trapped DNA molecules can already be tracked with localization accuracy in the sub-10 nm range at tensions above 1 pN. These experiments by us and others demonstrate the enormous potential of this combination of single-molecule techniques for the investigation of complex DNA-protein interactions.
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Affiliation(s)
- Andrea Candelli
- Institute for Lasers, Life and Biophotonics Amsterdam and Department of Physics and Astronomy, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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DeSantis MC, Li JL, Wang YM. Protein sliding and hopping kinetics on DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:021907. [PMID: 21405863 PMCID: PMC3683889 DOI: 10.1103/physreve.83.021907] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Indexed: 05/16/2023]
Abstract
Using Monte Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (i) in each diffusion trajectory, a protein makes on average hundreds of alternating slides and hops with a mean sliding time of several tens of milliseconds; (ii) sliding dominates the root-mean-square displacement of fast diffusion trajectories, whereas hopping dominates slow ones; (iii) flow and variations in salt concentration have limited effects on hopping kinetics, while in vivo DNA configuration is not expected to influence sliding kinetics; and (iv) the rate of occurrence for hops longer than 200 nm agrees with experimental data for EcoRV proteins.
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Affiliation(s)
- Michael C DeSantis
- Department of Physics, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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Simultaneous single-molecule measurements of phage T7 replisome composition and function reveal the mechanism of polymerase exchange. Proc Natl Acad Sci U S A 2011; 108:3584-9. [PMID: 21245349 DOI: 10.1073/pnas.1018824108] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of the molecular mechanisms underlying the functioning of large, multiprotein complexes requires experimental tools capable of simultaneously visualizing molecular architecture and enzymatic activity in real time. We developed a novel single-molecule assay that combines the flow-stretching of individual DNA molecules to measure the activity of the DNA-replication machinery with the visualization of fluorescently labeled DNA polymerases at the replication fork. By correlating polymerase stoichiometry with DNA synthesis of T7 bacteriophage replisomes, we are able to quantitatively describe the mechanism of polymerase exchange. We find that even at relatively modest polymerase concentration (∼2 nM), soluble polymerases are recruited to an actively synthesizing replisome, dramatically increasing local polymerase concentration. These excess polymerases remain passively associated with the replisome through electrostatic interactions with the T7 helicase for ∼50 s until a stochastic and transient dissociation of the synthesizing polymerase from the primer-template allows for a polymerase exchange event to occur.
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Ayaz MS, Kwak M, Alemdaroglu FE, Wang J, Berger R, Herrmann A. Synthesis of DNA block copolymers with extended nucleic acid segments by enzymatic ligation: cut and paste large hybrid architectures. Chem Commun (Camb) 2011; 47:2243-5. [PMID: 21225047 DOI: 10.1039/c0cc04746e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultra-high molecular weight DNA/polymer hybrid materials were prepared employing molecular biology techniques. Nucleic acid restriction and ligation enzymes were used to generate linear DNA di- and triblock copolymers that contain up to thousands of base pairs in the DNA segments.
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Affiliation(s)
- Meryem S Ayaz
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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Conformational dynamics of bacteriophage T7 DNA polymerase and its processivity factor, Escherichia coli thioredoxin. Proc Natl Acad Sci U S A 2010; 107:15033-8. [PMID: 20696935 DOI: 10.1073/pnas.1010141107] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene 5 of bacteriophage T7 encodes a DNA polymerase (gp5) responsible for the replication of the phage DNA. Gp5 polymerizes nucleotides with low processivity, dissociating after the incorporation of 1 to 50 nucleotides. Thioredoxin (trx) of Escherichia coli binds tightly (Kd = 5 nM) to a unique segment in the thumb subdomain of gp5 and increases processivity. We have probed the molecular basis for the increase in processivity. A single-molecule experiment reveals differences in rates of enzymatic activity and processivity between gp5 and gp5/trx. Small angle X-ray scattering studies combined with nuclease footprinting reveal two conformations of gp5, one in the free state and one upon binding to trx. Comparative analysis of the DNA binding clefts of DNA polymerases and DNA binding proteins show that the binding surface contains more hydrophobic residues than other DNA binding proteins. The balanced composition between hydrophobic and charged residues of the binding site allows for efficient sliding of gp5/trx on the DNA. We propose a model for trx-induced conformational changes in gp5 that enhance the processivity by increasing the interaction of gp5 with DNA.
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