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Schvartzman JB, Martínez V, Hernández P, Krimer DB, Fernández-Nestosa MJ. Changes in the topology of DNA replication intermediates: Important discrepancies between in vitro and in vivo. Bioessays 2021; 43:e2000309. [PMID: 33629756 DOI: 10.1002/bies.202000309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 11/08/2022]
Abstract
The topology of DNA duplexes changes during replication and also after deproteinization in vitro. Here we describe these changes and then discuss for the first time how the distribution of superhelical stress affects the DNA topology of replication intermediates, taking into account the progression of replication forks. The high processivity of Topo IV to relax the left-handed (+) supercoiling that transiently accumulates ahead of the forks is not essential, since DNA gyrase and swiveling of the forks cooperate with Topo IV to accomplish this task in vivo. We conclude that despite Topo IV has a lower processivity to unlink the right-handed (+) crossings of pre-catenanes and fully replicated catenanes, this is indeed its main role in vivo. This would explain why in the absence of Topo IV replication goes-on, but fully replicated sister duplexes remain heavily catenated.
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Affiliation(s)
- Jorge B Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Víctor Martínez
- Directorate of Research and Postgraduate Studies, Polytechnic School, National University of Asunción, P, San Lorenzo, Paraguay
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Dora B Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - María-José Fernández-Nestosa
- Directorate of Research and Postgraduate Studies, Polytechnic School, National University of Asunción, P, San Lorenzo, Paraguay
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Lin G, Weiss SC, Vergara S, Camacho C, Calero G. Transcription with a laser: Radiation-damage-free diffraction of RNA Polymerase II crystals. Methods 2019; 159-160:23-28. [PMID: 31029767 DOI: 10.1016/j.ymeth.2019.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
Well-diffracting crystals are essential to obtain relevant structural data that will lead to understanding of RNA Polymerase II (Pol II) transcriptional processes at a molecular level. Here we present a strategy to study Pol II crystals using negative stain transmission electron microscopy (TEM) and a methodology to optimize radiation damage free data collection using free electron laser (FEL) at the Linac Coherent Light Source (LCLS). The use of negative stain TEM allowed visualization and optimization of crystal diffraction by monitoring the lattice quality of crystallization conditions. Nano crystals bearing perfect lattices were seeded and used to grow larger crystals for FEL data collection. Moreover, the use of in house designed crystal loops together with ultra-violet (UV) microscopy for crystal detection facilitated data collection. Such strategy permitted collection of multiple crystals of radiation-free-damage data, resulting in the highest resolution of wild type (WT) Pol II crystals ever observed.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Simon C Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Sandra Vergara
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States
| | - Carlos Camacho
- Department of Computanional and Systems Biology, University of Pittsburgh School of Medicine, United States
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, United States.
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Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W. Characterizing metal-binding sites in proteins with X-ray crystallography. Nat Protoc 2018; 13:1062-1090. [PMID: 29674755 PMCID: PMC6235626 DOI: 10.1038/nprot.2018.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical, and diagnostic processes. Proper handling of metal-containing macromolecule samples for structural studies is not trivial, and failure to handle them properly is often a source of irreproducibility caused by issues such as pH changes, incorporation of unexpected metals, or oxidization/reduction of the metal. This protocol outlines the guidelines and best practices for characterizing metal-binding sites in protein structures and alerts experimenters to potential pitfalls during the preparation and handling of metal-containing protein samples for X-ray crystallography studies. The protocol features strategies for controlling the sample pH and the metal oxidation state, recording X-ray fluorescence (XRF) spectra, and collecting diffraction data sets above and below the corresponding metal absorption edges. This protocol should allow experimenters to gather sufficient evidence to unambiguously determine the identity and location of the metal of interest, as well as to accurately characterize the coordinating ligands in the metal binding environment within the protein. Meticulous handling of metal-containing macromolecule samples as described in this protocol should enhance experimental reproducibility in biomedical sciences, especially in X-ray macromolecular crystallography. For most samples, the protocol can be completed within a period of 7-190 d, most of which (2-180 d) is devoted to growing the crystal. The protocol should be readily understandable to structural biologists, particularly protein crystallographers with an intermediate level of experience.
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Affiliation(s)
- Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Ewa Niedzialkowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
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