1
|
Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion. Molecules 2021; 26:molecules26206224. [PMID: 34684805 PMCID: PMC8537808 DOI: 10.3390/molecules26206224] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/21/2022] Open
Abstract
Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.
Collapse
|
2
|
Böhning J, Bharat TAM. Towards high-throughput in situ structural biology using electron cryotomography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:97-103. [PMID: 32579969 DOI: 10.1016/j.pbiomolbio.2020.05.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 01/11/2023]
Abstract
Electron cryotomography is a rapidly evolving method for imaging macromolecules directly within the native environment of cells and tissues. Combined with sub-tomogram averaging, it allows structural and cell biologists to obtain sub-nanometre resolution structures in situ. However, low throughput in cryo-ET sample preparation and data acquisition, as well as difficulties in target localisation and sub-tomogram averaging image processing, limit its widespread usability. In this review, we discuss new advances in the field that address these throughput and technical problems. We focus on recent efforts made to resolve issues in sample thinning, improvement in data collection speed at the microscope, strategies for localisation of macromolecules using correlated light and electron microscopy and advancements made to improve resolution in sub-tomogram averaging. These advances will considerably decrease the amount of time and effort required for cryo-ET and sub-tomogram averaging, ushering in a new era of structural biology where in situ macromolecular structure determination will be routine.
Collapse
Affiliation(s)
- Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom.
| |
Collapse
|
3
|
Gusev Y, Mazilov S, Volokhina I, Chumakov M. Agrobacterial, Single-Stranded DNA-Binding Protein VirE2 and Its Complexes. J Comput Biol 2019; 27:675-682. [PMID: 31486677 DOI: 10.1089/cmb.2019.0243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
VirE2 from Agrobacterium tumefaciens is a single-stranded (ss) DNA-binding protein involved in delivery of ssT-DNA (single-stranded transfer DNA) from the agrobacterial Ti plasmid into the eukaryotic cell nucleus. The crystallized part of VirE2 was studied by X-ray diffraction, and the noncrystallized parts of the C- (40 amino acid residues [aars]) and N- (111 aars) termini of the protein, which are presumably disordered, were evaluated by computational methods. We did a molecular dynamics simulation of VirE2 without VirE1 and observed no large changes in domain orientation. The interaction of VirE2 with ssDNA and formation of ssDNA-VirE2 complexes in silico were studied. We also used computer-aided methods to design model complexes consisting from two- and four-subunit VirE2 proteins. We examined the implication of disordered sites in formation of two- and four-subunit VirE2 complexes. Formation of VirE2 dimers and tetramers within ssDNA-VirE2 complexes was demonstrated by computational methods. Using the Platinum program, we found that hydrophilic amino acids were predominant on the surface of the four-subunit VirE2 complex.
Collapse
Affiliation(s)
- Yury Gusev
- Bioengineering Laboratory, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov, Russia
| | - Svyatoslav Mazilov
- Bioengineering Laboratory, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov, Russia
| | - Irina Volokhina
- Bioengineering Laboratory, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov, Russia
| | - Mikhail Chumakov
- Bioengineering Laboratory, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, Saratov, Russia
| |
Collapse
|
4
|
Hepp C, Maier B. Bacterial Translocation Ratchets: Shared Physical Principles with Different Molecular Implementations: How bacterial secretion systems bias Brownian motion for efficient translocation of macromolecules. Bioessays 2017; 39. [PMID: 28895164 DOI: 10.1002/bies.201700099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/02/2017] [Indexed: 12/20/2022]
Abstract
Secretion systems enable bacteria to import and secrete large macromolecules including DNA and proteins. While most components of these systems have been identified, the molecular mechanisms of macromolecular transport remain poorly understood. Recent findings suggest that various bacterial secretion systems make use of the translocation ratchet mechanism for transporting polymers across the cell envelope. Translocation ratchets are powered by chemical potential differences generated by concentration gradients of ions or molecules that are specific to the respective secretion systems. Bacteria employ these potential differences for biasing Brownian motion of the macromolecules within the conduits of the secretion systems. Candidates for this mechanism include DNA import by the type II secretion/type IV pilus system, DNA export by the type IV secretion system, and protein export by the type I secretion system. Here, we propose that these three secretion systems employ different molecular implementations of the translocation ratchet mechanism.
Collapse
Affiliation(s)
- Christof Hepp
- Department of Physics Universität zu Köln, Köln, Nordrhein-Westfalen, Germany
| | - Berenike Maier
- Department of Physics Universität zu Köln, Köln, Nordrhein-Westfalen, Germany
| |
Collapse
|
5
|
Volokhina I, Gusev Y, Mazilov S, Moiseeva Y, Chumakov M. Computer evaluation of VirE2 protein complexes for ssDNA transfer ability. Comput Biol Chem 2017; 68:64-70. [DOI: 10.1016/j.compbiolchem.2017.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 01/23/2017] [Accepted: 01/23/2017] [Indexed: 11/16/2022]
|
6
|
Yaakov N, Barak Y, Pereman I, Christie PJ, Elbaum M. Direct fluorescence detection of VirE2 secretion by Agrobacterium tumefaciens. PLoS One 2017; 12:e0175273. [PMID: 28403156 PMCID: PMC5389803 DOI: 10.1371/journal.pone.0175273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 03/23/2017] [Indexed: 11/18/2022] Open
Abstract
VirE2 is a ssDNA binding protein essential for virulence in Agrobacterium tumefaciens. A tetracysteine mutant (VirE2-TC) was prepared for in vitro and in vivo fluorescence imaging based on the ReAsH reagent. VirE2-TC was found to be biochemically active as it binds both ssDNA and the acidic secretion chaperone VirE1. It was also biologically functional in complementing virE2 null strains transforming Arabidopsis thaliana roots and Nicotiana tabacum leaves. In vitro experiments demonstrated a two-color fluorescent complex using VirE2-TC/ReAsH and Alexa Fluor 488 labeled ssDNA. In vivo, fluorescent VirE2-TC/ReAsH was detected in bacteria and in plant cells at time frames relevant to transformation.
Collapse
Affiliation(s)
- Noga Yaakov
- Dept of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Barak
- Chemical Research Support Dept, Weizmann Institute of Science, Rehovot, Israel
| | - Idan Pereman
- Dept of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, UT-Houston Medical School, Houston, Texas, United States of America
| | - Michael Elbaum
- Dept of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
7
|
Bourras S, Rouxel T, Meyer M. Agrobacterium tumefaciens Gene Transfer: How a Plant Pathogen Hacks the Nuclei of Plant and Nonplant Organisms. PHYTOPATHOLOGY 2015; 105:1288-1301. [PMID: 26151736 DOI: 10.1094/phyto-12-14-0380-rvw] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Agrobacterium species are soilborne gram-negative bacteria exhibiting predominantly a saprophytic lifestyle. Only a few of these species are capable of parasitic growth on plants, causing either hairy root or crown gall diseases. The core of the infection strategy of pathogenic Agrobacteria is a genetic transformation of the host cell, via stable integration into the host genome of a DNA fragment called T-DNA. This genetic transformation results in oncogenic reprogramming of the host to the benefit of the pathogen. This unique ability of interkingdom DNA transfer was largely used as a tool for genetic engineering. Thus, the artificial host range of Agrobacterium is continuously expanding and includes plant and nonplant organisms. The increasing availability of genomic tools encouraged genome-wide surveys of T-DNA tagged libraries, and the pattern of T-DNA integration in eukaryotic genomes was studied. Therefore, data have been collected in numerous laboratories to attain a better understanding of T-DNA integration mechanisms and potential biases. This review focuses on the intranuclear mechanisms necessary for proper targeting and stable expression of Agrobacterium oncogenic T-DNA in the host cell. More specifically, the role of genome features and the putative involvement of host's transcriptional machinery in relation to the T-DNA integration and effects on gene expression are discussed. Also, the mechanisms underlying T-DNA integration into specific genome compartments is reviewed, and a theoretical model for T-DNA intranuclear targeting is presented.
Collapse
Affiliation(s)
- Salim Bourras
- First, second, and third authors: INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Thierry Rouxel
- First, second, and third authors: INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| | - Michel Meyer
- First, second, and third authors: INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, BP 01, F-78850 Thiverval-Grignon, France
| |
Collapse
|
8
|
Kim S, Zbaida D, Elbaum M, Leh H, Nogues C, Buckle M. Surface plasmon resonance imaging reveals multiple binding modes of Agrobacterium transformation mediator VirE2 to ssDNA. Nucleic Acids Res 2015; 43:6579-86. [PMID: 26044711 PMCID: PMC4513855 DOI: 10.1093/nar/gkv571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/20/2015] [Indexed: 11/20/2022] Open
Abstract
VirE2 is the major secreted protein of Agrobacterium tumefaciens in its genetic transformation of plant hosts. It is co-expressed with a small acidic chaperone VirE1, which prevents VirE2 oligomerization. After secretion into the host cell, VirE2 serves functions similar to a viral capsid in protecting the single-stranded transferred DNA en route to the nucleus. Binding of VirE2 to ssDNA is strongly cooperative and depends moreover on protein–protein interactions. In order to isolate the protein–DNA interactions, imaging surface plasmon resonance (SPRi) studies were conducted using surface-immobilized DNA substrates of length comparable to the protein-binding footprint. Binding curves revealed an important influence of substrate rigidity with a notable preference for poly-T sequences and absence of binding to both poly-A and double-stranded DNA fragments. Dissociation at high salt concentration confirmed the electrostatic nature of the interaction. VirE1–VirE2 heterodimers also bound to ssDNA, though by a different mechanism that was insensitive to high salt. Neither VirE2 nor VirE1–VirE2 followed the Langmuir isotherm expected for reversible monomeric binding. The differences reflect the cooperative self-interactions of VirE2 that are suppressed by VirE1.
Collapse
Affiliation(s)
- Sanghyun Kim
- Dept of Materials and Interfaces, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - David Zbaida
- Dept of Materials and Interfaces, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Michael Elbaum
- Dept of Materials and Interfaces, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Hervé Leh
- LBPA, Institut d'Alembert, ENS de Cachan, CNRS, 61, avenue du Président Wilson, F-94235 Cachan, France
| | - Claude Nogues
- LBPA, Institut d'Alembert, ENS de Cachan, CNRS, 61, avenue du Président Wilson, F-94235 Cachan, France
| | - Malcolm Buckle
- LBPA, Institut d'Alembert, ENS de Cachan, CNRS, 61, avenue du Président Wilson, F-94235 Cachan, France
| |
Collapse
|