Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance
Abstract
Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resistant staphylococci and streptococci infections posing major threats to human health. The MOBV family of relaxases accounts for approximately 85% of all relaxases found in Staphylococcus aureus isolates. Here, we present six structures of the MOBV relaxase MobM from the promiscuous plasmid pMV158 in complex with several origin of transfer DNA fragments. A combined structural, biochemical, and computational approach reveals that MobM follows a previously uncharacterized histidine/metal-dependent DNA processing mechanism, which involves the formation of a covalent phosphoramidate histidine-DNA adduct for cell-to-cell transfer. In conclusion, we discuss how the chemical features of the high-energy phosphorus-nitrogen bond shape the dominant position of MOBV histidine relaxases among small promiscuous plasmids and their preference toward Gram-positive bacteria.
- Authors:
-
- Barcelona Institute of Science and Technology, Barcelona (Spain); Molecular Biology Institute of Barcelona, Barcelona (Spain); International Institute of Molecular and Cell Biology in Warsaw, Warsaw (Poland)
- Barcelona Institute of Science and Technology, Barcelona (Spain); Molecular Biology Institute of Barcelona, Barcelona (Spain); CELLS-ALBA Synchrotron Light Source, Cerdanyola del Valles (Spain)
- Consejo Superior de Investigaciones Cientificas, Madrid (Spain)
- Barcelona Institute of Science and Technology, Barcelona (Spain); Molecular Biology Institute of Barcelona, Barcelona (Spain); SLAC National Accelerator Lab., Menlo Park, CA (United States)
- Barcelona Institute of Science and Technology, Barcelona (Spain); Barcelona Institute of Science and Technology, Barcelona (Spain)
- Barcelona Institute of Science and Technology, Barcelona (Spain); Molecular Biology Institute of Barcelona, Barcelona (Spain)
- Barcelona Institute of Science and Technology, Barcelona (Spain); Barcelona Institute of Science and Technology, Barcelona (Spain); Univ. of Barcelona, Barcelona (Spain)
- Publication Date:
- Research Org.:
- SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1390289
- Grant/Contract Number:
- AC02-76SF00515; SGR2009-1309; 2014-SGR134; 2014-SGR1530; GA No. 260644; ERC_SimDNA; BFU2008-02372/BMC; CSD-2006-23; BFU2011-22588; BIO2013-49148-C2-2-R; BFU2014-53550-P; BIO2015-69085-REDC; BIO2015-64802; CSD-2008/00013
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Volume: 114; Journal Issue: 32; Journal ID: ISSN 0027-8424
- Publisher:
- National Academy of Sciences, Washington, DC (United States)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; histidine relaxase; antibiotic resistance; horizontal gene transfer; X-ray structure; Staphylococcus aureus
Citation Formats
Pluta, Radoslaw, Boer, D. Roeland, Lorenzo-Diaz, Fabian, Russi, Silvia, Gomez, Hansel, Fernandez-Lopez, Cris, Perez-Luque, Rosa, Orozco, Modesto, Espinosa, Manuel, and Coll, Miquel. Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance. United States: N. p., 2017.
Web. doi:10.1073/pnas.1702971114.
Pluta, Radoslaw, Boer, D. Roeland, Lorenzo-Diaz, Fabian, Russi, Silvia, Gomez, Hansel, Fernandez-Lopez, Cris, Perez-Luque, Rosa, Orozco, Modesto, Espinosa, Manuel, & Coll, Miquel. Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance. United States. https://doi.org/10.1073/pnas.1702971114
Pluta, Radoslaw, Boer, D. Roeland, Lorenzo-Diaz, Fabian, Russi, Silvia, Gomez, Hansel, Fernandez-Lopez, Cris, Perez-Luque, Rosa, Orozco, Modesto, Espinosa, Manuel, and Coll, Miquel. Mon .
"Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance". United States. https://doi.org/10.1073/pnas.1702971114. https://www.osti.gov/servlets/purl/1390289.
@article{osti_1390289,
title = {Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance},
author = {Pluta, Radoslaw and Boer, D. Roeland and Lorenzo-Diaz, Fabian and Russi, Silvia and Gomez, Hansel and Fernandez-Lopez, Cris and Perez-Luque, Rosa and Orozco, Modesto and Espinosa, Manuel and Coll, Miquel},
abstractNote = {Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resistant staphylococci and streptococci infections posing major threats to human health. The MOBV family of relaxases accounts for approximately 85% of all relaxases found in Staphylococcus aureus isolates. Here, we present six structures of the MOBV relaxase MobM from the promiscuous plasmid pMV158 in complex with several origin of transfer DNA fragments. A combined structural, biochemical, and computational approach reveals that MobM follows a previously uncharacterized histidine/metal-dependent DNA processing mechanism, which involves the formation of a covalent phosphoramidate histidine-DNA adduct for cell-to-cell transfer. In conclusion, we discuss how the chemical features of the high-energy phosphorus-nitrogen bond shape the dominant position of MOBV histidine relaxases among small promiscuous plasmids and their preference toward Gram-positive bacteria.},
doi = {10.1073/pnas.1702971114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 32,
volume = 114,
place = {United States},
year = {Mon Jul 24 00:00:00 EDT 2017},
month = {Mon Jul 24 00:00:00 EDT 2017}
}
Web of Science
Works referenced in this record:
Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC
journal, November 2003
- Guasch, Alicia; Lucas, María; Moncalián, Gabriel
- Nature Structural & Molecular Biology, Vol. 10, Issue 12
Features of the Plasmid pMV158-encoded MobM, a Protein Involved in its Mobilization
journal, January 2004
- de Antonio, Carmen; Farı́as, Marı́a Eugenia; de Lacoba, Mario Garcı́a
- Journal of Molecular Biology, Vol. 335, Issue 3
Conjugative and mobilizable genomic islands in bacteria: evolution and diversity
journal, July 2014
- Bellanger, Xavier; Payot, Sophie; Leblond-Bourget, Nathalie
- FEMS Microbiology Reviews, Vol. 38, Issue 4
Initiation of replication of plasmid pMV158: mechanisms of DNA strand-transfer reactions mediated by the initiator RepB protein
journal, May 1997
- Moscoso, Miriam; Eritja, Ramón; Espinosa, Manuel
- Journal of Molecular Biology, Vol. 268, Issue 5
Coupling Factors in Macromolecular Type-IV Secretion Machineries
journal, May 2004
- Gomis-Ruth, F.; Sola, M.; Cruz, F.
- Current Pharmaceutical Design, Vol. 10, Issue 13
Bringing them together: Plasmid pMV158 rolling circle replication and conjugation under an evolutionary perspective
journal, July 2014
- Lorenzo-Díaz, Fabián; Fernández-López, Cris; Garcillán-Barcia, M. Pilar
- Plasmid, Vol. 74
Bacterial conjugation: a two-step mechanism for DNA transport
journal, July 2002
- Llosa, Matxalen; Gomis-Ruth, F. Xavier; Coll, Miquel
- Molecular Microbiology, Vol. 45, Issue 1
Plasmids as models for studying macromolecular interactions: the pMV158 paradigm
journal, April 2013
- Espinosa, Manuel
- Research in Microbiology, Vol. 164, Issue 3
Breaking and joining single-stranded DNA: the HUH endonuclease superfamily
journal, July 2013
- Chandler, Michael; de la Cruz, Fernando; Dyda, Fred
- Nature Reviews Microbiology, Vol. 11, Issue 8
Making and Breaking Nucleic Acids: Two-Mg2+-Ion Catalysis and Substrate Specificity
journal, April 2006
- Yang, Wei; Lee, Jae Young; Nowotny, Marcin
- Molecular Cell, Vol. 22, Issue 1
Mobilization Function of the pBHR1 Plasmid, a Derivative of the Broad-Host-Range Plasmid pBBR1
journal, March 2001
- Szpirer, C. Y.; Faelen, M.; Couturier, M.
- Journal of Bacteriology, Vol. 183, Issue 6
Unveiling the Molecular Mechanism of a Conjugative Relaxase: The Structure of TrwC Complexed with a 27-mer DNA Comprising the Recognition Hairpin and the Cleavage Site
journal, May 2006
- Boer, Roeland; Russi, Silvia; Guasch, Alicia
- Journal of Molecular Biology, Vol. 358, Issue 3
The mechanism and control of DNA transfer by the conjugative relaxase of resistance plasmid pCU1
journal, May 2010
- Nash, Rebekah Potts; Habibi, Sohrab; Cheng, Yuan
- Nucleic Acids Research, Vol. 38, Issue 17
A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin.
journal, December 1987
- Coll, M.; Frederick, C. A.; Wang, A. H.
- Proceedings of the National Academy of Sciences, Vol. 84, Issue 23
Mechanism for the Autophosphorylation of CheA Histidine Kinase: QM/MM Calculations
journal, October 2011
- Shi, Ting; Lu, Yunxiang; Liu, Xinyi
- The Journal of Physical Chemistry B, Vol. 115, Issue 41
Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus
journal, January 2013
- Edwards, J. S.; Betts, L.; Frazier, M. L.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 8
Inter- and Intramolecular Determinants of the Specificity of Single-Stranded DNA Binding and Cleavage by the F Factor Relaxase
journal, October 2005
- Larkin, Chris; Datta, Saumen; Harley, Matthew J.
- Structure, Vol. 13, Issue 10
The Structure of the Minimal Relaxase Domain of MobA at 2.1 Å Resolution
journal, February 2007
- Monzingo, Arthur F.; Ozburn, Angela; Xia, Shuangluo
- Journal of Molecular Biology, Vol. 366, Issue 1
The diversity of conjugative relaxases and its application in plasmid classification
journal, May 2009
- Garcillán-Barcia, María Pilar; Francia, María Victoria; de La Cruz, Fernando
- FEMS Microbiology Reviews, Vol. 33, Issue 3
TraG Encoded by the pIP501 Type IV Secretion System Is a Two-Domain Peptidoglycan-Degrading Enzyme Essential for Conjugative Transfer
journal, August 2013
- Arends, K.; Celik, E. -K.; Probst, I.
- Journal of Bacteriology, Vol. 195, Issue 19
Towards an integrated model of bacterial conjugation
journal, September 2014
- Cabezón, Elena; Ripoll-Rozada, Jorge; Peña, Alejandro
- FEMS Microbiology Reviews
Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis
journal, July 2011
- Lassila, Jonathan K.; Zalatan, Jesse G.; Herschlag, Daniel
- Annual Review of Biochemistry, Vol. 80, Issue 1
Nucleases: diversity of structure, function and mechanism
journal, September 2010
- Yang, Wei
- Quarterly Reviews of Biophysics, Vol. 44, Issue 1
Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains
journal, May 2009
- Boer, D. Roeland; Ruíz-Masó, José A.; López-Blanco, José R.
- The EMBO Journal, Vol. 28, Issue 11
Large-scale filter mating assay for intra- and inter-specific conjugal transfer of the promiscuous plasmid pMV158 in Gram-positive bacteria
journal, January 2009
- Lorenzo-Díaz, Fabián; Espinosa, Manuel
- Plasmid, Vol. 61, Issue 1
Nicking activity of the pMV158 MobM relaxase on cognate and heterologous origins of transfer
journal, July 2013
- Fernández-López, Cris; Lorenzo-Díaz, Fabián; Pérez-Luque, Rosa
- Plasmid, Vol. 70, Issue 1
Functional Properties and Structural Requirements of the Plasmid pMV158-Encoded MobM Relaxase Domain
journal, April 2013
- Fernandez-Lopez, C.; Pluta, R.; Perez-Luque, R.
- Journal of Bacteriology, Vol. 195, Issue 13
Assignment of Functional Amino Acids around the Active Site of Human DNA Topoisomerase IIα
journal, May 2000
- Okada, Yoshito; Ito, Yasutomo; Kikuchi, Akihiko
- Journal of Biological Chemistry, Vol. 275, Issue 32
Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow
journal, July 2010
- Wozniak, Rachel A. F.; Waldor, Matthew K.
- Nature Reviews Microbiology, Vol. 8, Issue 8
Plasmid rolling circle replication: identification of the RNA polymerase-directed primer RNA and requirement for DNA polymerase I for lagging strand synthesis
journal, September 1997
- Kramer, M. G.
- The EMBO Journal, Vol. 16, Issue 18
The MobM relaxase domain of plasmid pMV158: thermal stability and activity upon Mn2+ and specific DNA binding
journal, February 2011
- Lorenzo-Díaz, Fabián; Dostál, Lubomir; Coll, Miquel
- Nucleic Acids Research, Vol. 39, Issue 10
One cannot rule them all: Are bacterial toxins-antitoxins druggable?
journal, March 2015
- Chan, Wai Ting; Balsa, Dolors; Espinosa, Manuel
- FEMS Microbiology Reviews, Vol. 39, Issue 4
An equivalent metal ion in one- and two-metal-ion catalysis
journal, October 2008
- Yang, Wei
- Nature Structural & Molecular Biology, Vol. 15, Issue 11
Mobility of Plasmids
journal, August 2010
- Smillie, C.; Garcillan-Barcia, M. P.; Francia, M. V.
- Microbiology and Molecular Biology Reviews, Vol. 74, Issue 3
Focus on phosphohistidine
journal, November 2006
- Attwood, P. V.; Piggott, M. J.; Zu, X. L.
- Amino Acids, Vol. 32, Issue 1
Histidine phosphorylation in biological systems
journal, January 2008
- Puttick, Jennifer; Baker, Edward N.; Delbaere, Louis T. J.
- Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1784, Issue 1
Complete nucleotide sequence of pGO1, the prototype conjugative plasmid from the staphylococci
journal, July 2009
- Caryl, J. A.; O’Neill, A. J.
- Plasmid, Vol. 62, Issue 1
Cut and move: protein machinery for DNA processing in bacterial conjugation
journal, December 2006
- Gomis-Rüth, F. Xavier; Coll, Miquel
- Current Opinion in Structural Biology, Vol. 16, Issue 6
A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases
journal, June 2010
- Schmidt, Bryan H.; Burgin, Alex B.; Deweese, Joseph E.
- Nature, Vol. 465, Issue 7298
Contrasting lifestyles of rolling-circle phages and plasmids
journal, November 1998
- Novick, Richard P.
- Trends in Biochemical Sciences, Vol. 23, Issue 11
The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials
journal, April 2015
- Lanza, Val Fernández; Tedim, Ana P.; Martínez, José Luís
- Microbiology Spectrum, Vol. 3, Issue 2
Rapid detection and isolation of covalent DNA/protein complexes: application to topoisomerase I and II.
journal, March 1984
- Trask, D. K.; DiDonato, J. A.; Muller, M. T.
- The EMBO Journal, Vol. 3, Issue 3
Works referencing / citing this record:
Computational and mutational analysis of TatD DNase of Bacillus anthracis
journal, February 2019
- Singh, Damini; Rahi, Amit; Kumari, Romika
- Journal of Cellular Biochemistry, Vol. 120, Issue 7
Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation
journal, May 2019
- Tu, Jie; Chen, Ran; Yang, Ye
- Nature Chemical Biology, Vol. 15, Issue 6
DNA processing by the MOBH family relaxase TraI encoded within the gonococcal genetic island
journal, July 2019
- Heilers, Jan-Hendrik; Reiners, Jens; Heller, Eva-Maria
- Nucleic Acids Research, Vol. 47, Issue 15
Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs
journal, May 2019
- Soler, Nicolas; Robert, Emilie; Chauvot de Beauchêne, Isaure
- Mobile DNA, Vol. 10, Issue 1
Regulation of Gram-Positive Conjugation
journal, May 2019
- Kohler, Verena; Keller, Walter; Grohmann, Elisabeth
- Frontiers in Microbiology, Vol. 10
Complete labelling of pneumococcal DNA-binding proteins with seleno-L-methionine
journal, November 2019
- Lorenzo-Diaz, Fabián; Moreno-Córdoba, Inmaculada; Espinosa, Manuel
- Journal of Microbiological Methods, Vol. 166
The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation
journal, November 2017
- Miguel-Arribas, Andrés; Hao, Jian-An; Luque-Ortega, Juan R.
- Frontiers in Microbiology, Vol. 8
Relaxase MobM Induces a Molecular Switch at Its Cognate Origin of Transfer
journal, February 2018
- Lorenzo-Díaz, Fabián; Fernández-López, Cris; Guillén-Guío, Beatriz
- Frontiers in Molecular Biosciences, Vol. 5