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Lin DL, Traglia GM, Baker R, Sherratt DJ, Ramirez MS, Tolmasky ME. Functional Analysis of the Acinetobacter baumannii XerC and XerD Site-Specific Recombinases: Potential Role in Dissemination of Resistance Genes. Antibiotics (Basel) 2020; 9:E405. [PMID: 32668667 PMCID: PMC7399989 DOI: 10.3390/antibiotics9070405] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/09/2020] [Accepted: 07/11/2020] [Indexed: 12/12/2022] Open
Abstract
Modules composed of a resistance gene flanked by Xer site-specific recombination sites, the vast majority of which were found in Acinetobacter baumannii, are thought to behave as elements that facilitate horizontal dissemination. The A. baumannii xerC and xerD genes were cloned, and the recombinant clones used to complement the cognate Escherichia coli mutants. The complemented strains supported the resolution of plasmid dimers, and, as is the case with E. coli and Klebsiella pneumoniae plasmids, the activity was enhanced when the cells were grown in a low osmolarity growth medium. Binding experiments showed that the partially purified A. baumannii XerC and XerD proteins (XerCAb and XerDAb) bound synthetic Xer site-specific recombination sites, some of them with a nucleotide sequence deduced from existing A. baumannii plasmids. Incubation with suicide substrates resulted in the covalent attachment of DNA to a recombinase, probably XerCAb, indicating that the first step in the recombination reaction took place. The results described show that XerCAb and XerDAb are functional proteins and support the hypothesis that they participate in horizontal dissemination of resistant genes among bacteria.
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Affiliation(s)
- David L. Lin
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA; (D.L.L.); (M.S.R.)
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (R.B.); (D.J.S.)
| | - German M. Traglia
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República (UDeLaR), Montevideo 11600, Uruguay;
| | - Rachel Baker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (R.B.); (D.J.S.)
| | - David J. Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (R.B.); (D.J.S.)
| | - Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA; (D.L.L.); (M.S.R.)
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA; (D.L.L.); (M.S.R.)
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (R.B.); (D.J.S.)
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Ramirez MS, Iriarte A, Reyes-Lamothe R, Sherratt DJ, Tolmasky ME. Small Klebsiella pneumoniae Plasmids: Neglected Contributors to Antibiotic Resistance. Front Microbiol 2019; 10:2182. [PMID: 31616398 PMCID: PMC6764390 DOI: 10.3389/fmicb.2019.02182] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Klebsiella pneumoniae is the causative agent of community- and, more commonly, hospital-acquired infections. Infections caused by this bacterium have recently become more dangerous due to the acquisition of multiresistance to antibiotics and the rise of hypervirulent variants. Plasmids usually carry genes coding for resistance to antibiotics or virulence factors, and the recent sequence of complete K. pneumoniae genomes showed that most strains harbor many of them. Unlike large plasmids, small, usually high copy number plasmids, did not attract much attention. However, these plasmids may include genes coding for specialized functions, such as antibiotic resistance, that can be expressed at high levels due to gene dosage effect. These genes may be part of mobile elements that not only facilitate their dissemination but also participate in plasmid evolution. Furthermore, high copy number plasmids may also play a role in evolution by allowing coexistence of mutated and non-mutated versions of a gene, which helps to circumvent the constraints imposed by trade-offs after certain genes mutate. Most K. pneumoniae plasmids 25-kb or smaller replicate by the ColE1-type mechanism and many of them are mobilizable. The transposon Tn1331 and derivatives were found in a high percentage of these plasmids. Another transposon that was found in representatives of this group is the bla KPC-containing Tn4401. Common resistance determinants found in these plasmids were aac(6')-Ib and genes coding for β-lactamases including carbapenemases.
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Affiliation(s)
- Maria S. Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Facultad de Medicina, Universidad de la República de Uruguay, Montevideo, Uruguay
| | | | - David J. Sherratt
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Sciences, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA, United States
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Toleikis A, Webb MR, Molloy JE. oriD structure controls RepD initiation during rolling-circle replication. Sci Rep 2018; 8:1206. [PMID: 29352198 PMCID: PMC5775427 DOI: 10.1038/s41598-017-18817-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/18/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial antibiotic resistance is often carried by circular DNA plasmids that are copied separately from the genomic DNA and can be passed to other bacteria, spreading the resistance. The chloramphenicol-resistance plasmid pC221 from Staphylococcus aureus is duplicated by a process called asymmetric rolling circle replication. It is not fully understood how the replication process is regulated but its initiation requires a plasmid-encoded protein called RepD that nicks one strand of the parent plasmid at the double-stranded origin of replication (oriD). Using magnetic tweezers to control the DNA linking number we found RepD nicking occurred only when DNA was negatively supercoiled and that binding of a non-nicking mutant (RepDY188F) stabilized secondary structure formation at oriD. Quenched-flow experiments showed the inverted complementary repeat sequence, ICRII, within oriD was most important for rapid nicking of intact plasmids. Our results show that cruciform formation at oriD is an important control for initiation of plasmid replication.
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Affiliation(s)
- Algirdas Toleikis
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- WMS - Cell and Development Biology, University of Warwick, Coventry, CV4 7AL, UK
| | - Martin R Webb
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Justin E Molloy
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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Amikacin: Uses, Resistance, and Prospects for Inhibition. Molecules 2017; 22:molecules22122267. [PMID: 29257114 PMCID: PMC5889950 DOI: 10.3390/molecules22122267] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 12/16/2022] Open
Abstract
Aminoglycosides are a group of antibiotics used since the 1940s to primarily treat a broad spectrum of bacterial infections. The primary resistance mechanism against these antibiotics is enzymatic modification by aminoglycoside-modifying enzymes that are divided into acetyl-transferases, phosphotransferases, and nucleotidyltransferases. To overcome this problem, new semisynthetic aminoglycosides were developed in the 70s. The most widely used semisynthetic aminoglycoside is amikacin, which is refractory to most aminoglycoside modifying enzymes. Amikacin was synthesized by acylation with the l-(-)-γ-amino-α-hydroxybutyryl side chain at the C-1 amino group of the deoxystreptamine moiety of kanamycin A. The main amikacin resistance mechanism found in the clinics is acetylation by the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib], an enzyme coded for by a gene found in integrons, transposons, plasmids, and chromosomes of Gram-negative bacteria. Numerous efforts are focused on finding strategies to neutralize the action of AAC(6')-Ib and extend the useful life of amikacin. Small molecules as well as complexes ionophore-Zn+2 or Cu+2 were found to inhibit the acetylation reaction and induced phenotypic conversion to susceptibility in bacteria harboring the aac(6')-Ib gene. A new semisynthetic aminoglycoside, plazomicin, is in advance stage of development and will contribute to renewed interest in this kind of antibiotics.
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Muskhelishvili G, Travers A. The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity. Biophys Rev 2016; 8:5-22. [PMID: 28510220 PMCID: PMC5425797 DOI: 10.1007/s12551-016-0237-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023] Open
Abstract
We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.
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Affiliation(s)
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
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Higgins NP, Vologodskii AV. Topological Behavior of Plasmid DNA. Microbiol Spectr 2015; 3:10.1128/microbiolspec.PLAS-0036-2014. [PMID: 26104708 PMCID: PMC4480603 DOI: 10.1128/microbiolspec.plas-0036-2014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Indexed: 11/20/2022] Open
Abstract
The discovery of the B-form structure of DNA by Watson and Crick led to an explosion of research on nucleic acids in the fields of biochemistry, biophysics, and genetics. Powerful techniques were developed to reveal a myriad of different structural conformations that change B-DNA as it is transcribed, replicated, and recombined and as sister chromosomes are moved into new daughter cell compartments during cell division. This article links the original discoveries of superhelical structure and molecular topology to non-B form DNA structure and contemporary biochemical and biophysical techniques. The emphasis is on the power of plasmids for studying DNA structure and function. The conditions that trigger the formation of alternative DNA structures such as left-handed Z-DNA, inter- and intra-molecular triplexes, triple-stranded DNA, and linked catenanes and hemicatenanes are explained. The DNA dynamics and topological issues are detailed for stalled replication forks and for torsional and structural changes on DNA in front of and behind a transcription complex and a replisome. The complex and interconnected roles of topoisomerases and abundant small nucleoid association proteins are explained. And methods are described for comparing in vivo and in vitro reactions to probe and understand the temporal pathways of DNA and chromosome chemistry that occur inside living cells.
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Affiliation(s)
- N Patrick Higgins
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
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Plasmid-Mediated Antibiotic Resistance and Virulence in Gram-negatives: the Klebsiella pneumoniae Paradigm. Microbiol Spectr 2014; 2:1-15. [PMID: 25705573 DOI: 10.1128/microbiolspec.plas-0016-2013] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Plasmids harbor genes coding for specific functions including virulence factors and antibiotic resistance that permit bacteria to survive the hostile environment found in the host and resist treatment. Together with other genetic elements such as integrons and transposons, and using a variety of mechanisms, plasmids participate in the dissemination of these traits resulting in the virtual elimination of barriers among different kinds of bacteria. In this article we review the current information about physiology and role in virulence and antibiotic resistance of plasmids from the gram-negative opportunistic pathogen Klebsiella pneumoniae. This bacterium has acquired multidrug resistance and is the causative agent of serious communityand hospital-acquired infections. It is also included in the recently defined ESKAPE group of bacteria that cause most of US hospital infections.
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Small plasmids harboring qnrB19: a model for plasmid evolution mediated by site-specific recombination at oriT and Xer sites. Antimicrob Agents Chemother 2012; 56:1821-7. [PMID: 22290975 DOI: 10.1128/aac.06036-11] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasmids pPAB19-1, pPAB19-2, pPAB19-3, and pPAB19-4, isolated from Salmonella and Escherichia coli clinical strains from hospitals in Argentina, were completely sequenced. These plasmids include the qnrB19 gene and are 2,699, 3,082, 2,989, and 2,702 nucleotides long, respectively, and they share extensive homology among themselves and with other previously described small qnrB19-harboring plasmids. The genetic environment of qnrB19 in all four plasmids is identical to that in these other plasmids and in transposons such as Tn2012, Tn5387, and Tn5387-like. Nucleotide sequence comparisons among these and previously described plasmids showed a variable region characterized by being flanked by an oriT locus and a Xer recombination site. We propose that this arrangement could play a role in the evolution of plasmids and present a model for DNA swapping between plasmid molecules mediated by site-specific recombination events at oriT and a Xer target site.
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Cavalier-Smith T. Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution. Biol Direct 2010; 5:7. [PMID: 20132544 PMCID: PMC2837639 DOI: 10.1186/1745-6150-5-7] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/04/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. RESULTS I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. CONCLUSION Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.
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fpr, a deficient Xer recombination site from a Salmonella plasmid, fails to confer stability by dimer resolution: comparative studies with the pJHCMW1 mwr site. J Bacteriol 2009; 192:883-7. [PMID: 19966005 DOI: 10.1128/jb.01082-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella plasmid pFPTB1 includes a Tn3-like transposon and a Xer recombination site, fpr, which mediates site-specific recombination at efficiencies lower than those required for stabilizing a plasmid by dimer resolution. Mutagenesis and comparative studies with mwr, a site closely related to fpr, indicate that there is an interdependence of the sequences in the XerC binding region and the central region in Xer site-specific recombination sites.
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