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Abstract
Reversible site-specific DNA inversion reactions are widely distributed in bacteria and their viruses. They control a range of biological reactions that most often involve alterations of molecules on the surface of cells or phage. These programmed DNA rearrangements usually occur at a low frequency, thereby preadapting a small subset of the population to a change in environmental conditions, or in the case of phages, an expanded host range. A dedicated recombinase, sometimes with the aid of additional regulatory or DNA architectural proteins, catalyzes the inversion of DNA. RecA or other components of the general recombination-repair machinery are not involved. This chapter discusses site-specific DNA inversion reactions mediated by the serine recombinase family of enzymes and focuses on the extensively studied serine DNA invertases that are stringently controlled by the Fis-bound enhancer regulatory system. The first section summarizes biological features and general properties of inversion reactions by the Fis/enhancer-dependent serine invertases and the recently described serine DNA invertases in Bacteroides. Mechanistic studies of reactions catalyzed by the Hin and Gin invertases are then discussed in more depth, particularly with regards to recent advances in our understanding of the function of the Fis/enhancer regulatory system, the assembly of the active recombination complex (invertasome) containing the Fis/enhancer, and the process of DNA strand exchange by rotation of synapsed subunit pairs within the invertasome. The role of DNA topological forces that function in concert with the Fis/enhancer controlling element in specifying the overwhelming bias for DNA inversion over deletion and intermolecular recombination is emphasized.
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Affiliation(s)
- Reid C. Johnson
- Department of Biological Chemistry, UCLA School of Medicine, Los Angeles, CA 90095-1737, Phone: 310 825-7800, Fax: 310 206-5272
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Yun SH, Ji SC, Jeon HJ, Wang X, Kim SW, Bak G, Lee Y, Lim HM. The CnuK9E H-NS complex antagonizes DNA binding of DicA and leads to temperature-dependent filamentous growth in E. coli. PLoS One 2012; 7:e45236. [PMID: 23028867 PMCID: PMC3441716 DOI: 10.1371/journal.pone.0045236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/20/2012] [Indexed: 01/07/2023] Open
Abstract
Cnu (an OriC-binding nucleoid protein) associates with H-NS. A variant of Cnu was identified as a key factor for filamentous growth of a wild-type Escherichia coli strain at 37°C. This variant (CnuK9E) bears a substitution of a lysine to glutamic acid, causing a charge reversal in the first helix. The temperature-dependent filamentous growth of E. coli bearing CnuK9E could be reversed by either lowering the temperature to 25°C or lowering the CnuK9E concentration in the cell. Gene expression analysis suggested that downregulation of dicA by CnuK9E causes a burst of dicB transcription, which, in turn, elicits filamentous growth. In vivo assays indicated that DicA transcriptionally activates its own gene, by binding to its operator in a temperature-dependent manner. The antagonizing effect of CnuK9E with H-NS on DNA-binding activity of DicA was stronger at 37°C, presumably due to the lower operator binding of DicA at 37°C. These data suggest that the temperature-dependent negative effect of CnuK9E on DicA binding plays a major role in filamentous growth. The C-terminus of DicA shows significant amino acid sequence similarity to the DNA-binding domains of RovA and SlyA, regulators of pathogenic genes in Yersinia and Salmonella, respectively, which also show better DNA-binding activity at 25°C.
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Affiliation(s)
- Sang Hoon Yun
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Taejon, Republic of Korea
| | - Sang Chun Ji
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Taejon, Republic of Korea
| | - Heung Jin Jeon
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Taejon, Republic of Korea
| | - Xun Wang
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Taejon, Republic of Korea
| | - Si Wouk Kim
- Department of Environmental Engineering, Pioneer Research Center for Controlling of Harmful Algal Blooming, Chosun University, Gwangju, Republic of Korea
| | - Geunu Bak
- Department of Chemistry, KAIST, Daejeon, Republic of Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon, Republic of Korea
| | - Heon M. Lim
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Taejon, Republic of Korea
- * E-mail:
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Yun SH, Ji SC, Jeon HJ, Wang X, Lee Y, Choi BS, Lim HM. A mutational study of Cnu reveals attractive forces between Cnu and H-NS. Mol Cells 2012; 33:211-6. [PMID: 22358512 PMCID: PMC3887714 DOI: 10.1007/s10059-012-0006-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 01/09/2012] [Indexed: 10/28/2022] Open
Abstract
Cnu is a small 71-amino acid protein that complexes with H-NS and binds to a specific sequence in the replication origin of the E. coli chromosome. To understand the mechanism of interaction between Cnu and H-NS, we used bacterial genetics to select and analyze Cnu variants that cannot complex with H-NS. Out of 2,000 colonies, 40 Cnu variants were identified. Most variants (82.5%) had a single mutation, but a few variants (17.5%) had double amino acid changes. An in vitro assay was used to identify Cnu variants that were truly defective in H-NS binding. The changes in these defective variants occurred exclusively at charged amino acids (Asp, Glu, or Lys) on the surface of the protein. We propose that the attractive force that governs the Cnu-H-NS interaction is an ionic bond, unlike the hydrophobic interaction that is the major attractive force in most proteins.
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Affiliation(s)
- Sang Hoon Yun
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 305-764,
Korea
| | - Sang Chun Ji
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 305-764,
Korea
- Present address: Department of Pharmacology and Clinical Pharmacology, Seoul National University College of Medicine and Hospital, Seoul 110-799,
Korea
| | - Heung Jin Jeon
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 305-764,
Korea
| | - Xun Wang
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 305-764,
Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Byong-Seok Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Heon M. Lim
- Department of Biology, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 305-764,
Korea
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Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Mol Biol 2007; 8:44. [PMID: 17531098 PMCID: PMC1904230 DOI: 10.1186/1471-2199-8-44] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 05/25/2007] [Indexed: 01/11/2023] Open
Abstract
Background The genetic code imposes a dilemma for cells. The DNA must be long enough to encode for the complexity of an organism, yet thin and flexible enough to fit within the cell. The combination of these properties greatly favors DNA collisions, which can knot and drive recombination of the DNA. Despite the well-accepted propensity of cellular DNA to collide and react with itself, it has not been established what the physiological consequences are. Results Here we analyze the effects of recombined and knotted plasmids in E. coli using the Hin site-specific recombination system. We show that Hin-mediated DNA knotting and recombination (i) promote replicon loss by blocking DNA replication; (ii) block gene transcription; and (iii) cause genetic rearrangements at a rate three to four orders of magnitude higher than the rate for an unknotted, unrecombined plasmid. Conclusion These results show that DNA reactivity leading to recombined and knotted DNA is potentially toxic and may help drive genetic evolution.
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Kim MS, Bae SH, Yun SH, Lee HJ, Ji SC, Lee JH, Srivastava P, Lee SH, Chae H, Lee Y, Choi BS, Chattoraj DK, Lim HM. Cnu, a novel oriC-binding protein of Escherichia coli. J Bacteriol 2005; 187:6998-7008. [PMID: 16199570 PMCID: PMC1251610 DOI: 10.1128/jb.187.20.6998-7008.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have found, using a newly developed genetic method, a protein (named Cnu, for oriC-binding nucleoid-associated) that binds to a specific 26-base-pair sequence (named cnb) in the origin of replication of Escherichia coli, oriC. Cnu is composed of 71 amino acids (8.4 kDa) and shows extensive amino acid identity to a group of proteins belonging to the Hha/YmoA family. Cnu was previously discovered as a protein that, like Hha, complexes with H-NS in vitro. Our in vivo and in vitro assays confirm the results and further suggest that the complex formation with H-NS is involved in Cnu/Hha binding to cnb. Unlike the hns mutants, elimination of either the cnu or hha gene did not disturb the growth rate, origin content, and synchrony of DNA replication initiation of the mutants compared to the wild-type cells. However, the cnu hha double mutant was moderately reduced in origin content. The Cnu/Hha complex with H-NS thus could play a role in optimal activity of oriC.
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Affiliation(s)
- Myung Suk Kim
- Department of Biology, School of Biological Sciences and Biotechnology, Chungnam National University, Taejon, 305-764 Korea
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Sanders ER, Johnson RC. Stepwise dissection of the Hin-catalyzed recombination reaction from synapsis to resolution. J Mol Biol 2004; 340:753-66. [PMID: 15223318 DOI: 10.1016/j.jmb.2004.05.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 05/03/2004] [Accepted: 05/05/2004] [Indexed: 10/26/2022]
Abstract
The Hin DNA invertase promotes a site-specific DNA recombination reaction in the Salmonella chromosome. The native Hin reaction exhibits overwhelming selectivity for promoting inversions between appropriately oriented recombination sites and requires the Fis regulatory protein, a recombinational enhancer, and a supercoiled DNA substrate. Here, we report a robust recombination reaction employing oligonucleotide substrates and a hyperactive mutant form of Hin. Synaptic complex intermediates purified by gel electrophoresis were found to contain four Hin protomers bound to two recombination sites. Each Hin protomer is associated covalently with a cleaved DNA end. The cleaved complexes can be ligated into both parental and recombinant orientations at equivalent frequencies, provided the core residues can base-pair, and are readily disassembled into separated DNA fragments bound by Hin dimers. Kinetic analyses reveal that synapsis occurs rapidly, followed by comparatively slow Hin-catalyzed DNA cleavage. Subsequent steps of the reaction, including DNA exchange and ligation, are fast. Thus, post-synaptic step(s) required for DNA cleavage limit the overall rate of the recombination reaction.
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Affiliation(s)
- Erin R Sanders
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA
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