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Lee HH, Hsu CC, Lin YL, Chen CW. Linear plasmids mobilize linear but not circular chromosomes in Streptomyces: support for the ‘end first’ model of conjugal transfer. Microbiology (Reading) 2011; 157:2556-2568. [DOI: 10.1099/mic.0.051441-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Gram-positive bacteria of the genus Streptomyces possess linear chromosomes and linear plasmids capped by terminal proteins covalently bound to the 5′ ends of the DNA. The linearity of Streptomyces chromosomes raises the question of how they are transferred during conjugation, particularly when the mobilizing plasmids are also linear. The classical rolling circle replication model for transfer of circular plasmids and chromosomes from an internal origin cannot be applied to this situation. Instead it has been proposed that linear Streptomyces plasmids mobilize themselves and the linear chromosomes from their telomeres using terminal-protein-primed DNA synthesis. In support of this ‘end first’ model, we found that artificially circularized Streptomyces chromosomes could not be mobilized by linear plasmids (SLP2 and SCP1), while linear chromosomes could. In comparison, a circular plasmid (pIJ303) could mobilize both circular and linear chromosomes at the same efficiencies. Interestingly, artificially circularized SLP2 exhibited partial self-transfer capability, indicating that, being a composite replicon, it may have acquired the additional internal origin of transfer from an ancestral circular plasmid during evolution.
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Affiliation(s)
- Hsuan-Hsuan Lee
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Chin-Chen Hsu
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Yen-Ling Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Carton W. Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
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Boitz JM, Ullman B. Amplification of adenine phosphoribosyltransferase suppresses the conditionally lethal growth and virulence phenotype of Leishmania donovani mutants lacking both hypoxanthine-guanine and xanthine phosphoribosyltransferases. J Biol Chem 2010; 285:18555-64. [PMID: 20363738 PMCID: PMC2881781 DOI: 10.1074/jbc.m110.125393] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 03/31/2010] [Indexed: 11/06/2022] Open
Abstract
Leishmania donovani cannot synthesize purines de novo and obligatorily scavenge purines from the host. Previously, we described a conditional lethal Deltahgprt/Deltaxprt mutant of L. donovani (Boitz, J. M., and Ullman, B. (2006) J. Biol. Chem. 281, 16084-16089) that establishes that L. donovani salvages purines primarily through hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and xanthine phosphoribosyltransferase (XPRT). Unlike wild type L. donovani, the Deltahgprt/Deltaxprt knock-out cannot grow on 6-oxypurines and displays an absolute requirement for adenine or adenosine and 2'-deoxycoformycin, an inhibitor of parasite adenine aminohydrolase activity. Here, we demonstrate that the ability of Deltahgprt/Deltaxprt parasites to infect mice was profoundly compromised. Surprisingly, mutant parasites that survived the initial passage through mice partially regained their virulence properties, exhibiting a >10-fold increase in parasite burden in a subsequent mouse infection. To dissect the mechanism by which Deltahgprt/Deltaxprt parasites persisted in vivo, suppressor strains that had regained their capacity to grow under restrictive conditions were cloned from cultured Deltahgprt/Deltaxprt parasites. The ability of these suppressor clones to grow in and metabolize 6-oxypurines could be ascribed to a marked amplification and overexpression of the adenine phosphoribosyltransferase (APRT) gene. Moreover, transfection of Deltahgprt/Deltaxprt cells with an APRT episome recapitulated the suppressor phenotype in vitro and enabled growth on 6-oxypurines. Biochemical studies further showed that hypoxanthine, unexpectedly, was an inefficient substrate for APRT, evidence that could account for the ability of the suppressors to metabolize hypoxanthine. Subsequent analysis implied that APRT amplification was also a potential contributory mechanism by which Deltahgprt/Deltaxprt parasites displayed persistence and increased virulence in mice.
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Affiliation(s)
- Jan M. Boitz
- From the Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239
| | - Buddy Ullman
- From the Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239
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Li A, Chen X, Ugaz VM. Miniaturized System for Rapid Field Inversion Gel Electrophoresis of DNA with Real-Time Whole-Gel Detection. Anal Chem 2010; 82:1831-7. [DOI: 10.1021/ac902490e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Airong Li
- College of Chemical Engineering, Sichuan University, Chengdu, PR China, and Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, 77843-3122
| | - Xiaojia Chen
- College of Chemical Engineering, Sichuan University, Chengdu, PR China, and Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, 77843-3122
| | - Victor M. Ugaz
- College of Chemical Engineering, Sichuan University, Chengdu, PR China, and Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, 77843-3122
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Chen X, Ugaz VM. Investigating DNA migration in pulsed fields using a miniaturized FIGE system. Electrophoresis 2008; 29:4761-7. [DOI: 10.1002/elps.200800113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sellek RE, Escudero R, Gil H, Rodríguez I, Chaparro E, Pérez-Pastrana E, Vivo A, Anda P. In vitro culture of Borrelia garinii results in loss of flagella and decreased invasiveness. Infect Immun 2002; 70:4851-8. [PMID: 12183529 PMCID: PMC128296 DOI: 10.1128/iai.70.9.4851-4858.2002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A virulent, low-passage culture of a tick-derived strain of Borrelia garinii was subjected to serial in vitro passages, from which inoculations were made into C3H/HeN mice. A full display of pathogenicity was observed through passage 4, as measured by cultures of ear punch biopsy samples and internal organs and determination of tibiotarsal joint swelling. Decreased dissemination through skin and infection of internal organs were observed beginning at passage 6. These losses correlated with both the selection of clones harboring 21% less flagella than the parent strain, as seen by electron microscopy, and loss of the motility of the higher passages, as demonstrated by a swarm assay. However, during the chronic phase (3 months after infection), spirochetes were cultured from the bladder and kidney of a mouse inoculated with passage 12. The kidney isolate had the same number of flagella and motility as the original low-passage isolate. Although we can't exclude the possibility that other subtle variations may be arising given the uncloned nature of the isolate, we have found a strong association between loss of flagella and decreased invasiveness. Arthritogenicity progressively decreased with passages, so that only 12.5% of chronically infected mice inoculated with passage 29 still presented with joint swelling, concurrent with a decrease in the staining intensity in a Southern blot with a vlsE-based probe. These results suggest a multifactorial model in which the number of flagella drives the invasiveness of this agent, while plasmid-associated factors are responsible for triggering arthritogenicity.
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Affiliation(s)
- Ricela E Sellek
- Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220-Majadahonda, Madrid, Spain
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Ito T, Hohjoh H, Sakaki Y. Pulsed-field polyacrylamide gel electrophoresis: basic phenomena and applications. Electrophoresis 1993; 14:278-82. [PMID: 8500458 DOI: 10.1002/elps.1150140149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Pulsed-field gel electrophoresis (PFGE) using polyacrylamide gels, termed pulsed-field polyacrylamide gel electrophoresis (PF-PAGE), had been developed for the effective separation of linear DNAs from circular ones [1]. The first generation PF-PAGE employed horizontal polyacrylamide gels run in a contour-clamped homogeneous electric field (CHEF) apparatus. The second generation system, using a vertical slab gel in a discontinuous buffer system and field inversion gel electrophoresis (FIGE), was found to be easier to handle and requires a much shorter time for separation than the previous one [2]. In this report, basic aspects of the second generation PF-PAGE, such as the effects of a discontinuous buffer system and field inversion on the DNA migration in polyacrylamide gels, were investigated. The results indicate that the periodic inversion of electric field can broaden the resolving capability of polyacrylamide gels, enabling DNAs that otherwise fail to enter polyacrylamide gels to be resolved in such systems. Successful and possible applications of PF-PAGE techniques are also discussed.
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Affiliation(s)
- T Ito
- Laboratory of Molecular Medicine, University of Tokyo, Japan
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Turmel C, Noolandi J. Effect of one-dimensional pulsed-field gel electrophoresis on linear and circular DNA. Electrophoresis 1993; 14:304-12. [PMID: 8500461 DOI: 10.1002/elps.1150140153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A summary of the three main one-dimensional pulsed-field strategies (zero-integrated field, forward-biased field, and high frequency modulation) used for separating DNA molecules without band inversion within a preselected size range is given. Each of these strategies has size-specific features which make separations up to 6 Mbp possible. We applied the same methodology to circular DNAs varying in size from 2 kbp to about 4 Mbp. The migration of intermediate-sized circular plasmids (50 kbp-400 kbp) under these pulse conditions remains unexplained. On the other hand, preliminary results show that the migration of very large molecules, which are expected to be circular, comigrate with linear chromosomes of the same size under certain pulse conditions. We hypothesize that sample preparation, or the effect of the pulsed field, can create breakage and linearize very large circular DNAs, or that very large circular DNAs (> 2 Mbp) act like linear DNAs of the same size when submitted to one-dimensional pulsed-field gel electrophoresis conditions. The most likely possibility is that some of the circular DNAs have been linearized with one break during sample preparation, giving rise to a band at about 4 Mbp. The circular DNAs with more than one break may form an indistinguishable smear.
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Affiliation(s)
- C Turmel
- Xerox Research Centre, Mississauga, Ontario, Canada
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Smith DR, Smyth AP, Strauss WM, Moir DT. Incorporation of copy-number control elements into yeast artificial chromosomes by targeted homologous recombination. Mamm Genome 1993; 4:141-7. [PMID: 8439726 DOI: 10.1007/bf00352229] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have developed a pair of vectors for exchanging yeast artificial chromosome (YAC) arms by targeted homologous recombination. These conversion vectors allow the introduction of copy-number control elements into YACs constructed with pYAC4 or related vectors. YACs modified in this way provide an enriched source of DNA for genetic or biochemical studies. A LYS2 gene on the conversion vector provides a genetic selection for the modified YACs after transformation with appropriately prepared vector. A background of Lys+ clones that do not contain modified YACs is also present. However, clones with converted YACs can be distinguished from this background by counter-screening for loss of the original p YAC4 TRP1 arm (Trp- phenotype). The elimination of yeast replication origins (ARS elements) from the conversion vectors increased the frequency of Lys+ Trp- clones, but resulted in weaker amplification. Several YACs have been converted with these vectors, and the fate of the transformed DNA and of the resident YAC DNA has been systematically investigated.
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Affiliation(s)
- D R Smith
- Collaborative Research, Inc., Waltham, Massachusetts 02154
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Sobral BW, Honeycutt RJ, Atherly AG, McClelland M. Electrophoretic separation of the three Rhizobium meliloti replicons. J Bacteriol 1991; 173:5173-80. [PMID: 1860826 PMCID: PMC208210 DOI: 10.1128/jb.173.16.5173-5180.1991] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The megaplasmids and the chromosome from the bacterium Rhizobium meliloti 1021 were separated in preparative quantities by using transverse alternating-field gel electrophoresis. The genetic content of each electrophoretically separated band was determined by Southern hybridization with replicon-specific probes and by comparison with Agrobacterium tumefaciens transconjugants harboring either pSym-a or pSym-b megaplasmids. Pulsed-field gel electrophoresis analyses of PacI (5'-TTAATTAA-3') and SwaI (5'-ATTTAAAT-3') digests of the whole genome and of the separated replicons were used to calculate genome sizes in two R. meliloti strains. In these strains, PacI digestion yielded only four fragments for the entire genome. The sizes of the PacI fragments from R. meliloti 1021 in megabase pairs (Mb) were 3.32 +/- 0.30, 1.42 +/- 0.13, 1.21 +/- 0.10, and 0.55 +/- 0.08, for a total genome size of 6.50 +/- 0.61 Mb. Southern hybridization with replicon-specific probes assigned one PacI fragment to the chromosome of R. meliloti 1021, one to pRme1021a, and two to pRme1021b. PacI digestion of A. tumefaciens pTi-cured, pSym transconjugants confirmed these assignments. In agreement with PacI data, the addition of the six SwaI fragments from R. meliloti 1021 gave a genome size of 6.54 +/- 0.43 Mb. pRme1021a was calculated to be 1.42 +/- 0.13 Mb, 1.34 +/- 0.09 Mb, and 1.38 +/- 0.12 Mb on the basis of PacI digestion, SwaI digestion, and the migration of uncut pRme1021a, respectively. pRme1021b was calculated to be 1.76 +/- 0.18 Mb, 1.65 +/- 0.10 Mb, and 1.74 +/- 0.13 Mb on the basis of PacI digestion, SwaI digestion, and the migration of uncut pRme1021B, respectively. The R. meliloti 1021 chromosome was calculated to be 3.32 +/- 0.30 Mb, 3.55 +/- 0.24 Mb, and 3.26 +/- 0.46 Mb on the basis of PacI data, SwaI data, and the migration of uncut chromosome, respectively.
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Affiliation(s)
- B W Sobral
- California Institute of Biological Research, La Jolla 92037
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