1
|
Dunn KL, Rao CV. High-throughput sequencing reveals adaptation-induced mutations in pentose-fermenting strains ofZymomonas mobilis. Biotechnol Bioeng 2015; 112:2228-40. [DOI: 10.1002/bit.25631] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/22/2015] [Accepted: 04/29/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Kori L. Dunn
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
| | - Christopher V. Rao
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; Urbana Illinois 61801
| |
Collapse
|
2
|
Carrasco B, Yadav T, Serrano E, Alonso JC. Bacillus subtilis RecO and SsbA are crucial for RecA-mediated recombinational DNA repair. Nucleic Acids Res 2015; 43:5984-97. [PMID: 26001966 PMCID: PMC4499154 DOI: 10.1093/nar/gkv545] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/12/2015] [Indexed: 11/13/2022] Open
Abstract
Genetic data have revealed that the absence of Bacillus subtilis RecO and one of the end-processing avenues (AddAB or RecJ) renders cells as sensitive to DNA damaging agents as the null recA, suggesting that both end-resection pathways require RecO for recombination. RecA, in the rATP·Mg(2+) bound form (RecA·ATP), is inactive to catalyze DNA recombination between linear double-stranded (ds) DNA and naked complementary circular single-stranded (ss) DNA. We showed that RecA·ATP could not nucleate and/or polymerize on SsbA·ssDNA or SsbB·ssDNA complexes. RecA·ATP nucleates and polymerizes on RecO·ssDNA·SsbA complexes more efficiently than on RecO·ssDNA·SsbB complexes. Limiting SsbA concentrations were sufficient to stimulate RecA·ATP assembly on the RecO·ssDNA·SsbB complexes. RecO and SsbA are necessary and sufficient to 'activate' RecA·ATP to catalyze DNA strand exchange, whereas the AddAB complex, RecO alone or in concert with SsbB was not sufficient. In presence of AddAB, RecO and SsbA are still necessary for efficient RecA·ATP-mediated three-strand exchange recombination. Based on genetic and biochemical data, we proposed that SsbA and RecO (or SsbA, RecO and RecR in vivo) are crucial for RecA activation for both, AddAB and RecJ-RecQ (RecS) recombinational repair pathways.
Collapse
Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| | - Tribhuwan Yadav
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| |
Collapse
|
3
|
Deletion formation mutations in plasmid expression vectors are unfavored by runaway amplification conditions and differentially selected under kanamycin stress. J Biotechnol 2009; 143:231-8. [DOI: 10.1016/j.jbiotec.2009.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 07/17/2009] [Accepted: 08/03/2009] [Indexed: 01/03/2023]
|
4
|
Lee PC, Park IY, Kim MS, Kim SC. Effect of the replication mode of a plasmid on the stability of multimeric endoxylanase genes in Bacillus subtilis. J Biotechnol 1998; 62:177-85. [PMID: 9729802 DOI: 10.1016/s0168-1656(98)00059-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Effect of the replication mode of a plasmid on the stability of tandemly multimerized endoxylanase genes and a gene dose-dependent expression of the endoxylanase were studied in Bacillus subtilis. The structural genes encoding an endoxylanase, carrying its original promoter and ribosomal binding sequence, were tandemly multimerized and cloned into the Escherichia coli-B. subtilis shuttle plasmid, pJH27 delta 88 or pMTL500e, which has a rolling circle-replicon or a theta (theta)-replicon in B. subtilis, respectively. The cloned dimers in pJH27 delta 88, which has a rolling circle-replicon, spontaneously rearranged to monomers in B. subtilis DB104, whereas those in pMTL500e, having a theta (theta)-replicon, were stably maintained. Expression level of the endoxylanase was proportional to the gene dosage in multimers. The endoxylanase activity in the supernatant increased from 80 U ml-1 with pMTL-1x containing a monomer of the gene to 165 U ml-1 with pMTL-4x containing a tetramer. These results indicate that high level expression of the endoxylanase gene can be obtained by tandemly multimerizing the genes in a plasmid with a theta (theta)-replicon.
Collapse
Affiliation(s)
- P C Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Taejon, South Korea
| | | | | | | |
Collapse
|
5
|
Meima R, Haijema BJ, Dijkstra H, Haan GJ, Venema G, Bron S. Role of enzymes of homologous recombination in illegitimate plasmid recombination in Bacillus subtilis. J Bacteriol 1997; 179:1219-29. [PMID: 9023205 PMCID: PMC178819 DOI: 10.1128/jb.179.4.1219-1229.1997] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The structural stability of plasmid pGP1, which encodes a fusion between the penicillinase gene (penP) of Bacillus licheniformis and the Escherichia coli lacZ gene, was investigated in Bacillus subtilis strains expressing mutated subunits of the ATP-dependent nuclease, AddAB, and strains lacking the major recombination enzyme, RecA. Strains carrying a mutation in the ATP-binding site of the AddB subunit exhibited high levels of plasmid instability, whereas a comparable mutation in the A subunit did not affect plasmid stability. Using an alternative plasmid system, pGP100, we were able to demonstrate that the differences in stability reflected differences in initial recombination frequencies. Based on a comparison of endpoint sequences observed in the various hosts, we speculate that at least two different mechanisms underlie the deletion events involved, the first (type I) occurring between nonrepeated sequences, and the second (type II) occurring between short direct repeats (DRs). The latter event was independent of single-strand replication intermediates and the mode of replication and possibly requires the introduction of double-strand breaks (DSBs) between the repeats. In the absence of functional AddAB complex, or the AddB subunit, DSBs are likely to be processed via a recA-independent mechanism, resulting in intramolecular recombination between the DRs. In wild-type cells, such DSBs are supposed to be either repaired by a mechanism involving AddAB-dependent recombination or degraded by the AddAB-associated exonuclease activity. Plasmid stability assays in a recA mutant showed that (i) the level of deletion formation was considerably higher in this host and (ii) that deletions between short DRs occurred at higher frequencies than those described previously for the parental strain. We propose that in wild-type cells, the recA gene product is involved in recombinational repair of DSBs.
Collapse
Affiliation(s)
- R Meima
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands
| | | | | | | | | | | |
Collapse
|
6
|
Meima R, Haijema BJ, Venema G, Bron S. Overproduction of the ATP-dependent nuclease AddAB improves the structural stability of a model plasmid system in Bacillus subtilis. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:391-8. [PMID: 7565602 DOI: 10.1007/bf02191638] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The effect of the ATP-dependent exonuclease AddAB complex on the structural stability of plasmid pGP1 in Bacillus subtilis was studied. Using deletion mutagenesis and gene amplification techniques, B. subtilis strains were constructed either lacking or overproducing the AddAB complex, a key enzyme in homologous recombination. The deletion mutant possessed no residual ATP-dependent nuclease activity; in contrast, the nuclease activity was up to 30 times higher in lysates of strains carrying multiple copies of the addAB genes in the chromosome. Southern blot analyses of these strains indicated that a linear relationship exists between the number of chromosomal gene copies and the level of AddAB activity. The structural stability of pGP1 was analyzed in the AddAB-deficient and over-producing backgrounds. Frequencies of deletion formation in the plasmid, as monitored by the expression of the pGP1-encoded penP-lacZ fusion on media containing X-gal, were shown to be increased at least 25-fold in the addAB knock-out mutant, whereas the stability of pGP1 was improved up to 15-fold in strains overproducing the AddAB enzyme. A possible explanation for these findings is that interactions between AddAB and plasmid molecules prevent the formation of secondary structures that constitute potential deletion target sites, and thereby enhance the structural stability of plasmids.
Collapse
Affiliation(s)
- R Meima
- Groningen Biomolecular Sciences and Biotechnology Institute, Department of Genetics, University of Groningen, Haren, The Netherlands
| | | | | | | |
Collapse
|
7
|
Alonso JC, Stiege AC, Lüder G. Genetic recombination in Bacillus subtilis 168: effect of recN, recF, recH and addAB mutations on DNA repair and recombination. MOLECULAR & GENERAL GENETICS : MGG 1993; 239:129-36. [PMID: 8510642 DOI: 10.1007/bf00281611] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A recN- (recN1) strain of Bacillus subtilis was constructed. The effects of this and recF, recH and addAB mutations on recombination proficiency were tested. Mutations in the recN, recF, recH and addAB genes, when present in an otherwise Rec+ B. subtilis strain, did not affect genetic exchange. Strains carrying different combinations of mutations in these genes were constructed and examined for their sensitivity to 4-nitroquinoline-1-oxide (4NQO) and recombination proficiency. The recH mutation did not affect the 4NQO sensitivity of recN and recF cells and it only marginally affected that of addA addB cells. However, it reduced genetic recombination in these cells 10(2)- to 10(4)-fold. The addA addB mutations increased the 4NQO sensitivity of recF and recN cells, but completely blocked genetic recombination of recF cells and marginally affected recombination in recN cells. The recN mutation did not affect the recombinational capacity of recF cells. These data indicate that the recN gene product is required for DNA repair and recombination and that the recF, recH and addAB genes provide overlapping activities that compensate for the effects of single mutants proficiency. We proposed that the recF, recH, recB and addA gene products define four different epistatic groups.
Collapse
Affiliation(s)
- J C Alonso
- Max-Planck-Institut für molekulare Genetik, Berlin, Germany
| | | | | |
Collapse
|
8
|
Alonso JC, Lüder G, Trautner TA. Intramolecular homologous recombination in Bacillus subtilis 168. MOLECULAR & GENERAL GENETICS : MGG 1992; 236:60-4. [PMID: 1494351 DOI: 10.1007/bf00279643] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Plasmid resolution from a phage::plasmid chimera was used to measure directly intramolecular recombination in Bacillus subtilis. The system is based on a sigma-replicating plasmid (pC194) cloned into a dispensable region of the lytic bacteriophage SPP1. The plasmid, which confers chloramphenicol resistance, is resolved when SPP1::pC194 phages infect B. subtilis cells, provided the chimera carries a functional, intact copy of the plasmid repH gene. Intramolecular homologous recombination was independent of the RecA and RecL-RecR functions, but dependent on RecF, RecB, RecG, RecP, RecH and AddAB functions. These results are consistent with the hypothesis that B. subtilis has multiple pathways for genetic recombination and allow us to tentatively place the recB and recG genes into a new epistatic group epsilon.
Collapse
Affiliation(s)
- J C Alonso
- Max-Planck-Institut für molekulare Genetik, Berlin, FRG
| | | | | |
Collapse
|
9
|
Abstract
The replication of covalently closed circular supercoiled (form I) DNA in prokaryotes is generally controlled at the initiation level by a rate-limiting effector. Once initiated, replication proceeds via one of two possible modes (theta or sigma replication) which do not rely on functions involved in DNA repair and general recombination. Recently, a novel plasmid replication mode, leading to the accumulation of linear multigenome-length plasmid concatemers in both gram-positive and gram-negative bacteria, has been described. Unlike form I DNA replication, an intermediate recombination step is most probably involved in the initiation of concatemeric plasmid DNA replication. On the basis of structural and functional studies, we infer that recombination-dependent plasmid replication shares important features with phage late replication modes and, in several aspects, parallels the synthesis of plasmid concatemers in phage-infected cells. The characterization of the concatemeric plasmid replication mode has allowed new insights into the mechanisms of DNA replication and recombination in prokaryotes.
Collapse
Affiliation(s)
- J F Viret
- Max-Planck-Institut für molekulare Genetik, Berlin, Germany
| | | | | |
Collapse
|
10
|
Abstract
For the analysis of parameters affecting plasmid stability in Bacillus subtilis, we used a pUB 110-derived shuttle plasmid containing direct and inverted nucleotide repeats (DRs and IRs). Deletions of up to 6 kb were found to occur between DRs of 7 to 16 bp. IRs as small as 43 or 58 bp were shown to stimulate the formation of these deletions in their neighbourhood. However, these structural features (DRs and IRs) per se were not responsible for plasmid instability. The unstable recombinant plasmids, but not their deletion-carrying (delta) derivatives, were found to impair the growth of the host and to accumulate high amounts of linear plasmid multimers [high mol. wt. (hmw) DNA]. We propose that the accumulation of hmw DNA may be the major reason for the selective pressure against recombinant plasmids, and the enrichment of delta-plasmids. Host mutations and other parameters increasing the stability of recombinant plasmids in B. subtilis are described.
Collapse
Affiliation(s)
- H Leonhardt
- Max-Planck-Institut für Molekulare Genetik, Berlin, F.R.G
| | | |
Collapse
|
11
|
Abstract
Recombination in Bacillus subtilis requires the products of numerous rec loci. To dissect the various mechanisms which may be involved in genetic recombination, we constructed a series of isogenic strains containing more than one mutant rec allele. On the basis of their impairment in genetic exchange, the various loci (represented by specific rec alleles) were classified into different epistatic groups. Group alpha consists of rec genes represented by recB, recD, recF, recG, recL, and recR mutations, while group beta comprises the addA and addB mutations. Group gamma consists of the recH and recP mutations. These results suggest that B. subtilis has multiple pathways for genetic recombination and that the products of the genes within the alpha, beta, and gamma epistatic groups are involved in these alternative recombination pathways. The RecA protein is required in all three pathways of intermolecular recombination.
Collapse
Affiliation(s)
- J C Alonso
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | | | | |
Collapse
|
12
|
Bron S, Holsappel S, Venema G, Peeters BP. Plasmid deletion formation between short direct repeats in Bacillus subtilis is stimulated by single-stranded rolling-circle replication intermediates. MOLECULAR & GENERAL GENETICS : MGG 1991; 226:88-96. [PMID: 1903505 DOI: 10.1007/bf00273591] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The effects of the rolling-circle mode of replication and the generation of single-stranded DNA (ss DNA) on plasmid deletion formation between short direct repeats in Bacillus subtilis were studied. Deletion units consisting of direct repeats (9, 18, or 27 bp) that do or do not flank inverted repeats (300 bp) were introduced into various plasmid replicons that generate different amounts of ss DNA (from 0% to 40% of the total plasmid DNA). With ss DNA-generating rolling-circle-type plasmids, deletion frequencies between the direct repeats were 3- to 13-fold higher than in plasmids not generating ss DNA. When the direct repeats flanked inverted repeats the deletion frequencies in ss DNA-generating plasmids were increased by as much as 20- to 140-fold. These results support models for deletion formation based on template-switching errors during complementary strand synthesis of rolling-circle-type plasmids. The structural instability (deletion formation between short direct repeats) of the ss DNA-generating plasmid pTA1060 in B. subtilis was very low in the presence of a functional initiation site for complementary strand synthesis (minus origin). This observation suggests that it will be possible to develop stable host-vector cloning systems for B. subtilis.
Collapse
Affiliation(s)
- S Bron
- Department of Genetics, University of Groningen, Haren, The Netherlands
| | | | | | | |
Collapse
|
13
|
Mollet B, Delley M. Spontaneous deletion formation within the beta-galactosidase gene of Lactobacillus bulgaricus. J Bacteriol 1990; 172:5670-6. [PMID: 2120187 PMCID: PMC526881 DOI: 10.1128/jb.172.10.5670-5676.1990] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To investigate the genetic stability of the dairy organism Lactobacillus bulgaricus, we have analyzed 107 spontaneous mutations of the beta-galactosidase gene of this organism. Ten of these mutations were DNA rearrangements giving rise to different deletions, located predominantly within a small hot spot area. The DNA sequences of the different deletion junctions have been determined. The analysis showed that the deletions can be divided into two classes, depending on the presence of short direct-repeat sequences at the deletion endpoints and on the length of the deleted sequences. Possible mechanisms of these deletion formations and the involvement of inverted-repeat sequences that may enhance slipped DNA mispairing are discussed.
Collapse
Affiliation(s)
- B Mollet
- Nestlé Research Centre, Nestec Ltd., Lausanne, Switzerland
| | | |
Collapse
|