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    Evolutionary history of the phl gene cluster in the plant-associated bacterium Pseudomonas fluorescens
    Moynihan, J.A. ; Morrissey, J.P. ; Coppoolse, E. ; Stiekema, W.J. ; O'Gara, F. ; Boyd, E.F. - \ 2009
    Applied and Environmental Microbiology 75 (2009)7. - ISSN 0099-2240 - p. 2122 - 2131.
    complete genome sequence - antifungal metabolite 2,4-diacetylphloroglucinol - resident soil populations - pv. tomato dc3000 - black root-rot - biocontrol agent - compound 2,4-diacetylphloroglucinol - transcriptional repressor - arabidopsis-thaliana - biosynthesis
    Pseudomonas fluorescens is of agricultural and economic importance as a biological control agent largely because of its plant-association and production of secondary metabolites, in particular 2, 4-diacetylphloroglucinol (2, 4-DAPG). This polyketide, which is encoded by the eight gene phl cluster, has antimicrobial effects on phytopathogens, promotes amino acid exudation from plant roots, and induces systemic resistance in plants. Despite its importance, 2, 4-DAPG production is limited to a subset of P. fluorescens strains. Determination of the evolution of the phl cluster and understanding the selective pressures promoting its retention or loss in lineages of P. fluorescens will help in the development of P. fluorescens as a viable and effective inoculant for application in agriculture. In this study, genomic and sequence-based approaches were integrated to reconstruct the phylogeny of P. fluorescens and the phl cluster. It was determined that 2, 4-DAPG production is an ancestral trait in the species P. fluorescens but that most lineages have lost this capacity through evolution. Furthermore, intragenomic recombination has relocated the phl cluster within the P. fluorescens genome at least three times but the integrity of the cluster has always been maintained. The possible evolutionary and functional implications for retention of the phl cluster and 2, 4-DAPG production in some lineages of P. fluorescens are discussed
    Genetic and functional characterization of the gene cluster directing the biosynthesis of putisolvin I and II in Pseudomonas putida strain PCL1445
    Dubern, J.F. ; Coppoolse, E.R. ; Stiekema, W.J. ; Bloemberg, G.V. - \ 2008
    Microbiology 154 (2008). - ISSN 1350-0872 - p. 2070 - 2083.
    nonribosomal peptide-synthesis - escherichia-coli - lipopeptide production - rhizobium-meliloti - biofilm formation - system - synthetases - syringae - sequence - bacteria
    Pseudomonas putida PCL1445 secretes two cyclic lipopeptides, putisolvin I and putisolvin II, which possess a surface-tension-reducing ability, and are able to inhibit biofilm formation and to break down biofilms of Pseudomonas species including Pseudomonas aeruginosa. The putisolvin synthetase gene cluster (pso) and its surrounding region were isolated, sequenced and characterized. Three genes, termed psoA, psoB and psoC, were identified and shown to be involved in putisolvin biosynthesis. The gene products encode the 12 modules responsible for the binding of the 12 amino acids of the putisolvin peptide moiety. Sequence data indicate that the adenylation domain of the 11th module prioritizes the recognition of Val instead of Leu or Ile and consequently favours putisolvin I production over putisolvin II. Detailed analysis of the thiolation domains suggests that the first nine modules recognize the D form of the amino acid residues while the two following modules recognize the L form and the last module the L or D form, indifferently. The psoR gene, which is located upstream of psoA, shows high similarity to luxR-type regulatory genes and is required for the expression of the pso cluster. In addition, two genes, macA and macB, located downstream of psoC were identified and shown to be involved in putisolvin production or export.
    Size does matter: Cre-mediated somatic deletion efficiency depends on the distance between the target lox-sites
    Coppoolse, E.R. ; Vroomen, M.J. de; Gennip, F. van; Hersmus, B.J.M. ; Haaren, M.J. van - \ 2005
    Plant Molecular Biology 58 (2005)5. - ISSN 0167-4412 - p. 687 - 698.
    transgenic tomato plants - chromosome rearrangements - gene cloning - recombination - genome - expression - dna - identification - biotechnology - transposition
    Cre/lox recombination in vivo has become an important tool to induce chromosomal rearrangements like deletions. Using a combination of Ds transposition and Cre/lox recombination in two independent experiments on chromosomes 6 and 7 of tomato, two sets of somatic deletions up to a size of 200 kb were obtained. The efficiency of somatic deletion decreased with increasing deletion size. The largest germinally transmitted deletion had a size of only 55 kb. The results show that Cre-mediated deletion in somatic cells is less efficient when the lox sites are separated over larger distances. A further drop of the deletion efficiency after germinal transmission of the larger deletions can be explained by the probable loss of genes that are of vital importance to gametophyte function. Plasmid rescue of an 8.4 kb circularised deleted DNA showed that the Cre-mediated deletion takes place in tomato as expected. Since the circular Cre-deleted DNA could only be PCR amplified in plant cells where the deletion was not complete, the double-stranded DNA circle is assumed to be instable.
    A high-resolution map of the H1 locus harbouring resistance to the potato cyst nematode Globodera rostochiensis
    Bakker, E.H. ; Achenbach, U. ; Bakker, J.D. ; Vliet, J.M. van; Peleman, J. ; Segers, B. ; Heijden, S. van der; Linde, P. van der; Graveland, R. ; Hutten, R.C.B. ; Eck, H.J. van; Coppoolse, E.R. ; Vossen, E.A.G. van der; Goverse, A. - \ 2004
    Theoretical and Applied Genetics 109 (2004)1. - ISSN 0040-5752 - p. 146 - 152.
    gene conferring resistance - broad-spectrum resistance - disease resistance - markers - tomato - virus - cluster - identification - strategy - andigena
    The resistance gene H1 confers resistance to the potato cyst nematode Globodera rostochiensis and is located at the distal end of the long arm of chromosome V of potato. For marker enrichment of the H1 locus, a bulked segregant analysis (BSA) was carried out using 704 AFLP primer combinations. A second source of markers tightly linked to H1 is the ultra-high-density (UHD) genetic map of the potato cross SH x RH. This map has been produced with 387 AFLP primer combinations and consists of 10,365 AFLP markers in 1,118 bins (http://www.dpw.wageningen-ur.nl/uhd/). Comparing these two methods revealed that BSA resulted in one marker/cM and the UHD map in four markers/cM in the H1 interval. Subsequently, a high-resolution genetic map of the H1 locus has been developed using a segregating F-1 SH x RH population consisting of 1,209 genotypes. Two PCR-based markers were designed at either side of the H1 gene to screen the 1,209 genotypes for recombination events. In the high-resolution genetic map, two of the four co-segregating AFLP markers could be separated from the H1 gene. Marker EM1 is located at a distance of 0.2 cM, and marker EM14 is located at a distance of 0.8 cM. The other two co-segregating markers CM1 (in coupling) and EM15 (in repulsion) could not be separated from the H1 gene.
    Cre recombinase expression can result in phenotypic aberrations in plants
    Coppoolse, E. ; Vroomen, M.J. de; Roelofs, D. ; Smit, J. ; Gennip, F. van; Hersmus, B.J.M. ; Nijkamp, H.J.J. ; Haaren, M.J. van - \ 2003
    Plant Molecular Biology 51 (2003)2. - ISSN 0167-4412 - p. 263 - 279.
    site-specific recombination - agrobacterium-tumefaciens - transgenic tobacco - gene-transfer - dna - genome - transformation - selection - vectors - lox
    The cre recombinase gene was stably introduced and expressed in tomato, petunia and Nicotiana tabacum. Some plants expressing the cre gene driven by a CaMV 35S promoter displayed growth retardation and a distinct pattern of chlorosis in their leaves. Although no direct relation can be proven between the phenotype and cre expression, aberrant phenotypes always co-segregate with the transgene, which strongly suggests a correlation. The severity of the phenotype does not correlate with the level of steady-state mRNA in mature leaves, but with the timing of cre expression during organogenesis. The early onset of cre expression in tomato is correlated with a more severe phenotype and with higher germinal transmission frequencies of site-specific deletions. No aberrant phenotype was observed when a tissue-specific phaseolin promoter was used to drive the cre gene. The data suggest that for the application of recombinases in plants, expression is best limited to specific tissues and a short time frame.[12pt] Abbreviations: bar, the phosphinotricin acetyltransferase gene; CAM, chloramphenicol resistance gene; Ds 5 & Ds 3, borders of the Ds transposable element from maize forming a functional transposable element that embodies the interjacent DNA; gus, the -glucoronidase gene; gus-int, the gus gene interrupted by a plant intron; hpt, the hygromycin phosphotransferase gene; nptII, the neomycin phosphotransferase gene; ORI, bacterial origin for plasmid replication in Escherichia coli of plasmid p15A Cre recombinase - lox P - petunia - site-specific recombination - tobacco - tomato - toxicity
    High-resolution mapping of the H1 locus conferring resistance to the potato cyst nematode globodera rostochiensis using an ultra-dense genetic map
    Bakker, E.H. ; Bakker, J.D. ; Vliet, J.M. van; Coppoolse, E.R. ; Vossen, E.A.G. van der; Eck, H.J. van; Bakker, J. ; Goverse, A. - \ 2003
    In: Plant and Animal Genome XI, Final abstract guide. - San Diego : - p. 202 - 202.
    Map based cloning of the durable nematode resistance gene H1 of potato
    Coppoolse, E.R. ; Vossen, E. van der; Bakker, J. ; Stiekema, W.J. - \ 2000
    In: Durable disease resistance, Key to sustainable agriculture : Durable resistance, Ede-Wageningen 2000 Wageningen : - p. 50 - 50.
    Tomato chromosome 6: a high resolution map of the long arm and construction of a composite integrated marker-order map.
    Wordragen, M.F. van; Weide, R.L. ; Coppoolse, E. ; Koornneef, M. ; Zabel, P. - \ 1996
    Theoretical and Applied Genetics 92 (1996). - ISSN 0040-5752 - p. 1065 - 1072.
    Tomato chromosome 6: a high resolution map of the long arm and construction of a composite integrated marker-order map.
    Wordragen, M. van; Weide, R. ; Coppoolse, E. ; Koornneef, M. ; Zabel, P. - \ 1996
    In: Abstract Plant Genome 4. Int. Conf. on The status of plant genome research. San Diego, Ca, USA (1996) - p. 222 - 222.
    The effect of low hufa and high hufa enriched Artemia, fed at different feeding levels, on growth, survival, tissue fatty acids and liver histology of Clarias gariepinus larvae.
    Verreth, J. ; Coppoolse, J. ; Segner, H. - \ 1994
    Aquaculture 126 (1994). - ISSN 0044-8486 - p. 137 - 150.
    Ileale aminozuurverteerbaarheid en voederwaarde van aardappeleiwit en mais = Ileal amino acid digestibility and nutritive value of potato protein and maize
    Lenis, N.P. ; Diepen, J.T.M. van; Coppoolse, J. - \ 1992
    Lelystad : IVVO-DLO (Rapport / IVVO-DLO nr. 232) - 20
    bijproducten - voer - voedingswaarde - varkens - aardappelen - eiwitten - solanum tuberosum - zetmeelverwerkende industrie - byproducts - feeds - nutritive value - pigs - potatoes - proteins - solanum tuberosum - starch industry
    The effect of feeding level on growth and survival of larvae of the jaguar guapote (Cichlasoma managuense) fed Artemia nauplii in the primary nursing phase.
    Gunther, J. ; Galvez-Hidalgo, N. ; Ulloa-Rojas, J. ; Coppoolse, J. ; Verreth, J.A.J. - \ 1992
    Aquaculture 107 (1992). - ISSN 0044-8486 - p. 347 - 358.
    Verlaging van het eiwitgehalte van vleesvarkensvoeder onder aanvulling van synthetische aminozuren = Lowering dietary protein for growing pigs with supplementation of crystalline amino acids
    Coppoolse, J. ; Lenis, N.P. ; Diepen, J.T.M. van - \ 1990
    Lelystad : IVVO (Rapport IVVO no. 212) - 22
    vleesproductie - voer - eiwitten - aminozuren - meat production - feeds - proteins - amino acids
    Ileaal verteerbare aminozuren in rantsoenen voor varkens = Ileal digestible amino acids in pig feeds
    Lenis, N.P. ; Coppoolse, J. ; Schutte, J.B. - \ 1990
    Lelystad : IVVO (I.V.V.O. rapport no. 215) - 20
    voer - eiwitten - varkens - feeds - proteins - pigs
    Simulatie van groei en groeisamenstelling bij vleesvarkens.
    Peet-Schwering, C. van der; Peet, G.F.V. van der; Verstegen, M.W.A. ; Smits, C. ; Kanis, E. ; Vries, A.G. de; Coppoolse, J. ; Jongbloed, A. - \ 1990
    In: Verslag 15e studiedag Nederlandstalige Voedingsonderzoekers, Utrecht - p. 29 - 30.
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