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dc.contributor.authorTomasch, Jürgen
dc.contributor.authorWang, Hui
dc.contributor.authorHall, April T K
dc.contributor.authorPatzelt, Diana
dc.contributor.authorPreusse, Matthias
dc.contributor.authorPetersen, Jörn
dc.contributor.authorBrinkmann, Henner
dc.contributor.authorBunk, Boyke
dc.contributor.authorBhuju, Sabin
dc.contributor.authorJarek, Michael
dc.contributor.authorGeffers, Robert
dc.contributor.authorLang, Andrew S
dc.contributor.authorWagner-Döbler, Irene
dc.date.accessioned2018-02-07T10:13:28Z
dc.date.available2018-02-07T10:13:28Z
dc.date.issued2018-01-01
dc.identifier.citationPackaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random. 2018, 10 (1):359-369 Genome Biol Evolen
dc.identifier.issn1759-6653
dc.identifier.pmid29325123
dc.identifier.doi10.1093/gbe/evy005
dc.identifier.urihttp://hdl.handle.net/10033/621266
dc.description.abstractGene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world's oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a "headful" type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated.
dc.language.isoenen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.titlePackaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random.en
dc.typeArticleen
dc.contributor.departmentHelmholtz-Zentrum for Infektion Research GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany.en
dc.identifier.journalGenome biology and evolutionen
refterms.dateFOA2018-06-13T01:01:26Z
html.description.abstractGene transfer agents (GTAs) are phage-like particles which contain a fragment of genomic DNA of the bacterial or archaeal producer and deliver this to a recipient cell. GTA gene clusters are present in the genomes of almost all marine Rhodobacteraceae (Roseobacters) and might be important contributors to horizontal gene transfer in the world's oceans. For all organisms studied so far, no obvious evidence of sequence specificity or other nonrandom process responsible for packaging genomic DNA into GTAs has been found. Here, we show that knock-out of an autoinducer synthase gene of Dinoroseobacter shibae resulted in overproduction and release of functional GTA particles (DsGTA). Next-generation sequencing of the 4.2-kb DNA fragments isolated from DsGTAs revealed that packaging was not random. DNA from low-GC conjugative plasmids but not from high-GC chromids was excluded from packaging. Seven chromosomal regions were strongly overrepresented in DNA isolated from DsGTA. These packaging peaks lacked identifiable conserved sequence motifs that might represent recognition sites for the GTA terminase complex. Low-GC regions of the chromosome, including the origin and terminus of replication, were underrepresented in DNA isolated from DsGTAs. DNA methylation reduced packaging frequency while the level of gene expression had no influence. Chromosomal regions found to be over- and underrepresented in DsGTA-DNA were regularly spaced. We propose that a "headful" type of packaging is initiated at the sites of coverage peaks and, after linearization of the chromosomal DNA, proceeds in both directions from the initiation site. GC-content, DNA-modifications, and chromatin structure might influence at which sides GTA packaging can be initiated.


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