Compositional discordance between prokaryotic plasmids and host chromosomes

van Passel, Mark WJ; Bart, Aldert; Luyf, Angela CM; van Kampen, Antoine HC; van der Ende, Arie
January 2006
BMC Genomics;2006, Vol. 7, p26
Academic Journal
Background: Most plasmids depend on the host replication machinery and possess partitioning genes. These properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. Hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. However, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, suggesting dinucleotide composition dissimilarity between plasmid and host genome. We compared the dinucleotide composition of a large collection of plasmids with that of their host genomes to shed more light on this enigma. Results: The dinucleotide frequency, coined the genome signature, facilitates the identification of putative horizontally transferred DNA in complete genome sequences, since it was found to be typical for a certain genome, and similar between related species. By comparison of the genome signature of 230 plasmid sequences with that of the genome of each respective host, we found that in general the genome signature of plasmids is dissimilar from that of their host genome. Conclusion: Our results show that the genome signature of plasmids does not resemble that of their host genome. This indicates either absence of amelioration or a less stable relationship between plasmids and their host. We propose an indiscriminate lifestyle for plasmids preserving the genome signature discordance between these episomes and host chromosomes.


Related Articles

  • The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Rabus, Ralf; Kube, Michael; Heider, Johann; Beck, Alfred; Heitmann, Katja; Widdel, Friedrich; Reinhardt, Richard // Archives of Microbiology;Jan2005, Vol. 183 Issue 1, p27 

    Recent research on microbial degradation of aromatic and other refractory compounds in anoxic waters and soils has revealed that nitrate-reducing bacteria belonging to the Betaproteobacteria contribute substantially to this process. Here we present the first complete genome of a metabolically...

  • The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation. Guglielmini, Julien; Quintais, Leonor; Garcillán-Barcia, Maria Pilar; de la Cruz, Fernando; Rocha, Eduardo P. C. // PLoS Genetics;Aug2011, Vol. 7 Issue 8, Special section p1 

    Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity...

  • SeqEntropy: Genome-Wide Assessment of Repeats for Short Read Sequencing. Chu, Hsueh-Ting; Hsiao, William WL.; Tsao, Theresa TH.; Hsu, D. Frank; Chen, Chaur-Chin; Lee, Sheng-An; Kao, Cheng-Yan // PLoS ONE;Mar2013, Vol. 8 Issue 3, p1 

    Background: Recent studies on genome assembly from short-read sequencing data reported the limitation of this technology to reconstruct the entire genome even at very high depth coverage. We investigated the limitation from the perspective of information theory to evaluate the effect of repeats...

  • Next-generation CRISPRs. Rusk, Nicole // Nature Methods;Jan2015, Vol. 12 Issue 1, p36 

    The article focuses on the use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas system is a prokaryotic immune system which confers resistance to foreign genetic elements like plasmids and phages.

  • Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns". Larsabal, Etienne; Danchin, Antoine // BMC Bioinformatics;2005, Vol. 6, p206 

    Background: The genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given genome, both in coding and non-coding sequences. Until now this bias remained of unknown origin. Results: Using...

  • Complex prokaryotic genome structure: rapid evolution of chromosome II. Bavishi, Anish; Abhishek, Ankur; Lin, Lin; Choudhary, Madhusudan // Genome;Sep2010, Vol. 53 Issue 9, p675 

    Although many bacteria with two chromosomes have been sequenced, the roles of such complex genome structuring are still unclear. To uncover levels of chromosome I (CI) and chromosome II (CII) sequence divergence, Mauve 2.2.0 was used to align the CI- and CII-specific sequences of bacteria with...

  • A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation.  // BMC Research Notes;2012, Vol. 5 Issue 1, p80 

    The article focuses on a study conducted to test various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes, which found that a cost-effective way for prokaryotic whole genome sequencing is a single end 454 Jr. run combined with a paired end 454 Jr. run. Solution to...

  • Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations. Ming-Chun Lee; Marx, Christopher J. // PLoS Genetics;May2012, Vol. 8 Issue 5, Special section p1 

    Genome reduction has been observed in many bacterial lineages that have adapted to specialized environments. The extreme genome degradation seen for obligate pathogens and symbionts appears to be dominated by genetic drift. In contrast, for free-living organisms with reduced genomes, the...

  • The Importance of the Expendable: Toxin--Antitoxin Genes in Plasmids and Chromosomes. Díaz-Orejas, Ramón; Espinosa, Manuel; Chew Chieng Yeo // Frontiers in Microbiology;8/4/2017, p1 

    Toxin--antitoxin (TA) genes were first reported in plasmids and were considered expendable genetic cassettes involved in the stable maintenance of the plasmid replicon by interfering with growth and/or viability of bacteria in which the plasmid was lost. TAs were later found in bacterial...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics