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The mechanisms for lateral gene transfer in nature as reflected in prokaryote genomes

The mechanisms for lateral gene transfer in nature as reflected in prokaryote genomes

Objective

Lateral gene transfer (LGT) is the process by which prokaryotes acquire DNA across wide taxonomic boundaries and incorporate it into their genome. Accumulating evidence shows that LGT plays a major role in prokaryote evolution. The biological and evolutionary significance of lateral gene transfer has broad implications for our understanding of microbial biology, not only in terms of evolution, but also in terms of human health.
Mechanisms of lateral gene transfer include: transformation, transduction, conjugation, and gene transfer agents. Each of these transfer mechanisms leaves distinct and recognizable molecular footprints in genome sequences. The molecular details of these footprints betray the workings of the corresponding mechanisms in nature, but their relative contributions to the evolution of sequenced genomes have so far not been investigated. By identifying these footprints one can specify and quantify the relative contribution of the different LGT mechanisms during prokaryote genome evolution and thereby uncover more of the biology underlying prokaryote evolution in nature. The goal of this proposal is to quantify those contributions and to bring forth a general computer-based model of prokaryote genome evolution that approximates the underlying evolutionary process far more realistically than phylogenetic trees alone possibly can.
Here I propose to apply directed networks to the study of prokaryotic genome evolution in an evolutionary model that allows both for vertical inheritance and for lateral gene transfer events. With methods to identify gene donors, all recent LGTs can be described in a single directed network. This is a fundamentally new, biologically more realistic and evolutionarily more accurate, general computational model of prokaryote genome evolution. Such a model will substantially enrich our ability to understand the process of prokaryote evolution as it is recorded in genomic and metagenomic data.
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Principal Investigator

Tal Dagan (Prof.)

Host institution

CHRISTIAN-ALBRECHTS-UNIVERSITAET ZU KIEL

Address

Olshausenstrasse 40
24118 Kiel

Germany

Activity type

Higher or Secondary Education Establishments

EU Contribution

€ 1 415 507,20

Principal Investigator

Tal Dagan (Prof.)

Administrative Contact

Linda Piálek (Ms.)

Beneficiaries (2)

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CHRISTIAN-ALBRECHTS-UNIVERSITAET ZU KIEL

Germany

EU Contribution

€ 1 415 507,20

HEINRICH-HEINE-UNIVERSITAET DUESSELDORF

Germany

EU Contribution

€ 84 492,80

Project information

Grant agreement ID: 281357

Status

Closed project

  • Start date

    1 July 2012

  • End date

    30 June 2018

Funded under:

FP7-IDEAS-ERC

  • Overall budget:

    € 1 500 000

  • EU contribution

    € 1 500 000

Hosted by:

CHRISTIAN-ALBRECHTS-UNIVERSITAET ZU KIEL

Germany