Are protein domains modules of lateral genetic transfer?

Chan, Cheong Xin, Darling, Aaron E., Beiko, Robert G. and Ragan, Mark A. (2009) Are protein domains modules of lateral genetic transfer?. PLoS One, 4 2: e4524.1-e4524.8. doi:10.1371/journal.pone.0004524

Author Chan, Cheong Xin
Darling, Aaron E.
Beiko, Robert G.
Ragan, Mark A.
Title Are protein domains modules of lateral genetic transfer?
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2009-02-20
Year available 2009
Sub-type Article (original research)
DOI 10.1371/journal.pone.0004524
Open Access Status DOI
Volume 4
Issue 2
Start page e4524.1
End page e4524.8
Total pages 8
Editor I. Jordan King
Place of publication San Francisco, CA
Publisher Public Library of Science
Collection year 2010
Language eng
Subject C1
97 Expanding Knowledge
970106 Expanding Knowledge in the Biological Sciences
060408 Genomics
Formatted abstract

In prokaryotes and some eukaryotes, genetic material can be transferred laterally among unrelated lineages and recombined into new host genomes, providing metabolic and physiological novelty. Although the process is usually framed in terms of gene sharing (e.g. lateral gene transfer, LGT), there is little reason to imagine that the units of transfer and recombination correspond to entire, intact genes. Proteins often consist of one or more spatially compact structural regions (domains) which may fold autonomously and which, singly or in combination, confer the protein's specific functions. As LGT is frequent in strongly selective environments and natural selection is based on function, we hypothesized that domains might also serve as modules of genetic transfer, i.e. that regions of DNA that are transferred and recombined between lineages might encode intact structural domains of proteins.

Methodology/Principal Findings

We selected 1,462 orthologous gene sets representing 144 prokaryotic genomes, and applied a rigorous two-stage approach to identify recombination breakpoints within these sequences. Recombination breakpoints are very significantly over-represented in gene sets within which protein domain-encoding regions have been annotated. Within these gene sets, breakpoints significantly avoid the domain-encoding regions (domons), except where these regions constitute most of the sequence length. Recombination breakpoints that fall within longer domons are distributed uniformly at random, but those that fall within shorter domons may show a slight tendency to avoid the domon midpoint. As we find no evidence for differential selection against nucleotide substitutions following the recombination event, any bias against disruption of domains must be a consequence of the recombination event per se.


This is the first systematic study relating the units of LGT to structural features at the protein level. Many genes have been interrupted by recombination following inter-lineage genetic transfer, during which the regions within these genes that encode protein domains have not been preferentially preserved intact. Protein domains are units of function, but domons are not modules of transfer and recombination. Our results demonstrate that LGT can remodel even the most functionally conservative modules within genomes.
Q-Index Code C1
Q-Index Status Confirmed Code
Additional Notes Article number: e4524

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2010 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 33 times in Thomson Reuters Web of Science Article | Citations
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Created: Fri, 29 Jan 2010, 10:35:06 EST by Susan Allen on behalf of Institute for Molecular Bioscience