Volume 19, Issue 20, Pages 1683-1691 (November 2009) Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence  Teresa Nogueira, Daniel J. Rankin, Marie Touchon, François Taddei, Sam P. Brown, Eduardo P.C. Rocha  Current Biology  Volume 19, Issue 20, Pages 1683-1691 (November 2009) DOI: 10.1016/j.cub.2009.08.056 Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 1 The Influence of Population Structure and Relatedness on Bacterial Social Traits in a Subpopulation A cooperative gene coding for a public good is represented by “x” and can be carried either by the chromosome (A and B) or a plasmid (C). (A) A small bacterial population where all individuals have the cooperative gene on the chromosome. (B) Only one individual (B) posseses the gene and produces the public good. A, C, and D benefit from B's actions. (C) The cooperative gene is carried on the plasmid so individuals A and B both produce the trait. A and B will now have a high genetic relatedness (r > 0) because relatedness is defined as the probability that two individuals bear the same gene. Thus relatedness is influenced by the rate at which the plasmid spreads through the subpopulation. The greater the plasmid infection rate, the more “related” the hosts will be because more individuals within the subpopulation will share the same genes, albeit on the plasmid. This illustrates that it is the focal locus that ultimately matters when dealing with social dilemmas such as public good production. Current Biology 2009 19, 1683-1691DOI: (10.1016/j.cub.2009.08.056) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 2 Effect of Migration and Transfer Rates on Relatedness Top: Effect of the probability of horizontal gene transfer on relatedness within a patch under different gene loss probabilities (s = 0, s = 0.25, s = 0.5, s = 0.75), where m = 0.1 and n = 50. Bottom: Effect of the migration rate m on relatedness for different degrees of horizontal gene transfer (β = 0, β = 0.25, β = 0.5, β = 0.75), where s = 0 and n = 50. Current Biology 2009 19, 1683-1691DOI: (10.1016/j.cub.2009.08.056) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 3 Distribution of Core, Ancestral, and Recent Genes among the Localization Classes The differences are highly significant (χ2 test, p < 0.0001). Current Biology 2009 19, 1683-1691DOI: (10.1016/j.cub.2009.08.056) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 4 Percentage of Nonancestral E. coli Genes with Homologs in Human Gut Metagenome The bars correspond to secreted and outer membrane proteins (black bars) and other localizations (white bars), when separating the set of unweaned babies from the sets containing other individuals and when including all data [23]. Current Biology 2009 19, 1683-1691DOI: (10.1016/j.cub.2009.08.056) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 5 Biosynthetic Energetic Cost per Residue in Proteins The large horizontal line indicates the average and the two small lines indicate its 95% interval of confidence. The dashed line indicates the cost of the 10% highest expressed genes via the codon adaptation index (see Figure S4 for details). The distribution is significantly different from the expected (χ2 test, p < 0.0001). Current Biology 2009 19, 1683-1691DOI: (10.1016/j.cub.2009.08.056) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 6 Positioning of Genes Coding for Secreted and Outer Membrane Proteins Frequency of genes that are not in the core genome within three types of genome positioning: plasmids, chromosomal hotspots, and other locations in the genome. The differences are highly significant (χ2 test, p < 0.0001). Current Biology 2009 19, 1683-1691DOI: (10.1016/j.cub.2009.08.056) Copyright © 2009 Elsevier Ltd Terms and Conditions

Figure 7 Functions in the Neighborhood of Genes Coding for Localized Proteins Observed/expected co-occurrence of genes that are not in the core genome coding for proteins localized in different cellular regions with integrases, restriction/modification systems, and toxin/antitoxin systems. The distributions are significantly different from the expected values for all three types of genes (χ2 test, p < 0.0001). Current Biology 2009 19, 1683-1691DOI: (10.1016/j.cub.2009.08.056) Copyright © 2009 Elsevier Ltd Terms and Conditions