Irgm1 in cell-autonomous immunity.

<p><b>(Left)</b> In the wild-type, IFNγ-treated cell, IRG proteins are induced and both <i>T. gondii</i> (A) and mycobacteria (B) are killed. Many IRG proteins accumulate around the <i>T. gondii</i> vacuole (indicated in red at (A)), while only the normally Golgi-associated Irgm1 (green) is thought to accumulate around the mycobacterial phagosome <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001008#ppat.1001008-MacMicking1" target="_blank">[6]</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001008#ppat.1001008-Tiwari1" target="_blank">[36]</a>. There is little doubt that destruction of <i>T. gondii</i> is initiated by an IRG protein–mediated direct attack on the parasitophorous vacuole membrane <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001008#ppat.1001008-Martens1" target="_blank">[21]</a>. It has been argued that Irgm1 on the mycobacterial phagosome membrane is directly responsible for fast acidification of the phagosome by lysosomal fusion (<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001008#ppat.1001008-MacMicking1" target="_blank">[6]</a>, indicated in grey at (B)) and perhaps also for initiation of autophagy <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001008#ppat.1001008-Gutierrez1" target="_blank">[10]</a>. <b>(Right)</b> Loss of Irgm1 results in loss of control of both <i>T. gondii</i> and mycobacteria. However, Irgm1 is one of three essential regulatory proteins belonging to the GMS subfamily of IRG proteins (Irgm1, Irgm2, Irgm3), that prevent premature activation of the GKS subfamily IRG proteins (Irga6, Irgb6, Irgd, etc.; red) in IFNγ-induced cells <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001008#ppat.1001008-Hunn1" target="_blank">[19]</a>. Loss of Irgm1 causes the normally markedly cytosolic GKS proteins (shaded red on the left) to form large, GTP-bound, non-functional aggregates (red dots) in IFNγ-induced cells <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001008#ppat.1001008-Henry2" target="_blank">[14]</a> with striking cytopathic effects, especially on cells of the lymphomyeloid system <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001008#ppat.1001008-Feng1" target="_blank">[7]</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1001008#ppat.1001008-Feng2" target="_blank">[15]</a>. We argue that this, rather than loss of Irgm1 from the mycobacterial phagosome, is the main reason for the dramatic immune impairment of Irgm1-deficient mice, including loss of mycobacterial resistance.</p

Correction: Phosphorylation of Mouse Immunity-Related GTPase (IRG) Resistance Proteins Is an Evasion Strategy for Virulent <i>Toxoplasma gondii</i>

<p>Correction: Phosphorylation of Mouse Immunity-Related GTPase (IRG) Resistance Proteins Is an Evasion Strategy for Virulent <i>Toxoplasma gondii</i></p

Ancestral protein kinases are extensively lost during arthropod evolution.

<p><i>S. maritima</i> is an exception and retains the largest number of ancestral kinases. Numbers of kinase subfamilies in selected species are shown in parentheses after species names. The gains, losses, and inferred content of common ancestors are listed on internal branches. Kinases found in at least two species from human, <i>C. elegans</i> and <i>Nematostella vectenesis</i> were used as an outgroup.</p

Conserved macro synteny signal between <i>S. maritima</i> and the chordate lancelet <i>B. floridae</i> clustered into ancestral linkage groups.

<p>Each dot represents a pair of genes, one in <i>B. floridae</i>, one in <i>S. maritima</i>, assigned to the same gene family by our orthology analysis. The ancestral linkage group identifiers refer to groups of scaffolds from the <i>S. maritima</i> (SmALG) or <i>B. floridae</i> (BfALG) assemblies, as detailed in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005.s066" target="_blank">File S2</a>. The identification of ALGs is described in the SI. Note that two <i>S. maritima</i> scaffolds were divided across ALGs, and so appear multiple times in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005.s066" target="_blank">File S2</a>.</p

Arthropod phylogenetic tree (with nematode outgroup) showing selected events of gene loss, gene gain, and gene family expansions.

<p>Main taxa are listed on the tips, with representative species for which there is a fully sequenced genome listed below. Major nodes are also named. Data from the genome of <i>S. maritima</i> allow us to map when in arthropod evolution these events occurred, even when these events did not occur on the centipede lineage. A plausible node for the occurrence of each event is marked and colour-coded, with the possible range marked with a thin line of the same colour. The events, listed from left to right are: (1) Dscam alternative splicing as a strategy for increasing immune diversity is known from <i>D. melanogaster</i>, as well as the crustacean <i>D. pulex</i>, and thus probably evolved in the lineage leading to pancrustacea, after the split from centipedes. (2) Several wnt genes have been lost in holometabolous insects, leaving only seven of the 13 ancestral families. This loss occurred gradually over arthropod evolution, but reached its peak at the base of the Holometabola. (3) Selenoproteins are rare in insects. The presence of a large number of selenoproteins in <i>S. maritima</i> as well as in other non-insect arthropods suggests that the loss of many selenoproteins occurred at the base of the Insecta. (4) Expansion of chemosensory gene families occurred independently in different arthropod lineages as they underwent terrestrialisation. The OR family is expanded in insects only. (5) Chemosensory genes of the GR and IR genes have undergone a lineage specific expansion in the genome of <i>S. maritima</i>. As these are probably also linked with terrestrialisation we suggest that this expansion happened at the base of the Chilopoda, but it could have also occurred later in the lineage leading to <i>S. maritima</i>. (6) Cuticular proteins of the RR-1 family are numerous in the <i>S. maritima</i> genome. They are found in other arthropods, but not in chelicerates nor in any non-arthropod species. This suggests that the RR-1 subfamily evolved at the base of the Mandibulata. (7) The genome of <i>S. maritima</i> has a large complement of wnt genes, but is missing <i>wnt8</i>. Since this gene is found in the Diplopod <i>G. marginata</i> (a species without a fully sequenced genome), the loss most likely occurred at the base of the Chilopoda. (8) Unlike the situation in <i>D. melanogaster</i>, immune diversity in the <i>S. maritima</i> genome is achieved through multiple copies of the Dscam gene. This expansion of the family could have happened at any time after the split between Myriapoda and Pancrustacea. (9) Both circadian rhythm genes and many light receptors are missing in <i>S. maritima</i>. These losses are most likely due to the subterranean life style of geophilomorph centipedes and are probably specific to this group. However, we cannot rule out the possibility that they were lost somewhere in the lineage leading to myriapods. (10) The existence of JH signalling in <i>S. maritima</i> as well as in all other arthropods studied to date strengthens the idea that this signalling system evolved with the exoskeleton of arthropods, though its origins could be even more ancient and date back to the origin of moulting at the base of the Ecdysozoa.</p

Expansion of chemosensory receptor families.

<p>(A) Phylogenetic relationships among <i>S. maritima</i> (Smar), <i>I. scapularis</i> (Isca), <i>D. pulex</i> (Dpul), and a few insect GRs that encode for sugar, fructose, and carbon dioxide receptors (Dmel, <i>D. melanogaster</i>, and Amel, <i>A. mellifera</i>). (B) Phylogenetic relationships among <i>S. maritima</i>, <i>I. scapularis</i>, and a few <i>D. melanogaster</i> IRs and IgluR genes (the suffix at the end of the protein names indicates: i, incomplete and p, pseudogene).</p

Presence and absence of immunity genes in different arthropods.

<p>Counts of immune genes are shown for <i>S. maritima</i>, <i>D. pulex</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-McTaggart1" target="_blank">[131]</a>, <i>A. mellifera</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-Evans1" target="_blank">[86]</a>, <i>T. castaneum</i>, <i>Anopheles gambiae</i>, and <i>D. melanogaster</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-Dasmahapatra1" target="_blank">[132]</a>. ∼, identity of the gene is uncertain; -, not investigated.</p

Dscam diversity caused either by gene and/or exon duplication in different Metazoa.

<p>^aOnly canonical Dscam paralogues were considered. ^bIn <i>D. melanogaster</i> and <i>D. pulex</i> the paralogue Dscam-L2 has two Ig7 alternative coding exons. ^cPotential number of Dscam isoforms, circulating in one individual, produced by mutually exclusive alternative splicing of duplicated exons.</p

Frequency histogram of CpG_(o/e) observed in <i>S. maritima</i> gene bodies.

<p>The y-axis depicts the number of genes with the specific CpG_(o/e) values given on the x-axis. The distribution of CpG_(o/e) in <i>S. maritima</i> is a trimodal distribution, with a low-CpG_(o/e) peak consistent with the presence of historical DNA methylation in <i>S. maritima</i> and the presence of a high CpG_(o/e) peak. The data underlying this plot are available in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005.s068" target="_blank">File S4</a>.</p

Instances of homeobox gene clustering and linkage.

<p>Instances of homeobox gene clustering and linkage.</p