Figure 2

Comparison of sequences and chromosomal positions of TRIM and MHC genes between species. (a) Human MHC-paralogous regions. The 1pq, 6p21 and 9q segments are the classical MHC-paralogous regions [8]. For simplicity only selected markers are shown, particularly MHC markers shared with the fish markers shown in Figure 1. For the purposes of this article I identified a set of genes on human chromosome 11p so far not considered as a MHC-paralogous region but that indeed seem to correspond to a group of MHC-paralogous genes that are missing from the group present on chromosome 19p13. Asterisks indicate genes for which paralogs have also been identified on chromosome 12p13, which is also known to contain some MHC-paralogous genes. Two chromosomes also have ATP5L homologs (green) linked to TRIM genes, as also found for three fish species in [6]. TRIMs in blue are those with antiviral activity. Lines indicate paralogous loci. (b) Alignment of B30.2 (Pry-Spry) domains across metazoa. Invertebrates are represented by the following sequences: a diploblastic cnidarian (sea anemone, Nematostella, XM_001632290), a protostome insect (Drosophila, NP_723600.2), a chelicerate (tick, Ixodes, EEC02812), a deuterostome echinoderm (sea urchin, Strongylocentrotus, XR_026371), a tunicate (sea squirt, Ciona, XM_002126032) and a cephalochordate (amphioxus, Branchiostoma, XM_002222150). Vertebrates are represented by: a teleost fish TRIM-B30.2 (zebrafish, Danio, XM_001332270), human CD277 (Homo, NP_001138480, given as an example of B30.2 associated with a molecule other than TRIMs), and rat Trim9 (Rattus, NP_569104, of which several invertebrate TRIMs are close homologs). Red, residues conserved in more than 50% of the sequences; blue, regions considered as signatures of the B30.2 domain [2]. Strand prediction (shown above the sequences) is taken from the Phyre server [17]. (c) Schematic representations using SMART [18] of TRIM-related proteins from Nematostella (close to class I of [5]) and Branchiostoma (close to class IV of [6]). The Pry domain is not always suggested by the graphic SMART program, as for Nematostella here, but it is visible in the alignment. Data obtained from the ENSEMBL [19], UCSC [20] and Vectorbase [21] servers.