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PLoS One
2014 Nov 06;911:e110330. doi: 10.1371/journal.pone.0110330.
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Evolution of an expanded mannose receptor gene family.
Staines K
,
Hunt LG
,
Young JR
,
Butter C
.
Abstract
Sequences of peptides from a protein specifically immunoprecipitated by an antibody, KUL01, that recognises chicken macrophages, identified a homologue of the mammalian mannose receptor, MRC1, which we called MRC1L-B. Inspection of the genomic environment of the chicken gene revealed an array of five paralogous genes, MRC1L-A to MRC1L-E, located between conserved flanking genes found either side of the single MRC1 gene in mammals. Transcripts of all five genes were detected in RNA from a macrophage cell line and other RNAs, whose sequences allowed the precise definition of spliced exons, confirming or correcting existing bioinformatic annotation. The confirmed gene structures were used to locate orthologues of all five genes in the genomes of two other avian species and of the painted turtle, all with intact coding sequences. The lizard genome had only three genes, one orthologue of MRC1L-A and two orthologues of the MRC1L-B antigen gene resulting from a recent duplication. The Xenopus genome, like that of most mammals, had only a single MRC1-like gene at the corresponding locus. MRC1L-A and MRC1L-B genes had similar cytoplasmic regions that may be indicative of similar subcellular migration and functions. Cytoplasmic regions of the other three genes were very divergent, possibly indicating the evolution of a new functional repertoire for this family of molecules, which might include novel interactions with pathogens.
Figure 2. Structure of paralogous MRC1 genes in the chicken genome.Exons are shown to scale as rectangles. Introns are drawn to 1/10 of the exon scale, except for the shortest which are expanded for visibility. Orange and blue exons are the CysR and FNII domains in all genes except D. The terminal green exon contains transmembrane and cytoplasmic regions. The central array of exons encodes the eight CTLDs indicated by the black bars above each gene.
Figure 3. C type lectin domains of the avian MRC1 orthologue gene products.Sequences are labelled on the left, M being the mouse MRC1 sequence while the chicken genes are labelled A to E in genome order in the direction of their transcription, with sequential numbers to indicate the domains in order. Dashes indicate missing residues in the alignment. The short linker peptides between domains are omitted from this figure. Residues reported [20], [51] to be conserved throughout the mannose receptor family are indicated above the sequences using the symbols Ω, aromatic or aliphatic; φ, aromatic; θ, aliphatic; C, E, G, P, W, N, D the standard amino acid codes; O, carbonyl oxygen containing (DNEQ). The corresponding residues in the sequences are shaded, yellow for cysteine and purple for the others. Additional cysteine residues in domains 2, 3, 4, 6 and 8 are also shaded. Likely locations of secondary structural features in the mouse sequence [52] are indicated by blue arrows above the sequence; β, beta strand; α alpha helix; L loop.
Figure 4. Arrangement the MRC1 orthologue locus in different species.Species are labelled at the left, with a numeral indicating the chromosome where that is known. Black arrowheads indicate the relative orientations of the reference genome maps. The conserved flanking genes SLC39A12 and STAM are indicated in red and green respectively. An additional gene TMEM236, found only in mammalian genomes, is coloured yellow. Predicted MRC1 paralogues are shown in blue. Vertical lines represent the exons of each gene. All the genomes are represented at the same scale, so that the region between vertical dotted lines is 300 kilobase pairs, except in the case of the Painted Turtle, where it represents 600 kilobase pairs. The location in megabase pairs of the right hand end of the map in the chromosome, or other map segment, is indicated at the right. The coding sequences of all genes shown run from right to left in this map, as indicated by arrowheads.
Figure 5. Evolutionary relationships of avian MRC1L genes.A maximum likelihood phylogenetic tree was constructed from predicted exons encoding all the CTLDs, using the Tamura-Nei model in the MEGA software, with 100 bootstrap datasets. All nodes with bootstrap values less than 100 were coalesced into multifurcations. Leaves are labelled with a three letter species code (chk, chicken (Gallus gallus); tky, turkey (Maleagris gallopavo); zfn, zebrafinch (Taeniopygia guttata); ttl, painted turtle (Chrysemys picta bellii); liz, lizard (Anolis carolinensis); xen, Xenopus tropicalis; hum, human (Homo sapiens); mou, mouse (Mus musculus); followed by either a letter or a number indicating the order of the genes in the direction of transcription. Clades representing orthologues of the MRC1 (human) and KUL01 (chicken) genes are surrounded by dotted lines.
Figure 6. Alignments of cytoplasmic regions of MRC-like genes from various species.Gene names are as described in the legend to figure 5. Shaded residues show the locations of peptide motifs that may be involved in targeting to the endocytic pathway; green for the φxNxxY, red and blue for the (DE)xxxLZ motif, and purple for YxxZ (φ indicating a bulky hydrophobic residue and Z indicating a hydophobic residue). Light green shading indicates an overlapping potential di-aromatic endosome sorting motif in the MRC1 and MRC1L-A sequences.
Figure 7. Relative levels of each MRC1 orthologue mRNA in different tissues, measured by quantitative PCR.Tissues, as labelled at the left, are grouped according to preponderance of immune function. For each gene, relative levels of mRNAs are plotted horizontally using a logarithmic scale with arbitrary origins. Circles are individual measurements from each of six birds. Boxes are centered on the means, and their ends indicate the standard errors of those means. All measurements were normalised relative to a constant level of 28S rRNA in each sample and adjusted to the log2 scale using the measured PCR efficiency of standard dilution series, before calculation of means and standard errors. Grey vertical lines and small scale bars at the bottom indicate two-fold differences in relative mRNA measurements.
Figure 1. KUL01 specifically precipitates a molecule with apparent molecular weight 180 kDa.Track M contains molecular weight standards. The other tracks contain materials absorbed from a precleared lysate of the HD11 macrophage cell line, by agarose beads to which were attached either KUL01, an isotype matched control antibody, or no antibody, and eluted at low pH. The open arrowhead points to the band(s) specifically absorbed by the KUL01 antibody, which were analysed by mass spectroscopy.
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