Open Access Research article

The evolution of the class A scavenger receptors

Fiona J Whelan1, Conor J Meehan2, G Brian Golding3, Brendan J McConkey4 and Dawn M E Bowdish1*

Author Affiliations

1 Department of Pathology and Molecular Medicine, McMaster University, 1200 Main Street West, Hamilton, L8N 3Z5, Ontario, Canada

2 Faculty of Biochemistry and Molecular Biology, Dalhousie University, 5080 College Street, Halifax, Nova Scotia, Canada, B3H 4R2

3 Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada

4 Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, N2L 3G1, Ontario, Canada

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BMC Evolutionary Biology 2012, 12:227  doi:10.1186/1471-2148-12-227

Published: 27 November 2012

Additional files

Additional file 1:

Table S2. Domain boundaries of the representative class A scavenger receptors in Homo sapiens. Probabilities for the cytoplasmic and transmembrane domains were determined using the TMHMM software tool. The α-helical domain with coiled-coil motifs was determined using the JUFO Server and PSIPred [JUFO;PSIPRED]. The collagenous, SRCR, and C-type lectin domains were determined using NCBI’s CDD. ∧ indicate that probabilities were measured by the corresponding software for each amino acid in the domain and a range is given. P(H) and P(C) represent the probability of a helix or coil at each amino acid (aa) in the domain. ∗ indicate that there were multiple hits in NCBI’s CDD, for which a range of E-values is presented.

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Additional file 2:

Table S1. Class A scavenger receptor mRNA and protein sequence information. Novel sequences are indicated with bold font; those sequences marked as only predicted in GenBank and Ensembl databases are labeled with an asterisk. Proteins for which only partial sequence information is available is indicated with italics.

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Additional file 3:

Figure S1. Phylogenetic trees of known and novel class A scavenger receptors indicate conservation of these receptors in a subset of vertebrate genomes. Phylogenies were created based on full-length cA-SR protein sequences. Novel sequences are indicated with bold font; those sequences marked as only predicted in GenBank and Ensembl databases are labeled with an asterisk. MARCO (a) was discovered in avian and mammalian genomes. SRAI (b) was found in organisms from Xenopus to mammals; no SRAI sequences were found in publicly available avian genomes. SCARA5 (c) was more phylogenetically diverse as 3 additional instances of this receptor were found in fish genomes. SCARA3 (d) was found in 2 Teleost fish genomes, Danio rerio and Tetraodon nigroviridis. SCARA4 (e) is the most phylogenetically widespread of the cA-SRs, present in 4 distinct fish species including the early bony fish of the superorder Acanthopterygii. Tree topologies were determined using both Bayesian and maximum likelihood methods and are supported by posterior probabilities and bootstrap values as indicated on node labels [BY/ML]. All phylogenies are midpoint rooted; scale bar indicates the number of substitutions per site.

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Additional file 4:

Table S3. Exon structure for 3 representative species (human Hs, mouse Mm, and opossum Md) containing each of the 5 class A scavenger receptors. Exons are annotated as 5’UTR (untranslated region), CYTO (cytosolic), TM (transmembrane), AH (α-helical region), COL (collagenous region), SRCR (SRCR domain), LEC (Lectin domain), and 3’UTR (untranslated region). Accession numbers are from Ensembl Transcripts or mapping of mRNA to NCBI genomic sequence for XM_001370497. Numbers represent exon length in nucleotides, with values in brackets representing identified untranslated regions.

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