Sequence Diversity, Locus Structure, and Evolutionary History of the SpTransformer Genes in the Sea Urchin Genome

Abstract

The generation of large immune gene families is often driven by evolutionary pressure exerted on host genomes by their pathogens, which has been described as the immunological arms race. The SpTransformer (SpTrf) gene family from the California purple sea urchin, Strongylocentrotus purpuratus, is upregulated upon immune challenge and encodes the SpTrf proteins that interact with pathogens during an immune response. Native SpTrf proteins bind both bacteria and yeast, and augment phagocytosis of a marine Vibrio, while a recombinant SpTrf protein (rSpTrf-E1) binds a subset of pathogens and a range of pathogen associated molecular patterns. In the sequenced sea urchin genome, there are four SpTrf gene clusters for a total of 17 genes. Here, we report an in-depth analysis of these genes to understand the sequence complexities of this family, its genomic structure, and to derive a putative evolutionary history for the formation of the gene clusters. We report a detailed characterization of gene structure including the intron type and UTRs with conserved transcriptional start sites, the start codon and multiple stop codons, and locations of polyadenylation signals. Phylogenetic and percent mismatch analyses of the genes and the intergenic regions allowed us to predict the last common ancestral SpTrf gene and a theoretical evolutionary history of the gene family. The appearance of the gene clusters from the theoretical ancestral gene may have been driven by multiple duplication and deletion events of regions containing SpTrf genes. Duplications and ectopic insertion events, indels, and point mutations in the exons likely resulted in the extant genes and family structure. This theoretical evolutionary history is consistent with the involvement of these genes in the arms race in responses to pathogens and suggests that the diversification of these genes and their encoded proteins have been selected for based on the survival benefits of pathogen binding and host protection.

The complex set of internal repeats in SpTransformer protein sequences result in multiple but limited alternative alignments

“…The structure of the SpTrf gene family in the sequenced sea urchin genome shows tight clustering, sequence similarity, segmental duplications of the DNA that include entire genes, repeats in the second exon, and short tandem repeats in the flanking regions ( 2 , 22 , 26 , 27 ). The genes in this family are short (< 2 kb) and are composed of two exons and a short intron.…”

“…The element mosaicism is further complicated by the presence of six types of repeats (R) (Types 1 – 6), which are found in the coding sequence of the second exon ( 11 , 13 , 29 ). Two categories of genes have been identified and termed the long genes and the short genes ( 21 , 27 ). These categories are based on the length of these genes as determined by the number of elements that they contain.…”

“…In general, these two categories of genes therefore encode long (L) and short (S) proteins. These characteristics lead to interesting questions regarding the evolution of this gene family given that the appearance of these highly variable mosaic genes have been proposed to require extensive insertions, deletions, and perhaps partial gene conversions in the coding regions ( 26 , 27 ). Previous work by Buckley et al.…”

“…New alignment tools may have the potential to produce different alignments of the SpTrf sequences that would avoid biases and errors that might be present in the manual alignments. This effort has the additional goal of identifying an alignment tool that is capable of streamlining the alignment of these genes for further downstream studies including evolutionary analysis and identification of potential genomic events that led to the generation of the unusual structure of the SpTrf genes that are composed of elements ( 2 , 22 , 27 ). Here we explore the ability of the MSA tool, phylogenetically-aware algorithm (PRANK) [ ( 33 )], to align the protein sequences deduced from the SpTrf genes that have been identified in the sea urchin genome ( 27 , 34 ).…”

“…This effort has the additional goal of identifying an alignment tool that is capable of streamlining the alignment of these genes for further downstream studies including evolutionary analysis and identification of potential genomic events that led to the generation of the unusual structure of the SpTrf genes that are composed of elements ( 2 , 22 , 27 ). Here we explore the ability of the MSA tool, phylogenetically-aware algorithm (PRANK) [ ( 33 )], to align the protein sequences deduced from the SpTrf genes that have been identified in the sea urchin genome ( 27 , 34 ). Although we used the DNA sequences as the input dataset, PRANK translates the sequences into deduced amino acid sequences, or aligns the DNA sequences based on codons, and reports the alignments as amino acid sequences.…”