The scientific question that has focused the research in the lab for many years has been ‘how do immune systems function in marine invertebrates?’ and is centered the innate immune system of the purple sea urchin, Strongylocentrotus purpuratus. Annotation of the sea urchin genome and the identification of genes encoding proteins that function in immunity demonstrated that innate immune system of this long-lived invertebrate is complex, robust, and sophisticated. Many of the immune response genes are expressed in the immune cells, or coelomocytes, that become activated in response to infection or injury. A number of immune genes are upregulated in activated coelomocytes in response to lipopolysaccharide (LPS), other pathogen associated molecular patterns, and heat-killed Vibrio diazotrophicus (a marine bacterium). These genes encode homologues of the complement cascade, lectins, a Tie receptor homologue (a putative growth factor receptor), antimicrobial peptides called SpStrongelocins, and a set of unique genes that are members of the SpTransformer (SpTrf; formerly Sp185/333) gene family that are only found in sea urchins.
The SpTrf genes are strongly upregulated in response to immune challenge. Sequences of the mRNAs and genes are unusual because optimal alignments require the insertion of large gaps that define 25-27 blocks of similar sequence called elements. The high level of sequence diversity among the messages and genes is primarily based on the presence and/or absence of elements that generate mosaics of recognizable element patterns, in addition to small indels and single nucleotide polymorphisms (SNPs). About half of the messages encode proteins with early stop codons resulting from SNPs and frameshifts that are not present in the genes. This suggests that the messages are edited, primarily prior to immune challenge when truncated proteins are produced, in which there is a preponderance of C to U substitutions in genes compared to messages. These results indicate that editing, perhaps by a cytidine deaminase, broadens the sequence diversity of the proteins.
The genes are 1.8 kb or less with two exons, of which the first encodes a leader sequence and the second encodes the mature protein. The second exon includes the mosaic pattern of elements in addition to a variety of both tandem and interspersed repeats. Computational analysis of the repeat and element sequences strongly suggests that the genes undergo frequent recombination, and molecular clock predictions suggest that the extant members of the family are evolutionarily young.
Although the sea urchin genome sequence predicts the presence of only six SpTrf genes, estimates suggest that there are 50 (+10) family members. Sequences of large genome clones called bacterial artificial chromosomes (BACs), show that the genes are tightly clustered (up to seven genes within 40 kb), and that each is surrounded by short tandem repeats (STRs). Sequencing multiple BAC inserts with SpTrf genes indicates that there are two loci of SpTrf genes with 2, 6 and 7 genes per cluster. Among the two loci, there are multiple segmental duplications that include genes and are bounded by GA STRs. The structure of the genomic regions harboring the clusters of SpTrf genes suggest significant levels of gene conversion, recombination, duplication, deletion, and general genomic instability. It is noteworthy that no pseudogenes with altered reading frames have been identified, which is very unusual for clustered genes that share sequence. These results present questions about possible mechanisms for promoting gene diversification while blocking both the formation of pseudogenes and the homogenization of entire regions from gene conversion. It is not clear whether the STRs are involved in maintaining the structure and sequence diversity of the region but their presence and positioning is intriguing, particularly the positioning of large GA STR islands in locus 2 that appear to correlate with deleted genes. The curious structure of the genomic region may be required for high rates of diversification of the SpTrf gene family, which would be beneficial to the sea urchin as an underlying mechanism to keep pace in the arms race with pathogen diversification.
The SpTrf proteins are expressed in the category of coelomocytes called phagocytes that make up about 65-75% of the cells in the coelomic (body) fluid. The SpTrf proteins are located within perinuclear vesicles of some phagocytes, and are present on the surface membrane of others. The number of SpTrf+ coelomocytes increases significantly after immune challenge, consistent with increases in gene expression, and anti-pathogen function. The proteins are secreted from the phagocytes, and opsonize marine bacteria that augments phagocytosis by the phagocytes. To date, seven recombinant (r)SpTrf proteins have been isolated, and the functions of one version (rSpTrf-E1) shows that it binds to a range of targets including Gram negative bacteria, lipopolysaccharide from E. coli, β-1,3-glucan from yeast, and phosphatidic acid that is a phospholipid without a head-group. rSpTrf-E1 does not bind to Gram positive bacteria or to peptidoglycan from Bacillus. This broad range of binding targets that have been identified for one version of the SpTrf proteins suggests that the collective functions of the variety of native proteins in sea urchins is extraordinarily effective in protecting sea urchins from the extensive range of microbes in marine systems.
The sequence diversity of immune gene families in metazoans is a consequence of the arms race between a host and its pathogens, and is directly related to the ecological niche in which it lives. The array of pathogens in contact with the host, including what the host eats and its mucosal microflora shapes the immune response and the genes that function within it over evolutionary time. Different hosts appear to have quite different means to diversify the proteins that function in pathogen detection and immune defense. Rearrangement of the immunoglobulin class of genes in higher vertebrates is a classic example of how protein sequences of antibodies and T cell receptors are diversified. The assembly of the variable lymphocyte receptors in cyclostomes is another example. However, the notion of genomic instability in a region that harbors immune genes such as the SpTrf genes is an intriguing idea for generating immune gene sequence diversity in animals that lack the molecular capabilities for gene rearrangement or assembly. There are a wide variety of how immune systems function to protect hosts from the diversity and variability of pathogens, and the sea urchin SpTrf gene family is one variation on this theme.
Shaw, CG, C Pavloudi, MA Barela Hudgell, RS Crow, JH Saw, RA Pyron, LC Smith. 2023. Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium. Pathogens and Disease, in press
Smith, LC, SA Boettger, M Byrne, A Hyland, DL Lipscomb, AJ Majeske, JP Rast, NW Schuh, L Song, G Tafesh, L Wang, Z Xue, Z Yu. 2022. Chapter 18; Echinoderm Diseases and Pathologies.In: Invertebrate Pathology. AF Rowley, CJ Coates, MMA Whitten, eds. Oxford University Press. pp. 505-562.
Smith, LC, V Arizza, MA Barela Hudgell, G Barone, AG Bodnar, KM Buckley, V Cunsolo, N Dheilly, N Franchi, SD Fugmann, R Furukawa, J Garcia-Arraras, JH Henson, T Hibino, ZH Irons, C Li, CM Lun, AJ Majeske, M Oren, P Pagliara, A Pinsino, DA Raftos, JP Rast, B Samasa, D Schillaci, CS Schrankel, L Stabili, K Stensväg, E Sutton. 2018. Echinodermata: The Complex Immune System in Echinoderms. In “Advances in Comparative Immunology”, EL Cooper, ed. Springer Publisher. Chapter 13, pp 409-501.
Oren, M, MA Barela Hudgell, P Golconda, CM Lun, LC Smith. 2016. Genomic instability and shared mechanisms for gene diversification in two distant immune gene families: the plant NBS-LRR genes and the echinoid 185/333 genes. In “The Evolution of the Immune System, Conservation and Diversification” (D Malagoli, ed.). Elsevier Inc. Academic Press, London. pp. 295-310.
Smith, L.C. 2005. Host responses to bacteria; innate immunity in invertebrates. In The Influence of Bacterial Communities on Host Biology (M. McFall-Ngai, N. Ruby, B. Henderson, eds.). Advances in Molecular and Cellular Microbiology 10: 293-320. Cambridge University Press.
Smith, L.C. 2001. The complement system in sea urchins. In Phylogenetic Perspectives on the Vertebrate Immune Systems (G. Beck, M. Sugumaran, E. Cooper, eds.). Advances in Experimental Medicine and Biology, 363-372. Kluwer Academic/Plenum Publishing Co.New York, NY.
B.A., Drake University, 1974
M.S., University of Minnesota, 1976
Ph.D., University of California, Los Angeles, 1985, with William Hildemann
Post-Doctoral Work: California Institute of Technology with Eric Davidson