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Dynamic evolution of toll-like receptor multigene families in echinoderms.

Buckley KM, Rast JP - Front Immunol (2012)

Bottom Line: Representatives of most of the S. purpuratus TLR subfamilies and homologs of the mccTLR sequences are found in L. variegatus, although the L. variegatus TLR gene family is notably smaller (68 TLR sequences).The phylogeny of these genes within sea urchins highlights lineage-specific expansions at higher resolution than is evident at the phylum level.These analyses identify quickly evolving TLR subfamilies that are likely to have novel immune recognition functions and other, more stable, subfamilies that may function more similarly to those of vertebrates.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology, Sunnybrook Research Institute, University of Toronto Toronto, ON, Canada.

ABSTRACT
The genome sequence of the purple sea urchin, Strongylocentrotus purpuratus, a large and long-lived invertebrate, provides a new perspective on animal immunity. Analysis of this genome uncovered a highly complex immune system in which the gene families that encode homologs of the pattern recognition receptors that form the core of vertebrate innate immunity are encoded in large multigene families. The sea urchin genome contains 253 Toll-like receptor (TLR) sequences, more than 200 Nod-like receptors and 1095 scavenger receptor cysteine-rich domains, a 10-fold expansion relative to vertebrates. Given their stereotypic protein structure and simple intron-exon architecture, the TLRs are the most tractable of these families for more detailed analysis. A role for these receptors in immune defense is suggested by their similarity to TLRs in other organisms, sequence diversity, and expression in immunologically active tissues, including phagocytes. The complexity of the sea urchin TLR multigene families is largely derived from expansions independent of those in vertebrates and protostomes, although a small family of TLRs with structure similar to that of Drosophila Toll can be traced to an ancient eumetazoan ancestor. Several other echinoderm sequences are now available, including Lytechinus variegatus, as well as partial sequences from two other sea urchin species. Here, we present an analysis of the invertebrate deuterostome TLRs with emphasis on the echinoderms. Representatives of most of the S. purpuratus TLR subfamilies and homologs of the mccTLR sequences are found in L. variegatus, although the L. variegatus TLR gene family is notably smaller (68 TLR sequences). The phylogeny of these genes within sea urchins highlights lineage-specific expansions at higher resolution than is evident at the phylum level. These analyses identify quickly evolving TLR subfamilies that are likely to have novel immune recognition functions and other, more stable, subfamilies that may function more similarly to those of vertebrates.

No MeSH data available.


TLR subfamilies are differentially expressed. RNA-Seq was used to analyze gene expression from larvae (A), immune cells (B), and gut (C). Phagocytic coelomocytes and gut were isolated from an animal 12 h after intracoelomic injection of a gut bacteria preparation. Larvae were exposed to V. diazotrophicus for 0, 6, 12, and 24 h, and collected for transcriptome sequencing. RPKM values were calculated for each of the TIR domains; the average RPKM for each group is shown. The sccTLR subfamilies correspond to those shown in Figure 2. Note that the scales are different for each graph. The divergent TLRs are indicated as follows: M, mccTLRs; S, short; Int, intron-containing (Figure 1). In phagocytic coelomocytes, TLRs from the Ib, IIa, and X subfamilies, as well as the mccTLR genes are most highly expressed. In contrast, the III TLRs are primarily expressed in the gut tissue. The TLRs are expressed at lower levels in the larvae, and little change in TLR expression in the larvae is observed in response to bacterial challenge. The predominantly expressed families at the larval stage are Id and VI, are different than those expressed in coelomocytes.
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Figure 5: TLR subfamilies are differentially expressed. RNA-Seq was used to analyze gene expression from larvae (A), immune cells (B), and gut (C). Phagocytic coelomocytes and gut were isolated from an animal 12 h after intracoelomic injection of a gut bacteria preparation. Larvae were exposed to V. diazotrophicus for 0, 6, 12, and 24 h, and collected for transcriptome sequencing. RPKM values were calculated for each of the TIR domains; the average RPKM for each group is shown. The sccTLR subfamilies correspond to those shown in Figure 2. Note that the scales are different for each graph. The divergent TLRs are indicated as follows: M, mccTLRs; S, short; Int, intron-containing (Figure 1). In phagocytic coelomocytes, TLRs from the Ib, IIa, and X subfamilies, as well as the mccTLR genes are most highly expressed. In contrast, the III TLRs are primarily expressed in the gut tissue. The TLRs are expressed at lower levels in the larvae, and little change in TLR expression in the larvae is observed in response to bacterial challenge. The predominantly expressed families at the larval stage are Id and VI, are different than those expressed in coelomocytes.

Mentions: The expression levels of the TLR subfamilies were analyzed in sea urchin larvae and adult immune cells and gut tissue using an RNA-Seq approach (Figure 5). A single batch of sea urchin larvae (9 dpf) was exposed to the marine bacterium V. diazotrophicus, and samples were collected at 0, 6, 12, and 24 h. For each time point, ∼75 million paired-end SOLiD sequencing reads were obtained. Additionally, an adult sea urchin was challenged using bacteria isolated from the digestive tract of another animal to mimic a perforation in the gut and systemic infection. This is intended as a physiologically relevant immune challenge that may be expected to induce a coordinated and complex immune response. Adult phagocytic coelomocytes and gut were isolated 12 h after challenge and used in RNA-Seq experiments, with approximately 130 million and 70 million paired-end reads obtained for each tissue, respectively. From this animal, ∼40 million phagocytes were collected, from which 1.5 μg of polyadenylated mRNA was isolated and used to generate cDNA for sequencing.


Dynamic evolution of toll-like receptor multigene families in echinoderms.

Buckley KM, Rast JP - Front Immunol (2012)

TLR subfamilies are differentially expressed. RNA-Seq was used to analyze gene expression from larvae (A), immune cells (B), and gut (C). Phagocytic coelomocytes and gut were isolated from an animal 12 h after intracoelomic injection of a gut bacteria preparation. Larvae were exposed to V. diazotrophicus for 0, 6, 12, and 24 h, and collected for transcriptome sequencing. RPKM values were calculated for each of the TIR domains; the average RPKM for each group is shown. The sccTLR subfamilies correspond to those shown in Figure 2. Note that the scales are different for each graph. The divergent TLRs are indicated as follows: M, mccTLRs; S, short; Int, intron-containing (Figure 1). In phagocytic coelomocytes, TLRs from the Ib, IIa, and X subfamilies, as well as the mccTLR genes are most highly expressed. In contrast, the III TLRs are primarily expressed in the gut tissue. The TLRs are expressed at lower levels in the larvae, and little change in TLR expression in the larvae is observed in response to bacterial challenge. The predominantly expressed families at the larval stage are Id and VI, are different than those expressed in coelomocytes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3367398&req=5

Figure 5: TLR subfamilies are differentially expressed. RNA-Seq was used to analyze gene expression from larvae (A), immune cells (B), and gut (C). Phagocytic coelomocytes and gut were isolated from an animal 12 h after intracoelomic injection of a gut bacteria preparation. Larvae were exposed to V. diazotrophicus for 0, 6, 12, and 24 h, and collected for transcriptome sequencing. RPKM values were calculated for each of the TIR domains; the average RPKM for each group is shown. The sccTLR subfamilies correspond to those shown in Figure 2. Note that the scales are different for each graph. The divergent TLRs are indicated as follows: M, mccTLRs; S, short; Int, intron-containing (Figure 1). In phagocytic coelomocytes, TLRs from the Ib, IIa, and X subfamilies, as well as the mccTLR genes are most highly expressed. In contrast, the III TLRs are primarily expressed in the gut tissue. The TLRs are expressed at lower levels in the larvae, and little change in TLR expression in the larvae is observed in response to bacterial challenge. The predominantly expressed families at the larval stage are Id and VI, are different than those expressed in coelomocytes.
Mentions: The expression levels of the TLR subfamilies were analyzed in sea urchin larvae and adult immune cells and gut tissue using an RNA-Seq approach (Figure 5). A single batch of sea urchin larvae (9 dpf) was exposed to the marine bacterium V. diazotrophicus, and samples were collected at 0, 6, 12, and 24 h. For each time point, ∼75 million paired-end SOLiD sequencing reads were obtained. Additionally, an adult sea urchin was challenged using bacteria isolated from the digestive tract of another animal to mimic a perforation in the gut and systemic infection. This is intended as a physiologically relevant immune challenge that may be expected to induce a coordinated and complex immune response. Adult phagocytic coelomocytes and gut were isolated 12 h after challenge and used in RNA-Seq experiments, with approximately 130 million and 70 million paired-end reads obtained for each tissue, respectively. From this animal, ∼40 million phagocytes were collected, from which 1.5 μg of polyadenylated mRNA was isolated and used to generate cDNA for sequencing.

Bottom Line: Representatives of most of the S. purpuratus TLR subfamilies and homologs of the mccTLR sequences are found in L. variegatus, although the L. variegatus TLR gene family is notably smaller (68 TLR sequences).The phylogeny of these genes within sea urchins highlights lineage-specific expansions at higher resolution than is evident at the phylum level.These analyses identify quickly evolving TLR subfamilies that are likely to have novel immune recognition functions and other, more stable, subfamilies that may function more similarly to those of vertebrates.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology, Sunnybrook Research Institute, University of Toronto Toronto, ON, Canada.

ABSTRACT
The genome sequence of the purple sea urchin, Strongylocentrotus purpuratus, a large and long-lived invertebrate, provides a new perspective on animal immunity. Analysis of this genome uncovered a highly complex immune system in which the gene families that encode homologs of the pattern recognition receptors that form the core of vertebrate innate immunity are encoded in large multigene families. The sea urchin genome contains 253 Toll-like receptor (TLR) sequences, more than 200 Nod-like receptors and 1095 scavenger receptor cysteine-rich domains, a 10-fold expansion relative to vertebrates. Given their stereotypic protein structure and simple intron-exon architecture, the TLRs are the most tractable of these families for more detailed analysis. A role for these receptors in immune defense is suggested by their similarity to TLRs in other organisms, sequence diversity, and expression in immunologically active tissues, including phagocytes. The complexity of the sea urchin TLR multigene families is largely derived from expansions independent of those in vertebrates and protostomes, although a small family of TLRs with structure similar to that of Drosophila Toll can be traced to an ancient eumetazoan ancestor. Several other echinoderm sequences are now available, including Lytechinus variegatus, as well as partial sequences from two other sea urchin species. Here, we present an analysis of the invertebrate deuterostome TLRs with emphasis on the echinoderms. Representatives of most of the S. purpuratus TLR subfamilies and homologs of the mccTLR sequences are found in L. variegatus, although the L. variegatus TLR gene family is notably smaller (68 TLR sequences). The phylogeny of these genes within sea urchins highlights lineage-specific expansions at higher resolution than is evident at the phylum level. These analyses identify quickly evolving TLR subfamilies that are likely to have novel immune recognition functions and other, more stable, subfamilies that may function more similarly to those of vertebrates.

No MeSH data available.