Molecular Evolution, Functional Variation, and Proposed Nomenclature of the Gene Family That Includes Sphingomyelinase D in Sicariid Spider Venoms
- ️Thu May 26 2005
Abstract
The venom enzyme sphingomyelinase D (SMase D) in the spider family Sicariidae (brown or fiddleback spiders [Loxosceles] and six-eyed sand spiders [Sicarius]) causes dermonecrosis in mammals. SMase D is in a gene family with multiple venom-expressed members that vary in functional specificity. We analyze molecular evolution of this family and variation in SMase D activity among crude venoms using a data set that represents the phylogenetic breadth of Loxosceles and Sicarius. We isolated a total of 190 nonredundant nucleotide sequences encoding 168 nonredundant amino acid sequences of SMase D homologs from 21 species. Bayesian phylogenies support two major clades that we name α and β, within which we define seven and three subclades, respectively. Sequences in the α clade are exclusively from New World Loxosceles and Loxosceles rufescens and include published genes for which expression products have SMase D and dermonecrotic activity. The β clade includes paralogs from New World Loxosceles that have no, or reduced, SMase D and no dermonecrotic activity and also paralogs from Sicarius and African Loxosceles of unknown activity. Gene duplications are frequent, consistent with a birth-and-death model, and there is evidence of purifying selection with episodic positive directional selection. Despite having venom-expressed SMase D homologs, venoms from New World Sicarius have reduced, or no, detectable SMase D activity, and Loxosceles in the Southern African spinulosa group have low SMase D activity. Sequence conservation mapping shows >98% conservation of proposed catalytic residues of the active site and around a plug motif at the opposite end of the TIM barrel, but α and β clades differ in conservation of key residues surrounding the apparent substrate binding pocket. Based on these combined results, we propose an inclusive nomenclature for the gene family, renaming it SicTox, and discuss emerging patterns of functional diversification.
Keywords: Loxosceles, Sicarius, duplication, toxin
Introduction
Spider venoms are complex mixtures of hundreds of proteins, peptides, and low-molecular-weight components. The composition of venom varies widely across species but includes cytotoxins, neurotoxins with specific neurophysiological targets, and antimicrobial components (reviews in Schulz 1997; Rash and Hodgson 2002; Kuhn-Nentwig 2003; Adams 2004; Tedford et al. 2004; Escoubas 2006; Estrada et al. 2007; King 2007). Much recent research has focused on the rich potential in spider venoms for discovery of novel toxic activities that may have pharmacological utility (recent review in Escoubas et al. 2008), but relatively little work has empirically analyzed evolutionary mechanisms that have influenced spider venom diversity (see Kordis and Gubensek 2000; Diao et al. 2003; Sollod et al. 2005; Escoubas 2006). The general types of toxins in spider venoms are similar to those in other animals that have independently evolved venom for prey capture, such as cone snails (reviews in Duda and Palumbi 2000; Espiritu et al. 2001; Olivera 2002), snakes (Fry et al. 2008), and scorpions (Rodríguez de la Vega and Possani 2004, 2005). Work on these toxins has uncovered interesting evolutionary patterns and mechanisms including accelerated evolution and hypermutation mechanisms (e.g., Kini and Chan 1999; Duda and Palumbi 2000; Espiritu et al. 2001; Calvete et al. 2005; Lynch 2007), diversification via birth-and-death processes (Fry et al. 2003; Li et al. 2005), toxin gene recruitment from a broad range of protein families (Fry 2005), and evolution of expression patterns of toxin genes (Duda and Remigio 2008). Comparably focused work on spider venom toxins is likely to discover similarly interesting evolutionary dynamics. Furthermore, understanding evolutionary dynamics of venom toxins should help with focusing bioprospecting efforts, understanding the distribution of taxa with dangerous bites, and developing treatments that are effective for the phylogenetic breadth of taxa with clinically important toxins.
Here, we present an evolutionary analysis of the gene family that includes the venom toxin sphingomyelinase D (SMase D). SMase D is expressed in venoms of Loxosceles (brown or violin spiders) and their sister genus Sicarius (six-eyed sand spiders). These two genera are supported by morphology to be each other's closest relatives, and they are the only two taxa in the family Sicariidae (Platnick et al. 1991). Loxosceles are famous for bites that cause dermonecrotic lesions in mammalian tissues (recent reviews in da Silva et al. 2004; Swanson and Vetter 2005; Vetter 2008), and venoms of some Sicarius species also cause dermonecrosis (Newlands and Atkinson 1988; Van Aswegen et al. 1997). The venom-expressed enzyme SMase D has been demonstrated to be a sufficient causative agent for lesion formation (Kurpiewski et al. 1981; Tambourgi et al. 1998, 2004; Fernandes-Pedrosa et al. 2002; Ramos-Cerrillo et al. 2004). Multiple members of the gene family that includes SMase D are expressed in individual venoms (Tambourgi et al. 1998; de Castro et al. 2004; Ramos-Cerrillo et al. 2004; Binford et al. 2005; Machado et al. 2005; Kalapothakis et al. 2007; Fernandes-Pedrosa et al. 2008), and these paralogs differ in substrate specificity (Tambourgi et al. 1998; Ramos-Cerrillo et al. 2004; Lee and Lynch 2005; Kalapothakis et al. 2007). A structure has been solved for a member of this gene family (PDB 1XX1) and active sites proposed (Murakami et al. 2005). The enzyme is an (α/β)8 barrel and apparently depends upon binding of a Mg2+ ion for catalysis. This set of homologous genes has been referred to as “SMase D” in the literature, but the fact that known venom-expressed homologs do not have SMase D activity has led Kalapothakis et al. (2007) to propose the broader name LoxTox for the gene family.
Many characteristics of the LoxTox gene family suggest it has had an interesting evolutionary history. SMase D is a highly derived member of the ubiquitous glycerophosphodiester phosphodiesterase (GDPD) protein domain family (Binford et al. 2005; Cordes and Binford 2006; Murakami et al. 2006). Comparative analyses have not detected SMase D activity in venoms outside of sicariid spiders, which is consistent with a single evolutionary origin of SMase D as a venom toxin in the most recent common ancestor (MRCA) of this lineage (Binford and Wells 2003). Homologous SMase Ds are expressed as an exotoxin in a few Corynebacteria (Soucek et al. 1967; Bernheimer et al. 1985; Truett and King 1993). A C-terminal structural motif that is unique to and shared by spider and bacterial SMase Ds is evidence that this disparate distribution of SMase D may be explained by a lateral transfer event (Cordes and Binford 2006). The recent discovery of a homologous gene expressed in tick saliva (Accession DQ411855) is consistent with the gene family having an ancient presence in arachnids and implies that a horizontal transfer event would have originated from an arachnid and moved into Corynebacteria.
Despite the interesting emerging picture of evolutionary phenomena, detailed mechanisms influencing diversification of the LoxTox gene family require comparative analyses with more dense taxon sampling within sicariids. To date, a detailed analysis has been hampered by limited taxon sampling and lack of understanding of species relationships in sicariids. The approximately 100 described species of Loxosceles are native to the Americas, Africa, and the Mediterranean (Gertsch and Ennik 1983), and the synanthropic species L. rufescens has colonized many other locations. Twenty-three described species of Sicarius are native to Africa and Central and South America (Gerschman and Schiapelli 1979; Platnick 2008). LoxTox gene family members have been isolated from three North American Loxosceles species from the reclusa species group and four species from South America that represent three species groups (summary and references in table 1). There are no published homologs from Old World Loxosceles or Sicarius.
Table 1.
Summary of All Known SMaseD DNA and Protein Sequences Published to Date with Summaries of Enzyme Activity, Dermonecrotic Activity, and Studies That Have Been Conducted with Recombinant Forms of the Protein.
Our goal was to analyze patterns of variation and mechanisms of molecular evolution of venom-expressed members of the LoxTox gene family in sicariid spiders. We use phylogenetic analyses, structural modeling of amino acid conservation, and analyses of positive selection of a data set of sequences of venom-expressed members of this gene family available from this and previous work. We complement phylogenetic analyses with comparative protein separations and enzyme activity assays of whole crude venoms. Our data set includes representatives from all identified species groups of Loxosceles and Sicarius with taxon sampling guided by recent species-level molecular systematic work on members of this lineage (Binford et al. 2008). Based on our results, we propose renaming this gene family SicTox, abbreviated from Sicariidae toxin, to accommodate the currently known breadth of species that express members of this gene family in venoms. We also propose an inclusive, phylogenetically based nomenclature with the goal of standardizing the language to facilitate efficient and unambiguous discussion of this gene family in the literature.
Materials and Methods
Taxonomic Sampling and Collection
The representation of taxa in different analyses is summarized in table 2. Our goal was to capture the breadth of diversity within Sicariidae, guided by previous phylogenetic work (Binford et al. 2008, fig. 1). To do this, we include at least one representative of every described species group in Loxosceles, representatives of each geographic region to which Sicarius is native, and the most appropriate and available outgroup for each particular analysis (table 2). Spiders in the genus Drymusa are putative close relatives of sicariids that have been previously shown to not express SMase D in their venom (Binford and Wells 2003).
Table 2.
Taxa of Loxosceles, Sicarius, and Drymusa for Which New Data are Presented in This Work
Species | Locality | SMaseD cDNA | SMaseD assay | SDS-PAGE |
Loxosceles | ||||
reclusa species group | ||||
Loxosceles arizonica | United States: Tucson, AZ | X | X | X |
Loxosceles apachea | United States: Stein's Ghost Town, NM | X | X | X |
Loxosceles sabina | United States: Bill's Cave, Vail, AZ | X | X | X |
Loxosceles deserta | United States: Granite Mtn, CA | X | X | X |
Loxosceles reclusa | United States: Oxford, MS | X | X | |
laeta species group | ||||
Loxosceles laeta | United States: Los Angeles, CA | X | X | X |
L. sp. nov. Catamarca | Argentina: Catamarca | X | X | X |
spadicea species group | ||||
Loxosceles intermedia | Argentina: El Palmar | X | X | |
Loxosceles hirsuta | Argentina: Chaco | X | X | X |
Loxosceles spadicea | Argentina: Catamarca | X | X | X |
gaucho species group | ||||
Loxosceles variegata | Argentina: Corrientes | X | ||
amazonica species group | ||||
Loxosceles amazonica | Peru: Loreto, Pevas | X | X | X |
rufescens species group | ||||
Loxosceles rufescens | United States: Indianapolis, IN | X | X | X |
vonwredei species group | ||||
Loxosceles vonwredei | Namibia: Uisib Farm Caves | X | X | |
spinulosa species group | ||||
L. sp. aff spinulosa | Namibia: Munsterland | X | X | X |
Loxosceles speluncarum | South Africa: Greensleeves Cave | X | X | X |
L. sp. aff. spinulosa | Namibia: Ruacana Falls | X | X | X |
Loxosceles spinulosa | Namibia: Grootfontein | X | X | X |
L. spinulosa | South Africa: Borakalalo | X | X | X |
L. sp. aff. spinulosa | Namibia: Windhoek | X | X | X |
Sicarius | ||||
Africa | ||||
S. sp. cf. damarensis | Namibia: Oorloogskloof | X | X | X |
S. sp. cf. hahni | Namibia: Strydpoort Mtns | |||
Sicarius dolichocephalus | Namibia: Ruacana Falls | X | ||
Sicarius damarensis | Namibia: Daan Viljoen Park | X | ||
S. sp. aff. damarensis | Namibia: Munsterland Farm | X | ||
Sicarius albospinosus | Namibia: Gobabeb | X | X | X |
S. albospinosus | Namibia: Wundergat | X | ||
South America | ||||
Sicarius terrosus | Argentina: Catamarca | X | X | |
S. terrosus | Argentina: Sierra de las Quijades | X | X | X |
Sicarius rupestris | Argentina: Corallito | X | X | |
Sicarius patagonicus | Argentina: Picun Leufo | X | X | X |
Sicarius peruensis | Peru: Lima - Pisco | X | X | |
S. peruensis | Peru: Olmos - Lambayeque | X | X | X |
Central America | ||||
Sicarius rugosus | Costa Rica: Palo Verde | X | X | |
Drymusa | ||||
Drymusa capensis | South Africa: Capetown | X | X | |
Drymusa serrana | Argentina: Merlo | X | X | |
Drymusa dinora | Costa Rica: Osa Peninsula | X |
FIG. 1.—
Relationships of species from which SicTox genes and venoms were included in our analysis. This is a summary composite from analyses of Binford et al. (2008).
All spiders were collected in the field by G.J.B. and colleagues. Details of collecting localities are available from G.J.B. by request. We restricted analyses to mature individuals to allow for proper species-level confirmation using morphology. We also retained legs of spiders for genomic DNA isolation to help with confirmation of species status. If animals were not mature when collected, we reared them to maturity in the laboratory at 35% humidity, 24 °C. Species-level systematics of some taxa we include is unclear, and their taxonomic nomenclature is being revised. This is particularly true of African sicariids. For this work, we follow the same nomenclatural framework used in Binford et al. (2008). Voucher specimens are maintained in the collection of G.J.B. and will be submitted to the California Academy of Sciences, and duplicates from the same populations will be sent to National Museums from the countries of origin upon completion of our work.
SMase D Homolog Sequencing and Analyses
Venom Tissue Gland Isolation and cDNA Synthesis
We used electrical stimulation to extract venom from all specimens used for cDNA analysis (table 2) as described in Binford and Wells (2003). Two to three days later, a time when we have previously isolated SMase D mRNAs (Binford et al. 2005), we anesthetized spiders in CO2, removed, and immediately flash-froze the venom glands in liquid nitrogen. We immediately isolated RNA from homogenized venom glands using the ChargeSwitch Total RNA Cell Kit (Invitrogen, Carlsbad, CA), or we stored glands at −70 °C until RNA isolation. We synthesized first-strand cDNA using an anchored oligo-dT primer targeted for annealing at the 3′-end of mRNAs (5′-ggccacgcgtcgactagtacttttttttttttttttt-3′) and SuperScript III Reverse Transcriptase (Invitrogen). We increased all reactions 5× from the manufacturer's protocol.
Amplification of SMase D Homologs
To amplify a diverse set of SMase D homologs from cDNA samples, we used two different degenerate primers that were designed to match the N-terminus of published members of this gene family. One of these we have previously used to amplify SMase D genes from Loxosceles arizonica (“sphing1f” 5′-tggathatgggncayatggt-3′, Binford et al. 2005). To amplify more divergent homologs, we designed another primer (“Lpara” 5′-gcncayatggtnaaygayt-3′) to match published and divergent homologs of SMase D (laetaH10, Fernandes-Pedrosa et al. 2002) and homologs for which expression products show little or no enzyme activity when tested (LiD1, Kalapothakis et al. 2002; Lb3, Ramos-Cerrillo et al. 2004; LiRecDT3, da Silveira et al. 2006; Ribeiro et al. 2007) (table 1). We used the same primer to amplify from the C-terminus in all reactions (5′-ccacgcgtcgactagtac-3′).
For polymerase chain reaction (PCR), we used 2× MasterAmp PreMix (Epicentre Technologies, Madison, WI), NEB Taq Polymerase (New England Biolabs, Ipswich, MA), and an annealing temperature of 51 °C for all reactions except those with the primer Lpara and templates from Loxosceles spinulosa (Borakalalo) and L. spinulosa (Ruacana) that were run at 45 °C. We cloned PCR products that were ∼1 kb (approximate size of the SMase D gene) into pCR4-TOPO vector using the TOPO TA Cloning Kit for Sequencing (Invitrogen). We screened bacterial transformants using whole colony PCR under the conditions used to initially amplify the inserts. From each cDNA template, we screened a minimum of 20 colonies and up to 152 for taxa that were low yielding (L sp. aff. spinulosa Windhoek). Colonies with products ≥700 bp were grown in selective media and purified using the QIAPrep spin mini-prep kit (Qiagen, Valencia, CA). Inserts were sequenced in both directions with T3 and T7 primers on an Applied Biosystems 3730xl DNA Analyzer (Foster City, CA) at the Genomic Analysis and Technology Core (University of Arizona).
Sequence Analysis
After trimming vector sequence, we confirmed homology to SMase D by submitting sequences to TBlastX searches in the NCBI gene database (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi). We assembled all sequences that were homologous to SMase D genes using Sequencher (version 4.7, Gene Codes Corp.). We aligned all nucleotide sequences we recovered with all sequences available in GenBank, using ClustalX (Thompson et al. 1997) and refined this manually using MacClade (version 4.06; Maddison and Maddison 2005) guided by color-coding nucleotides according to their translated amino acid. We used conserved published active sites as anchors in the alignment. Sequences that ended prematurely (10) had early stop codons (19), or frame-shifting indels (8) were removed from the data set.
Molecular Phylogenetics
We analyzed phylogenetic relationships of our nonredundant amino acid data set (196 taxa in the ingroup, 349 characters) using Neighbor-Joining (NJ) in PAUP* (Swofford 1998) and Bayesian analyses in MrBayes v.3.1.2 (Ronquist and Huelsenbeck 2003). We used an SMase D homolog isolated from Ixodes (Arachnida:Acari) (DQ411855) as an outgroup. We assessed confidence in branches using 1,000 nonparametric bootstrap replicates for NJ analyses. All Bayesian analyses consisted of two simultaneous runs, each with four Markov Chain Monte Carlo chains. The current tree at every increment of 100 generations was saved to a file. We used default cold and heated chain parameters and compared the separate runs every 1,000 generations to facilitate convergence. We ran this analysis for 2 million generations when we considered the sampling to be adequate based on average standard deviation of split frequencies being <0.01 (Ronquist et al. 2005). We determined the burn-in period as the set of trees saved prior to log likelihood stabilization and convergence as estimated using Tracer 1.4 (Drummond and Rambaut, 2007).
Criteria for Identifying Paralogs
For many species, we recovered multiple distinct but very similar sequences that Bayesian analyses resolved as each other's closest relatives, often in a polytomy. Without further analyses, it is difficult to distinguish whether these are allelic variants or paralogs resulting from recent duplication events. We estimate the number of paralogs by three different methods. Our most liberal estimate was to define sets of sequences from a given species that were monophyletic terminal polytomies on our tree as allelic variants of a single paralog. For comparison, we estimated distinct paralogs within terminal monophyletic intraspecific groups as distinct paralogs when amino acid sequence divergence among them was 2% or greater (∼5 amino acids different). For analyses that would be biased by redundancy (gene duplication analyses and models of structural conservation, see below), we analyze a subset of our data set only including intraspecific sequences that were minimally 5% divergent (∼14 amino acids different).
Species Tree Gene Tree Reconciliation Analysis
We estimated the number of gene duplications and losses required to reconcile the gene tree with an independently estimated species tree (fig. 1) using reconciliation analysis in Notung 2.5 (Chen et al. 2000; Durand et al. 2006; Vernot et al. 2007). To address biases in the analysis from overrepresentation of paralogs via allelic variants and underrepresentation of paralogs from our inexhaustive sampling methods, we did this analysis on our full data set (all terminal taxa in fig. 2), and repeated it on two reduced data sets culled to include sequences with a minimum of 2% and 5% amino acid divergence as described above. For analyses of each of these data sets, we used gene trees estimated using NJ in PAUP* that were rooted with the sequence from Ixodes. We removed Ixodes from the gene tree before reconciliation.
FIG. 2.—
Tree topology resulting from Bayesian analyses. Posterior probabilities are labeled above branches with a * indicating support >0.95. Labels below the branch indicate bootstrap support from NJ analyses with 1,000 bootstrap replicates with a * indicating >95%. The proposed SicTox nomenclature delineating major clades on the tree are indicated by labels next to branches. The terminal names indicate the SicTox nomenclature for terminal groups (summarized in supplemental table 1, Supplementary Material online). Colored branches distinguish species groups as delineated in tables 1 and 2. Triangles below branches illustrate branches that had ω > 1 in free-ratio codon likelihood analyses.
Tests for Positive Directional Selection
We tested for an influence of positive selection on divergence of SicTox nucleotide sequences using two codon-based likelihood analyses implemented in the Codeml package of PAML 3.14 (Yang 2007), branch models (Yang 1998) and site models (Yang et al. 2000). We did not test for selection at particular branches (branch-site model) (Yang and Nielsen 2002) because we had no a priori hypotheses of specific branches undergoing positive selection. To increase computational speed, we analyzed a data set that included a single representative of terminal, intraspecific, monophyletic sets of sequences that shared less than 5% sequence divergence, we analyzed the α and the β clades separately (47 and 29 sequences, respectively), and we set cleandata = 1, which only includes amino acids with no gaps. Our input trees that included only the sequences under analysis were estimated by NJ and rooted by Ixodes. Ixodes was removed from the tree before input into Codeml. For branch analyses, we estimated independent ω values for all branches (free-ratios model), we estimated a single value of ω under a constraint that ω remain constant (one-ratio model), and computed log likelihood values when ω was fixed at 1. We used likelihood ratio tests (LRTs) to determine if log likelihood estimates were significantly different when ω values were free to vary and when they were constrained to have a single value. We calculated this by comparing twice the difference between the log likelihood under the fixed model and the log likelihood of the free model to a χ2 distribution with one degree of freedom (Yang 1998; Yang and Nielsen 1998; Yang and Bielawski 2000). For tests of selection that consider variation in selection across sites, we used the following models: M0 (one ratio), M1a (Nearly Neutral), M2a (Positive Selection), M7 (beta), and M8 (beta & ω) (Yang et al. 2005). We used LRTs comparing M1a and M2a, and M7 and M8 using df = 2.
Comparative Protein Composition and SMase D Assays
Protein Gel Electrophoresis
For protein analyses, we pooled venom collected by electrostimulation (see above) among individuals within the same population. We diluted all venoms in 1× Amplex Red buffer (5 mM CaCl2, 50 mM Tris–Cl, pH 8) and quantified total venom protein using the Coomassie (Bradford) Protein Assay (Pierce, Rockford, IL).
We separated proteins from crude venom (3, 5, or 7 μg) using one-dimensional SDS-PAGE with precast Criterion 12.5% midi gels (Bio-Rad, Hercules, CA). Intensity of staining varied among lanes with 5 μg of protein loaded, so we ran select venoms with 3, 5, and 7 μg of total protein to determine the effect of staining intensity on visibility of bands. We used a broad range molecular weight marker (New England Biolabs, Ipswich, MA, P7702S) along with a low range silver stain standard (Bio-Rad, 161-0314) on each gel for size reference. For visualization, we stained the gels with silver stain using standard protocol.
Assays for SMase D Activity
We assayed SMase D activity using a modification of the Amplex Red Phospholipase D Assay Kit (Molecular Probes, Eugene, OR), as described in Binford and Wells (2003) with sphingomyelin (from chicken egg yolk, Sigma, St Louis, MO) as the substrate. We measured fluorescence emission from reactions (200 μl) in a quartz fluorimeter cell (10 mm, z = 15, Starna Cells, Inc., Hainault, UK) using a Perkin Elmer LS55 luminescence spectrometer (Waltham, MA).
Amino Acid Sequence Conservation
We analyzed amino acid conservation among a nonredundant set (no two members having higher than 95% amino acid sequence identity) of venom-expressed members of the SicTox gene family by visual inspection of alignments. Conservation levels were also mapped onto the solvent-exposed surface of Loxosceles laeta SMase D (PDB ID 1XX1, chain A) (Murakami et al. 2005) using the Multalign Viewer utility within the program Chimera (Pettersen et al. 2004).
Results and Discussion
We isolated homologs of SMase D from the set of taxa detailed in table 3. Although our sampling is far from exhaustive, we add sufficient phylogenetic inclusion of members for the gene family that includes SMase D to identify distinct phylogenetic groups and to detect frequent duplication events. We also detect variation in patterns of SMase D activity in whole crude venoms that correlates with phylogenetic patterns in our gene tree. Based on these data, we propose an inclusive phylogeny-based nomenclatural system for the gene family. We name the gene family SicTox, abbreviated from Sicariidae toxin, as an acknowledgment of the expression of members of this gene family in venoms of species across the spider family Sicariidae. We start with an overview of our naming system to create a language for reporting our results.
Table 3.
Taxa Screened for Venom-Expressed SMase D Homologs Organized by Species Group
Species | n in mRNA Pool | SMase D Homologs Recovered | Nonredundant Nucleotide Sequences | Nonredundant Amino Acid Sequences |
Loxosceles | ||||
reclusa species group | ||||
Loxosceles arizonica | 2 | 15 | 11 | 11 |
Loxosceles apachea | 8 | 22 | 11 | 10 |
Loxosceles sabina | 4 | 15 | 13 | 11 |
Loxosceles deserta | 1 | 23 | 18 | 16 |
laeta species group | ||||
Loxosceles laeta | 4 | 12 | 9 | 9 |
L sp. nov. Catamarca | 1 | 4 | 2 | 2 |
spadicea species group | ||||
Loxosceles hirsuta | 2 | 45 | 31 | 24 |
Loxosceles spadicea | 2 | 20 | 14 | 8 |
gaucho species group | ||||
Loxosceles variegata | 1 | 14 | 9 | 9 |
amazonica species group | ||||
Loxosceles amazonica | 4 | 9 | 4 | 4 |
rufescens species group | ||||
Loxosceles rufescens | 8 | 10 | 6 | 6 |
spinulosa species group | ||||
L. sp. aff. spinulosa (Munsterland) | 2 | 1 | 1 | 1 |
L. sp aff. spinulosa (Ruacana) | 3 | 4 | 2 | 2 |
Loxosceles spinulosa (Grootfontein) | 4 | 8 | 2 | 2 |
L. spinulosa (Borakolo) | 2 | 17 | 10 | 10 |
Sicarius | ||||
Africa | ||||
S. sp. cf.damarensis (Oorlogsk) | 2 | 27 | 21 | 21 |
Sicarius albospinosus (Gobabeb) | 4 | 3 | 1 | 1 |
South America | ||||
Sicarius terrosus (S. de las Quijades) | 1 | 4 | 2 | 2 |
S. patagonicus | 1 | 8 | 4 | 4 |
Sicarius peruensis (Olmos) | 1 | 26 | 19 | 15 |
Total | 291 | 190 | 168 |
Rationale for Proposed Nomenclature
Our nomenclatural system follows the general guidelines established by the Human Genome Organization (HUGO) gene nomenclatural committee (HGNC) (http://www.genenames.org/). This committee encourages using symbols to distinguish phylogenetically defined stem or root groupings and then using a hierarchical numbering system to distinguish individual members. Rather than create a rigid structure our goal is to establish a general working scaffold within which newly discovered homologs may easily be placed in a hierarchical structure representative of degree of relatedness. This will serve to standardize discussions in the literature and facilitate efficient characterization of structure and function of this gene family by targeting divergent lineages for further analyses. Recent work by Kalapothakis et al. (2007) provides an excellent starting place. The sequences used in their analysis are anchors in our phylogeny that inform hypotheses of the functional evolution within this family. A complete translation of previous published names for toxins in this family to the SicTox nomenclature is in table 1,and a complete list of all known SicTox family members is available in supplemental table 1, Supplementary Material online. We detail the nomenclature and the logic behind it as we describe the structure of diversity of the group.
Isolation and Identification of SMase D Paralogs
We isolated 329 sequences homologous to SMase D, 291 of which were full length. Of those, 190 were nonredundant at the nucleotide level (GenBank Accession numbers FJ17340–FJ17529, detailed in Supplemental table 1, Supplementary Material online), and 168 were nonredundant at the amino acid level. Of the distinct nucleotide sequences, 143 are from 16 species of Loxosceles, and 47 are from 5 species of Sicarius (table 3). Our PCR methods did not amplify any genes from our outgroup taxon, Drymusa serrana. There was a large range in the number of SMase D homologs discovered from within a single mRNA pool. We were particularly successful at amplifying diverse SMase D homologs from Loxosceles hirsuta, Loxosceles apachea, L. arizonica, S sp cf damarensis (Oorlogskloof), and Sicarius peruensis (Olmos) (table 3). The number of distinct paralogs that we isolated from within a single species ranged from 1 to a minimum of 12 (defined by 98% identity) in L. arizonica. Our differential recovery of sequences and paralogs among taxa is not easily explained by numbers of individual spiders whose venom glands were combined in the cDNA pool or by greater success in amplifying cDNAs from species closely related to the source species of the amino acid sequences we used to design degenerate primers (table 3). The primer sphing1f successfully amplified homologs across all taxa, whereas Lpara amplified 12 sequences nonredundant at the nucleotide and amino acid levels (1 in the α clade, L. apachea αIB1b, and 11 in the β clade, all from African Loxosceles in the spinulosa species group).
Phylogenetic Patterns and Delineation of Major Clades
Bayesian analyses resolved two distinct clades that we label α and β, with posterior probabilities of 1.0 and 0.99, respectively (fig. 2). NJ collapses the β clade into two clades, each with low bootstrap support, as an unresolved basal polytomy with the α clade. The average pairwise amino acid distance p-distance between the α and β clades is 0.537. We distinguish major lineages (groups) within the α and β clades by roman numerals (I–VII in α) and (I–III in β) (fig. 2). We delineate groups based on strong posterior probability support of monophyly (fig. 2) and high percent divergences among them (table 4). Some groups either include a large number of sequences structured into well-supported groups (e.g., αI), or include sequences that are highly divergent (e.g., βI & βII). We delineate subgroups within these groups with capital letters (A–C in αI, A–F in βI, and A–B in βII). The number of nonredundant amino acid sequences included in groups and subgroups ranges from 1 (αVI, βIC) to 47 (αIB).
Table 4.
Mean Amino Acid p-Distances within and among Groups and Subgroups of All Sequences in Our Nonredundant Data set (All Terminal Taxa in fig. 2)
αI | αII | αIII | αIV | αV | αVI | |
αI | ||||||
αII | 0.351 | |||||
αIII | 0.421 | 0.489 | ||||
αIV | 0.379 | 0.444 | 0.495 | |||
αV | 0.315 | 0.421 | 0.438 | 0.323 | ||
αVI | 0.418 | 0.475 | 0.520 | 0.433 | 0.325 | |
αVII | 0.370 | 0.435 | 0.492 | 0.406 | 0.335 | 0.413 |
αIA | αIB | |||||
αIA | ||||||
αIB | 0.177 | |||||
αIC | 0.216 | 0.210 | ||||
βIA | βIB | βIC | βID | βIE | ||
βIA | ||||||
βIB | 0.366 | |||||
βIC | 0.379 | 0.384 | ||||
βID | 0.461 | 0.446 | 0.439 | |||
βIE | 0.530 | 0.519 | 0.517 | 0.532 | ||
βIF | 0.470 | 0.461 | 0.477 | 0.503 | 0.496 | |
βI | βII | |||||
βI | ||||||
βII | 0.507 | |||||
βIII | 0.529 | 0.454 | ||||
α Clade | Mean Distance Within | n | ||||
α | 0.261 | 133 | ||||
αI | 0.156 | 98 | ||||
αIA | 0.093 | 36 | ||||
αIB | 0.095 | 48 | ||||
αIC | 0.161 | 14 | ||||
αII | 0.320 | 6 | ||||
αIII | 0.226 | 9 | ||||
αIV | 0.154 | 16 | ||||
αVI | 0.004 | 2 | ||||
β Clade | Mean Distance Within | n | ||||
β | 0.391 | 63 | ||||
βI | 0.434 | 28 | ||||
βIA | 0.129 | 4 | ||||
βIB | 0.106 | 7 | ||||
βIE | 0.317 | 11 | ||||
βIF | 0.314 | 4 | ||||
βII | 0.121 | 32 | ||||
βIIA | 0.047 | 11 | ||||
βIIB | 0.063 | 21 | ||||
βIII | 0.111 | 3 |
Structure within the α Clade
Our methods isolated more sequences in the α clade than the β clade. The α clade consists predominantly of genes from New World Loxosceles and includes published genes whose expression products have been demonstrated to cause dermonecrosis (table 1). Average amino acid differences among groups within the α clade range from 0.31 to 0.52 (table 4). Some subgroups within this clade contain sequences that are predominantly from single species groups. For example, the αIA clade includes genes isolated from South American Loxosceles in the spadicea and gaucho species groups. The only exception is Loxosceles reclusa αIA1 that Bayesian analyses resolve as a basal lineage of the αIA clade. Support for this placement is weak, and both parsimony and NJ resolve with weak support L. reclusa αIA1 as the basal lineage of the αIB clade. The αIB clade exclusively contains genes isolated from members of the reclusa species group. Although we isolated more sequences in the αIA and αIB clades than other clades, the average amino acid divergences within these clades are relatively low (table 4). The αIC clade consists exclusively of members of the gaucho, amazonica, and rufescens species groups. These lineages are well supported to share a close relationship despite the fact that gaucho and amazonica are native to South America and rufescens group members are native to the Old World (Binford et al. 2008, fig. 1).
The αII group contains clear paralogs of sequences in the αI group. Support for monophyly of αII is strong except for the inclusion of LoxTox i5 (SicTox L. intermedia αII2), which NJ resolves as polytomy with αI, the rest of the taxa in αII, and αIII. Conspicuously missing from the αI and αII clades are sequences from the L. laeta species group. This is surprising because species phylogenies tenuously support a closer relationship between members of the laeta and reclusa species groups than either of these lineages share with other American Loxosceles species groups (Binford et al. 2008, fig. 1). However, it is consistent with well-known patterns in the literature of laeta venom characteristics being divergent from those of other New World Loxosceles venoms that have been analyzed (see discussion below, Barbaro et al. 2005; de Roodt et al. 2007).
The rest of the groups in the α clade (IV–VII) contain paralogs of genes in αI–III. Group IV is the only one with more than one sequence. Bayesian analyses strongly support monophyly of group IV, but NJ breaks this clade into two, pulling all of the L. laeta, except L. laeta αIV3, out into a separate monophyletic group. NJ leaves these two groups in a basal polytomy within the α clade that includes the monophyetic clade of groups I–III and groups V, VI, and VII.
Structure within the β Clade
The β clade predominantly consists of Sicarius and African Loxosceles in the spinulosa species group within which clear paralogs are evident. This clade also includes a monophyletic group of published sequences from New World Loxosceles in the βIA clade (L. laeta H10, Loxosceles boneti P3, Loxosceles intermedia LiDT3, L. laeta βIA1, L. boneti βIA1, and L. intermedia βIA1 with our SicTox nomenclature, respectively), some of which have been demonstrated to have reduced or no SMase D or dermonecrotic activity (table 1 and references therein). Amino acid differences among groups are generally high, ranging from 0.37 to 0.52 (table 4). The only other New World sequence that falls in the β clade is LiDT5 (L. intermedia βID1). Bayesian and NJ analyses agree on inclusion of genes within the defined groups, but NJ weakly resolves a sister–taxon relationship between βII and βIII and collapses βID into a polytomy with a monophyletic group of βIA–C and a monophyletic group of βIE–F.
Duplication History in SicTox Gene Family
Although the SicTox gene tree has some clustering of sequences into clades consistent with species groups, duplications complicate this relationship. Recent duplications are most apparent in groups of closely related species for which we have extensive recovery of gene copies. This is particularly true for αIA and αIB members of the spadicea and reclusa groups, respectively. Our sampling includes the only three described species in the spadicea group, and there is solid support of spadicea and hirsuta being each other's closest relatives with intermedia sister to that pair (fig. 1). Within the αIA clade, there have been at least three duplication events since the MRCA of the spadecia group (fig. 2). Estimates of the age of the MRCA of the spadecia group range between 48 and 34 Ma (unpublished, methods as in Binford et al. 2008), meaning the minimally two duplications between the MRCA and hirsuta occurred within this time frame. The αIB clade includes only members of the North American reclusa group. Patterns of relationships among terminal paralog groups within αIB mirror species relationships in the reclusa group (fig. 1) and contain clear duplication events (fig. 2). An example is in the phylogenetic grade that includes L arizonica αIB2a, αIB2b, and αIB2c.
Panning out to a broad description of the history of duplications and losses in this lineage, reconciliation analyses (Notung) of a species tree (subset of fig. 1) with an SMase D gene tree (NJ) that includes all unique amino acid sequences (all taxa in fig. 1 except Ixodes) estimated 110 duplications and 84 losses (D/L score = 249.0). This likely overestimates duplications because of the inclusion of allelic variants in monophyletic terminal intraspecific groups. Repeating the analysis including only terminal paralogs defined by minimum amino acid divergence thresholds of 2% (105 sequences) and 5% (75 sequences) estimated 44 duplication events and 71 losses (D/L score = 137.0), and 30 duplications and 74 losses (D/L score = 119.0), respectively. The 5% threshold resulted in monophyletic, terminal intraspecific sets of sequences being reduced to single representatives and therefore eliminates the possibility of allelic variants but also will exclude very recent duplications.
It has been hypothesized that gene families encoding spider venom toxins are evolving via mechanisms similar to those driving Conus toxin diversification in which there is rapid duplication followed by adaptive divergence (Sollod et al. 2005; Escoubas 2006). In spiders, rapid duplication rates in toxin gene families are assumed based on large numbers of paralogs expressed in venoms (King et al. 2002; Sollod et al. 2005; Escoubas 2006; Jiang et al. 2008). Little work in any toxin lineage has attempted to quantify duplication rates, and reasonably so, given a long list of limitations including 1) lack of comprehensive knowledge of gene family size that would require a sequenced genome; 2) the complicating influences of concerted evolution and the evolution of expression patterns (Duda and Remigio 2008); and 3) few analyses with dense taxon sampling of genes among closely related species of known relationships and with known divergence times. Of these, our work only overcomes the limitation of having a species tree and broad SicTox gene sampling. Thus, although preliminary, estimates from reconciliation serve as a starting point for discussion of general patterns of duplication rates in venom evolution.
To translate our reconciliation results to inferred duplication rates, if duplications were evenly distributed across the 25 taxa in our analysis, the average species would have undergone 1.2 (5% threshold) to 4.4 (all data included) duplications in the evolutionary time frame encompassed. This assumption is unlikely to be true given the wide range of paralog numbers we recovered across taxa. Thus, these estimates are conservative. Molecular dating analyses and biogeographic patterns support the MRCA of Sicariidae predating the separation of South America and Africa meaning a conservative estimate of minimum age of the MRCA is 95 Ma and a maximum estimate is 157 Ma (Binford et al. 2008). This translates to 0.0126–0.0463 duplications per million years for the minimum age of sicariids and 0.0076–0.0280 duplications per million years for the maximum age.
These estimates of duplication rates are within ranges of estimates under the best of circumstances using comparisons of whole sequenced genomes, but minimizing the confounding influence of gene conversion by constraining analyses to include only pairs of duplicate genes. These include 0.028, 0.0014, and 0.024 duplications per million years in yeast, Drosophila and Caenorhabditis elegans, respectively (Gu et al. 2002 assuming a molecular clock), 0.01–0.06 duplications per billion years in yeast (not assuming molecular clock, Gao and Innan 2004), and 0.009 duplications per million years in humans (Lynch and Conery 2003). We can estimate duplication rates from a venom toxin in the four-loop conotoxin lineage. At least seven duplications have occurred since the divergence of Conus abbreviatus and Conus lividus (Duda and Palumbi 1999) whose MRCA is estimated to have lived approximately 27 Ma (Duda and Kohn 2005), which results in an average duplication rate of 0.269 duplications per million years. Within the spadecia group described above, estimated duplication rates of SicTox would be between 0.041 and 0.071 per million years, which is faster than any of our estimates from reconciliation and faster than rigorous estimates from model systems but slower than the estimates for Conus four-loop toxins.
A final notable pattern is that single species (L. intermedia, L. boneti, and L. laeta) have SicTox paralogs in both the α and β clades. These are descendents of a duplication event that must predate the MRCA of Sicariidae and thus the putative origin of SMase D as a venom toxin in sicariids (Binford and Wells 2003).
Evidence of Purifying Selection, Episodic Positive Directional Selection and Positively Selected Sites
LRTs indicate significant improvements in log likelihood values under the free-ratios model relative to the fixed ratios model for both the α and the β clades (table 5). They also support significant deviation of ω from 1. Estimated ω values under the fixed model (constrained to a single value across the lineage) were considerably less than 1 (0.250 and 0.193 for the α and β clades, respectively), consistent with predominantly purifying selection in the lineage. Reconstructed estimates of ω along branches under the free-ratios model are generally less than 1; however, scattered branches within both the α and the β clades have ω values greater than 1 (fig. 2). The significantly better fit of the free-ratios model and branches with ω > 1 is consistent with a pattern of episodic positive selection acting in this lineage. Branches with estimated ω > 1 are particularly concentrated in the αIB and the βIA and B clades.
Table 5.
Summary Statistics for Branch and Site Analyses
Parameters | Estimates | −ln L | χ2 | df |
P |
|||||||||||
Branch models | ||||||||||||||||
α | ω fix at 1 | 18,339.0 | ||||||||||||||
M0 (one ratio) | ω | 0.250 | 17,657.9 | |||||||||||||
M1 (free ratios) | ω | Varies | 17,512.2 | 291.4 | 1 | <0.0001 | ||||||||||
β | ω fix at 1 | 14,369.0 | ||||||||||||||
M0 (one ratio) | ω | 0.193 | 13,685.6 | |||||||||||||
M1 (free ratios) | ω | Varies | 13,607.9 | 155.4 | 1 | <0.0001 | ||||||||||
Site Models | Proportions | |||||||||||||||
α | M0 | ω | 0.258 | 16,920.0 | ||||||||||||
M1a (nearly neutral) | ω0 | 0.739 | 0.163 | 16,544.9 | ||||||||||||
ω1 | 0.261 | 1.000 | ||||||||||||||
M2a (positive selection) | ω0 | 0.727 | 0.165 | 16,538.7 | 12.2 | 2 | <0.005 | |||||||||
ω1 | 0.256 | 1.000 | ||||||||||||||
ω2 | 0.018 | 2.091 | ||||||||||||||
M7 (beta) | p | 0.576 | 16,364.8 | |||||||||||||
q | 1.351 | |||||||||||||||
M8 (beta & ω) | p0 | 0.949 | 0.730 | 16,348.3 | 33.0 | 2 | <0.001 | |||||||||
p | ||||||||||||||||
q | 2.284 | |||||||||||||||
ωs > 1 | 0.051 | 1.344 | ||||||||||||||
β | M0 | ω | 0.199 | 12,642.0 | ||||||||||||
M1a (nearly neutral) | ω0 | 0.793 | 0.158 | 12,452.0 | ||||||||||||
ω1 | 0.206 | 1.000 | ||||||||||||||
M2a (positive selection) | ω0 | 0.793 | 0.158 | 12,452.0 | 0.0 | 2 | ns | |||||||||
ω1 | 0.044 | 1.000 | ||||||||||||||
ω2 | 0.162 | 1.000 | ||||||||||||||
M7 (beta) | p | 0.672 | 12,280.2 | |||||||||||||
q | 2.188 | |||||||||||||||
M8 (beta & ω) | p0 | 0.969 | 12,278.9 | 2.6 | 2 | ns | ||||||||||
p | 0.743 | |||||||||||||||
q | 2.752 | |||||||||||||||
ωs > 1 | 0.031 | 1.000 | ||||||||||||||
Positively selected amino acid residues based on BEB (Yang et al. 2005) (P >0.95 in bold). | ||||||||||||||||
α | M2a | 18 | 151 | 204 | 208 | |||||||||||
M8 | 18 | 39 | 40 | 56 | 58 | 115 | 151 | 176 | 204 | 208 | 215 | 236 | 268 | |||
β | M8 | 39 | 60 | 259 |
Site model analyses support significant improvement of log likelihood values in the α clade under the M2a and M8 models relative to their nested models. In this clade, 1.8% and 5.1% of amino acids are identified as evolving under positive selection by M2a and M8 models, respectively (table 5). Thirteen amino acids were identified by Bayes Empirical Bayes (BEB) analyses (Yang et al. 2005) (table 5) as candidates for positively selected sites, three with posterior probabilities > 0.95 (18, 151, and 204, numbering according to PDB 1xx1 L laeta H17, αIII1i). Some of the weakly supported amino acids are near active sites in the protein; however, they all appear to be solvent-exposed positions that are neither in the active site nor in the plug region. We are investigating possible functional roles for these residues.
Analyses of the β clade did not detect significant improvement in models that support amino acids that are under positive selection across the lineage (table 5). However, BEB analyses under the M8 model identified three sites, 39, 60, and 259 as candidates for evolving under positive selection in this clade but with low posterior probabilities (ranging from 0.55 to 0.63) (table 5). Like the residues in the α clade, these are all solvent exposed, and their functional relevance is unclear. As we fill in our data set with more thorough taxon sampling and more resolution in functional diversity, we will pursue branch-site analyses that may be more sensitive at detecting amino acids that are under selection in particular lineages.
Major Species Lineages Vary in SMase D-Sized Proteins in Venoms and in SMase D Activity
Qualitative comparative protein composition data and quantitative SMase D enzyme activity data allow a preliminarily view of how differences in expression of SicTox gene family members may influence differences in excreted venoms. They also add to a growing body of comparative data of whole crude venoms (table 1 and references therein).
Expressed proteins from members of this gene family are between 31 and 35 kDa (see table 1 references). Using comparative SDS-PAGE, we detected proteins in this size range from all Loxosceles and Sicarius but not in either African or Argentine Drymusa (fig. 3b). Variation among taxa that have proteins in this size region correlates to some degree with species relatedness and patterns of relationships of SicTox gene family members. Among venoms from North America, L. reclusa has a concentrated region of proteins around 32 kDa, whereas other reclusa species group members from the desert southwest of the United States (L. arizonica, L. apachea, Loxosceles sabina, and Loxosceles deserta), have a broader range of proteins in that region (∼31–34 kDa) (fig. 3a). Banding patterns of L. laeta are strikingly different from all other New World venoms with the most dense banding at 31 kDa and a reduction in proteins larger than that (fig. 3a and c). The differences in banding between L. intermedia and L. hirsuta are notable given the putative close relationship between these species (fig. 3a). Banding patterns for the African species Loxosceles vonwredei are more similar to New World species than they are to the African spinulosa group (fig. 3a), which is consistent with patterns of species relationships (Binford et al. 2008, fig. 1). Venoms from the African spinulosa clade (from which we have only isolated SicTox genes in the β clade) tend to have higher molecular weight proteins than other Loxosceles venoms. Venom profiles from Sicarius, again with isolated SicTox genes only from the β clade, have notable differences between New World and Old World species (fig. 3b and c). Venoms from African Sicarius have a higher concentration of larger molecular weight proteins, comparable with the African Loxosceles venoms, whereas the South American Sicarius have a region of dense proteins at ∼31 kDa. This apparent size variation could be influenced by posttranslational modification (glycosylation), but it likely also reflects differences in the expressed SicTox genes. Disentangling these relative influences on protein variation will require paralog-specific expressions and Westerns, and a better understanding of posttranslational modifications.
FIG. 3.—
One-dimensional gel electrophoresis separations of 5 μg crude venoms from species of (a) Loxosceles; (b) Sicarius and Drymusa. Gels (12.5% acrylamide) were stained with silver nitrate; (c) repeated separations of crude venoms from select species loaded with 3, 5, and 7 μg of total protein to illustrate the effect of uneven loading of total venom protein on visibility of bands. The region of origin of species is indicated. *Loxosceles rufescens is native to the Mediterranean.
We assayed crude venoms from 36 taxa for SMase D activity (table 2). Sicarius species from Africa, all Loxosceles from the Americas, and Loxosceles rufescens have high SMase D activity using 0.5 or 1.0 μg of crude venom, whereas activity from venoms from African Loxosceles is generally lower (fig. 4a), and there is no activity in Drymusa venom. All of these patterns are consistent with previous work (Binford and Wells 2003). However, we detected little or no activity at these concentrations in venoms from South and Central American Sicarius (fig. 4a). When we repeated the experiment for South American Sicarius with concentrations of crude venom that were increased by two orders of magnitude (50 μg) enzyme activity increased but was never as high as in North American Loxosceles or South African Sicarius assayed at the original low concentrations (fig. 4b). The increase in SMase D activity with increasing amounts of venom from Argentine Sicarius terrosus (Quijades) and Sicarius patagonicus may reflect differences in substrate specificity of expressed SicTox members that results in a reduced binding efficacy for sphingomyelin. The fact that African Sicarius have strong SMase D signals and homologs for these species have only been recovered from the β clade suggests that at least some proteins in the β clade have strong efficacy for hydrolyzing sphingomyelin.
FIG. 4.—
Fluorescence intensity (proportional to SMase D activity) resulting from assays of crude venom: (a) fluorescence measured from reactions that contained 0.5 or 1.0 μg of crude venom; (b) fluorescence from reactions that contained 10 or 50 μg of venom with and without sphingomyelin (SM) as the substrate. Some samples were not analyzed under all conditions because of low venom availability. Buffer was substituted for venom in blank samples. The region of origin is indicated. *Loxosceles rufescens is native to the Mediterranean.
A growing body of work is indicating that defining the activities of venom-expressed members of this gene family as SMase D is inappropriately narrow, and there is variation in substrate specificity among homologs (Tambourgi et al. 1998; Lee and Lynch 2005; Murakami et al. 2005, da Silveira et al. 2006). Thus, our SMase D assay is a narrow assessment of the important biological activity in these venoms. Nonetheless, these assays may help identify patterns of variation in crude venom function that can focus further work to identify features of the molecules that are associated with the evolution of functional specificity. One pattern that emerges from the integration of comparative analyses of crude venoms, the gene family analysis, and published characterizations of expression products of SicTox genes is evidence of evolution of functional specificity in members of the SicTox β clade. For identifying specific changes in the molecule responsible for functional evolution, it may be particularly fruitful to investigate functional differences among paralogs from Sicarius. Given the striking difference in SMase D activity between African and American Sicarius, it is somewhat surprising that for every paralog we recovered from African Sicarius, we found orthologs in American Sicarius. In fact, our methods recovered one paralog in American Sicarius (the βIB lineage) for which we did not find a candidate ortholog in African Sicarius. Given the support for the sister–taxon relationship with βIA, and the reduced/low SMase D activity in American Sicarius, S. peruensis and S. terrosus βIB genes are good candidates of genes that have a function other than SMase D. Moreover, high levels of SMase D activity in African Sicarius suggest that, unless our method has missed capturing mRNAs of expressed α clade genes in these species, one of the other β clade paralogs must be SMase D active.
Patterns of Sequence and Structural Conservation
The structure solved for SicTox gene family member L. laeta αIII1 (H17) (Murakami et al. 2005) allows us to analyze sequence conservation in the context of structural position and proposed active sites (fig. 5). The most conserved solvent-exposed residues are at the two openings of the barrel, either in the vicinity of the active site at the top of the barrel, or in and around a previously described “plug motif” (Cordes and Binford 2006) that caps the bottom. In the active site, all residues proposed by Murakami et al. (2005, 2006) to be directly involved in phosphate or Mg2+ binding (His 12, Glu 32, Asp 34, His 47, Asp 91, Lys 93, and Trp 230; fig.5b in green) are >98% conserved across all homologs. An additional set of surface residues near the putative phosphate binding site (Pro 50, Cys 51, Asp 52, and Asn 252; fig. 5b in orange) also shows >98% conservation. Two of these (Asp 52 and Asn 252) are directly hydrogen bonded to His 12. Met 250 and Tyr 228 (fig. 5b in yellow), which line a deep cleft beneath the phosphate site, are also >98% conserved. Many of the residues listed above have been proposed to play some significant role in chemical catalysis; the remainder could be important for general aspects of substrate binding. The role of residues in the plug motif remains unknown, but their conservation across all SicTox homologs as well as in Ixodes and Corynebacterium relatives (Cordes and Binford 2006) suggests some vital role either in function or maintenance of structural integrity and stability.
FIG. 5.—
(a) Sequence conservation levels mapped onto the surface of Loxosceles laeta SMaseI (PDB ID 1XX1; chain A) for all spider sequences (left), the α clade (middle) and the β clade (right), for the top of the barrel containing the active site (top) and the bottom containing the conserved plug motif (bottom). Surface residues showing 60% conservation or less are shown in blue, whereas those showing 100% are shown in red. Intermediate levels of conservation show a range of color from blue to red, with 80% conservation appearing as white. Note that the levels of conservation observed in the α clade are higher than for the β clade. (b) Surface residues in and around the active site cleft showing >98% conservation (green, orange, and yellow groups) or clade-specific conservation (distal pocket residues in salmon). (c) Clade-specific sequence conservation patterns in the distal binding pocket. The residues shown for the α clade are >95% conserved within this group. Residue types in other clades that differ from the conserved residues in the α clade are underlined.
The distal side of the active site pocket (to the right of the Mg2+ and sulfate ions in fig 5a) contains a deep cleft whose role in substrate binding and/or catalysis is unclear at this point. Murakami et al. (2006) proposed that certain residues in this area, such as Pro 134, might contribute to substrate specificity. Interestingly, there is a contiguous set of residues in this cleft that shows >95% conservation within the α clade (Val 89, Ser 132, Pro 134, Asp 164, Ser 166, and Ser 195; see fig. 5b in salmon and fig. 5c), but subclade-specific sequence variation within the β clade. We hypothesize that these residues are involved in specific aspects of substrate binding, and consequently, we predict that members of the α clade will show relatively conserved substrate specificity profiles; by contrast, variation in these residues within the β clade may lead to more variable substrate specificity profiles among this group. It must be noted, however, that most of these residues also differ between the α clade and homologs in Corynebacterium (fig. 5c) even though both proteins are known to hydrolyze sphingomyelin substrates.
Summary of Inferred Evolutionary Mechanisms Influencing SicTox
Together our data indicate that evolutionary dynamics of the SicTox gene family are similar in some aspects and different in others from the emerging picture of evolutionary dynamics of other venom toxin lineages. Frequent duplications are consistent with a birth-and-death model of evolution (review in Nei and Rooney 2005) that has been described for other venom toxin families (e.g., Duda and Palumbi 1999; Espiritu et al. 2001; Fry et al. 2003; Lynch 2007); however, our estimates of SicTox duplications are lower than estimates for small peptide neurotoxins in Conus venoms. Once duplications occur, our data are consistent with purifying selection in the SicTox lineage with episodic directional selection. However, our data do not support the same level of high dN/dS values documented for other toxin lineages (e.g., Duda and Palumbi 1999; Kini and Chan 1999; Lynch 2007). In fact, recent estimates of average ω of 1.28 for the toxic enzyme PLA2s from snake venoms (Lynch 2007) are an order of magnitude higher than our estimates (table 5). The general pattern of SicTox genes having possibly lower duplication rates and lower levels of diversifying selection than other venom toxins is provocative with respect to understanding general principles that influence venom evolution. These patterns invite the consideration that some of the evolution of copy number may be best described under a model of genomic drift (Nogawa et al. 2007) in which the absolute number of paralogs is of little adaptive consequence. The little we know about the genome structure of SicTox is consistent with the genes lying in a region of high recombination within the genome. The coding region of SicTox genes in L. arizonica is compartmentalized into five exons, some of which are separated by large introns (Binford et al. 2005). Moreover, we have evidence that intron–exon boundaries are not conserved among paralogs (Binford GJ, unpublished data).
One limitation for understanding SicTox evolution is a lack of understanding of the functional role of these toxins in the complex dynamics of immobilization and/or digestion of arthropod prey. Recent expressed sequence tag analyses indicate that SicTox homologs are the most abundant transcripts in venoms of L. laeta (Fernandes-Pedrosa et al. 2008), consistent with an important functional role. Although a cytotoxic role is apparent, recent work indicates that SMase D and other phospholipase D can inhibit ion channels because of an interaction between the channel and the head groups of membrane phospholipids (Ramu et al. 2007; Xu et al. 2008). Thus, SicTox proteins may also have a neurotoxic effect on prey. As we gain insight into divergence in sequence, structure, and function more focused analyses of particular lineages and regions of the protein that have undergone directional selection will help clarify evolutionary dynamics in this lineage.
Relevance for Understanding Risks of Bites and Development of Treatments
Although the functional role of SicTox genes in prey capture remains unclear, the central role of SMase D activity in the pathology of human envenomation is well documented. The phylogenetic structure and diversity and insight into evolutionary dynamics of SicTox gene family members provides a framework for understanding the distribution of risks associated with bites from spiders in the sicariid lineage and for strategies of developing broadly effective treatments for bites.
The distribution of risks associated with bites of diverse species should be a function of the distribution of toxins in the venom of these species. The diverse set of SicTox homologs makes this pattern complex. It is clear that some SicTox gene family members are sufficient causative agents for causing dermonecrosis (table 1 and references therein), but there is much to learn about the role of the non-SMase D active members in the clinical syndrome of human envenomation. In particular, there is little understanding of the contribution of genes in the β clade. Bites from species of African Loxosceles from the spinulosa group and African Sicarius cause dermonecrotic lesions, and Sicarius envenomation can be particularly damaging (Newlands and Atkinson 1988; Van Aswegen et al. 1997). From both of these lineages, we only recovered genes in the β clade. There are no published records of the effects of bites from New World Sicarius; however, injection assays of venom into mice have yielded no lesions (Alegre et al. 1977). Comparative bioassays of crude venoms and expression products using well-established rabbit models will provide better estimates of whether or not reduced SMase D activity in South American Sicarius venoms correlates with potential risk of bites. Results of these analyses will be particularly informative about whether or not SMase D activity is necessary for causing dermonecrosis, and the contribution of other SicTox gene functions to the necrotic syndrome.
Much work has focused on patterns of antigenic cross-reactivity in venoms within Loxosceles with the goal of developing antibody-based treatments of bites (Barbaro et al. 1996, 2005; Gomez et al. 2001; Ramos-Cerrillo et al. 2004: Olvera et al. 2006; de Roodt et al. 2007). To date, these analyses have been restricted to a subset of New World Loxosceles. The data presented here may help direct future work to produce treatments that are broadly, perhaps even globally, effective for treating sicariid envenomations. One important example is the phylogenetic placement of the L. rufescens SicTox genes. Loxosceles rufescens is the most cosmopolitan of all Loxosceles species. They are native to Mediterranean Europe and have recently dispersed to all major continents. The placement of L. rufescens SicTox genes in the α clade make it reasonable to predict that antivenoms developed for North and South American Loxosceles (Barbaro et al. 2005; Olvera et al. 2006) may be effective for treating L. rufescens bites. This work may also help with the possibility of designing a treatment that is effective for bites of African Loxosceles spinulosa group members and Sicarius bites. The apparent lack of α clade genes in venoms of African spinulosa and Sicarius suggests that a divergent set of genes beyond those that have been well characterized (table 1) is responsible for the clinical effects of bites of these species. For any treatment to be globally effective, antibodies raised against a diverse set of β clade genes will likely also be necessary.
Conclusion
The SicTox gene family is large and diverse and has undergone frequent duplications and occasional functional evolution since co-option for venomous function in the sicariid lineage. Patterns of relationships within the gene family reflect species relationships to some degree, but this is complicated by frequent duplications and likely occasional losses. We hope the framework of diversity presented here, and our nomenclature for discussing it, serve as a scaffold for more detailed analyses of mechanisms of evolution within this gene family, and for guiding particularly informative targeted analyses that will increase understanding of clinical risks associated with particular species and development of treatments for bites.
Supplementary Material
Supplemental table 1 is available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).
Supplementary Material
[Supplementary Data]
Acknowledgments
For help with collecting specimens, we thank Andrew Merrell, Marjorie G. Weber, Williams Paredes, Lizette Tejada, Alfonzo Zavaleta (Peru); Facundo Labarque, Christopher Ellison, Jeremy Miller, Cristian Grismado (Argentina); Melissa Callahan, Pablo Berea Nunez, and Hartmut Kolb (Namibia); and Astri and John Leroy, Norman Larson, Wessel Pretorius, Rupert Harris, Gita Bodner (South Africa). We particularly thank Martín Ramírez and Christina Scioscia (Argentina); Tharina Bird, Helen Kolb, Joh Heschel, Leon Lotz (Namibia); Ansie Dippenaar-Schoeman, Leon Lotz (South Africa); and Gerardo Llamas and Williams Paredes (Peru) for help with obtaining collecting and export permits and with locality information. We thank Rebecca Duncan for help in the laboratory and Binford lab members, Greg Hermann and Michael Nachman, for helpful discussion and 3 anonymous reviewers for comments that improved the manuscript. Funding from Murdock Charitable Trust Life Sciences (G.J.B.), Murdock Partners in Science (S.B., G.J.B.), and NSF CAREER award IOB-0546858 (G.J.B.) supported research expenses and travel. Further support of travel was from the Student Academic Affairs Board at Lewis & Clark College (M.B., M.R.), Rogers Research Program at Lewis & Clark College (M.B., M.R.), and Instituto Bioclon S.A. de C.V. Molecular graphics images were produced using the UCSF Chimera package from the Computer Graphics Laboratory, University of California, San Francisco (supported by NIH P41 RR-01081).
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