Ice-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival at sub-zero temperatures. Intertidal invertebrates in temperate and polar regions frequently encounter sub-zero temperatures, yet there is little information on IBPs in these organisms. We hypothesized that there are far more IBPs than are currently known and that the occurrence of freezing in the intertidal zone selects for these proteins. We compiled a list of genome-sequenced invertebrates across multiple habitats and a list of known IBP sequences and used BLAST to identify a wide array of putative IBPs in those invertebrates. We found that the probability of an invertebrate species having an IBP was significantly greater in intertidal species than in those primarily found in open ocean or freshwater habitats. These intertidal IBPs had high sequence similarity to fish and tick antifreeze glycoproteins and fish type II antifreeze proteins. Previously established classifiers based on machine learning techniques further predicted ice-binding activity in the majority of our newly identified putative IBPs. We investigated the potential evolutionary origin of one putative IBP from the hard-shelled mussel Mytilus coruscus and suggest that it arose through gene duplication and neofunctionalization. We show that IBPs likely readily evolve in response to freezing risk and that there is an array of uncharacterized IBPs, and highlight the need for broader laboratory-based surveys of the diversity of ice-binding activity across diverse taxonomic and ecological groups.
For organisms to inhabit temperate and polar regions, low-temperature tolerance is a key trait (Sanmartín et al., 2001; Wiens and Donoghue, 2004). This is especially true for ectotherms that risk freezing of their body fluids and therefore have evolved strategies to survive otherwise lethal sub-zero body temperatures (Lee, 2010). While the physiology and biochemistry of low-temperature tolerance is diverse, one common biochemical mechanism present in a broad array of organisms ranging from bacteria to fish is the use of ice-binding proteins (IBPs; Davies, 2014; Bar Dolev et al., 2016). Initially described as ‘antifreeze proteins’, the IBP name now encompasses the understanding that IBPs have a wide variety of functions, including serving as an antifreeze (Davies, 2014; Bar Dolev et al., 2016).
As the name suggests, IBPs are proteins that can bind to ice (Davies, 2014; Bar Dolev et al., 2016). How these proteins bind to ice has been well addressed and is reviewed by Bar-Dolev et al. (2020) and Budke and Koop (2020). Regardless of the mechanisms of ice binding, these proteins promote survival at sub-zero temperatures through three primary means. First, ice binding can prevent further ice formation by effectively suppressing the freezing point relative to the melting point, resulting in thermal hysteresis (Davies, 2014; Bar Dolev et al., 2016). Thermal hysteresis is the first described IBP activity, discovered in Antarctic fish (DeVries and Wohlschlag, 1969). Thermal hysteresis is advantageous for freeze-avoidant organisms but can also be advantageous for freeze-tolerant organisms that want to prevent ice formation in particularly sensitive tissues or intracellular space (Davies, 2014; Bar Dolev et al., 2016). Second, ice binding can also prevent changes in the size of ice crystals through ice recrystallization inhibition (IRI; Knight et al., 1984; Davies, 2014; Bar Dolev et al., 2016). Ice recrystallization is the thermodynamically driven process whereby many small ice crystals present in early ice matrices become incorporated into each other to form fewer but larger ice crystals (Pronk et al., 2005; Balcerzak et al., 2014). This growth of ice crystals in the body can damage cells and tissues; thus, the IRI activity of IBPs is important for surviving internal ice formation (Knight and Duman, 1986; Davies, 2014; Bar Dolev et al., 2016). Third, IBPs can nucleate ice, promoting the formation of ice in the body (Davies, 2014; Bar Dolev et al., 2016). Ice nucleation activity can allow organisms to control when and where ice forms in the body, preventing uncontrolled ice formation in the body which could increase the risk of lethal freezing injury (Zachariassen and Hammel, 1976; Davies, 2014; Bar Dolev et al., 2016).
The variety of ways IBPs influence ice formation is mirrored by the diversity of organisms that utilize them, with examples of IBPs found throughout the tree of life (Bar Dolev et al., 2016). For example, IBPs with ice nucleation activity have been described in bacteria (Xu et al., 1998; Ling et al., 2018), with thermal hysteresis activity in fish (Fletcher et al., 2001) and with IRI activity in plants (John et al., 2009; reviewed in Bar Dolev et al., 2016). In fact, this list is ever-expanding, and novel IBPs are frequently discovered (Scholl et al., 2021). IBPs have evolved independently in multiple taxonomic groups, resulting in distinct groups of IBPs from beetles (Coleoptera) and moths (Lepidoptera) and have even evolved independently multiple times within a single taxon, including three unique IBP lineages in rye grasses and five lineages in teleost fishes (Bildanova et al., 2012). This structural diversity coincides with an array of evolutionary pathways that can produce IBPs (Bildanova et al., 2012). In teleosts alone there are examples of IBPs evolving de novo (Zhuang et al., 2019), through horizontal gene transfer (Graham et al., 2008) and through neofunctionalization (Deng et al., 2010). There are multiple progenitor proteins that have evolved into IBPs including C-type lectins for type II antifreeze proteins (AFPs) of fish (Gronwald et al., 1998), trypsinogen-like proteases for fish antifreeze glycoproteins (AFGPs; Chen et al., 1997), and multiple others (summarized in Bildanova et al., 2012). This combined diversity of functions, structures, evolutionary origins and organisms of origin for IBPs points to a relative ease of evolving an IBP for surviving temperate and polar habitats.
Despite this ready evolution of IBPs across the tree of life, there is a vast polyphyletic group that is thus far largely devoid of suspected IBPs: intertidal invertebrates (Storey and Storey, 2013). This is surprising as intertidal invertebrates in temperate regions experience freezing temperatures in the winter during low tide, and many species, especially the slow-moving and sessile ones, are freeze tolerant (Aarset, 1982). While it is possible for an organism to tolerate freezing without the use of IBPs, other known molecular strategies of freeze tolerance such as accumulating polyols and sugars are not believed to be possible for intertidal invertebrates as they are osmoconformers (Aarset, 1982; Storey and Storey, 1988, 2013; Duman et al., 1991; Ansart and Vernon, 2003). While osmolyte accumulation is an important correlate to freeze tolerance in the bay mussel (Mytilus trossulus), an intertidal species, it does not fully explain its freeze tolerance (Kennedy et al., 2020). This suggests high molecular weight cryoprotectants such as IBPs may play a role in their freeze tolerance (Kennedy et al., 2020). In addition to this, there is evidence for IBPs in both blue mussels (Mytilus edulis) and barnacles (Semibalanus balanoides; Theede et al., 1976; Marshall et al., 2018 preprint), and a partially characterized IBP with ice-nucleating activity found in an intertidal air-breathing snail (Madison et al., 1991). This, combined with the current scarcity of research on freeze tolerance in intertidal invertebrates, suggests that there is an array of IBPs waiting to be discovered in the intertidal zone (Storey and Storey, 2013), especially given the stressful habitat they reside in and the relative ease of evolving IBPs.
We hypothesized that IBPs are widespread and unreported in intertidal invertebrates, and that the intertidal habitat has selected for the evolution of IBPs. Given the examples of highly similar IBPs being acquired both convergently (Zhuang et al., 2019) and through horizontal gene transfer (Graham et al., 2008), we predicted that a BLAST search using sequenced and laboratory-characterized IBPs would return strong matches in the molecular sequence data of intertidal invertebrates. Expanding on this, we predicted that IBP matches would be biased towards species that occur in the intertidal zone relative to species in the same phylum found in different habitats. It should be noted that intertidal invertebrates may have novel IBPs, limiting our search potential in this study. As a result of these investigations, we systematically demonstrate that putative IBPs are broadly distributed through invertebrate taxa, that they were identified through sequence homology to fish type II AFPs, fish and tick AFGPs, and coleopteran AFPs, and that intertidal species are more likely to contain these putative IBPs than their non-intertidal conphyletics. Taken together, this suggests that IBPs readily evolve along the same evolutionary trajectory in response to low-temperature stress.
MATERIALS AND METHODS
To investigate the presence of putative IBPs in intertidal invertebrates, we first compiled a query list of known IBPs. Query list IBPs met two criteria: first, the IBP had to have amino acid sequence information available with an NCBI accession number; second, the IBP had to have literature documentation of ice-binding activity (Table S1).
Following the creation of this IBP query list, we produced a list of organisms to search for putative novel IBPs. We selected the following phyla of common intertidal invertebrates: Mollusca, Crustacea (subphylum of Arthropoda), Echinodermata, Annelida and Cnidaria. We opted only for the subphylum Crustacea as the vast majority of genome-sequenced arthropods are terrestrial. We then compiled a list of all species within these (sub)phyla that had a sequenced genome available at NCBI (https://www.ncbi.nlm.nih.gov/), and classified the habitat type of each search organism into ‘terrestrial’, ‘endoparasitic’, ‘intertidal’, ‘subtidal’, ‘estuarine’ or ‘other marine’ based on listings on SeaLifeBase (https://www.sealifebase.ca/), WoRMS (https://www.marinespecies.org/), and direct citations (Table 1; Table S2). In this study, ‘subtidal’ refers only to the shallow subtidal (≤1 m; Saier, 2002) while ‘other marine’ is a blanket term used in this study for all ocean habitats that do not fit within the intertidal, shallow subtidal or estuarine habitat types. For species found in a wide range of ocean habitats, their shallowest habitat type was used for categorization in this study (e.g. a species found in both the subtidal and intertidal would be designated intertidal for this study).
Search for putative IBPs
As there are no common ice-binding domains across all IBP types (Davies, 2014; Bar Dolev et al., 2016), we used the protein BLAST algorithm to identify any sequence homology between the query IBP list and the organism search list (Altschul et al., 1990). A protein BLAST (blastp) search was performed on the non-redundant protein sequence database filtered only to include the species in our organism search list. We set the Expect threshold to an E-value of 1×10−5 with a word size of six amino acids and enabling automatic adjustments for short query sequences. We used the standard BLOSUM62 matrix with conditional compositional score matrix adjustment method, gap existence cost of 11, and extension set to 1 to determine alignment scores (Henikoff and Henikoff, 1992). We binarily categorized each organism in the search list based on whether they contained an IBP hit conforming to the 1×10−5 Expect threshold from this search for later comparison of IBP presence among habitats and phyla.
To visualize potential phylogenetic patterns in IBP hits, we produced an unrooted phylogeny from the IBP query sequences. Query sequences were aligned in MEGA (Kumar et al., 2018) using the MUSCLE algorithm (Edgar, 2004). A maximum likelihood tree was produced from the aligned sequences using the WAG+G+F model (Whelan and Goldman, 2001). Our model selection for this and all future phylogenies in this study was determined by calculating maximum-likelihood fits in MEGA (Kumar et al., 2018) for 56 different amino acid substitution models, then selecting the model with the lowest Bayesian information criterion. We then mapped search organisms containing BLAST matches with high homology to query list IBPs on the tree based on habitat and phylum to guide our investigations into the potential evolutionary origin of the putative IBPs. We also produced a phylogeny of the organism search list through the taxonomy browser in NCBI, highlighting species bearing BLAST matches for IBPs to gain further insight into the evolution of putative IBPs.
Assessing putative IBPs
We then investigated the clades of query list IBPs that contained multiple hits against the organism search list to ensure matches were not due to ubiquitous IBP-like sequences found across organisms, including the progenitor proteins of the IBPs. To do this, sequences in each IBP clade were realigned using CLUSTAL W (Thompson et al., 1994) (see https://dtc-coding-dojo.github.io/main//blog/Ancestral_sequence_reconstruction/). We produced new maximum likelihood trees from these alignments, each using 50 bootstrap replicates and the WAG+G, WAG+G+F (Whelan and Goldman, 2001) and JTT (Jones et al., 1992) models for the coleopteran AFP, AFGP and teleost type II AFP clades, respectively. In the stead of an ice-binding domain search, we calculated ancestral sequences from these trees through MEGA (Kumar et al., 2018) using the same respective models mentioned above to obtain protein sequences bearing sequence regions shared across the respective IBPs in the clade. We searched for these ancestral sequences across the NCBI (https://www.ncbi.nlm.nih.gov/) non-redundant protein sequence database using blastp to investigate whether these had higher homology for IBPs and not the progenitor proteins of IBPs (Altschul et al., 1990). In the case of arthropod IBPs, progenitor proteins are unknown (Bildanova et al., 2012) but as the tick AFGPs are similar in sequence to fish AFGPs (Neelakanta et al., 2010), we assumed the same trypsinogen-like protease progenitor protein (Chen et al., 1997), although there are fish AFGPs that have evolved de novo (Zhuang et al., 2019). We then repeated the protein BLAST on the organism search list using the ancestral sequences to confirm a similar match profile with respect to which organisms bear matches (Altschul et al., 1990). We compiled hits from the ancestral sequence to the organism search list and used them to obtain separate trees and ancestral sequences as above to repeat the above progenitor protein verification. We searched for these ancestral sequences from the search organisms across the NCBI (https://www.ncbi.nlm.nih.gov/) non-redundant protein sequence database using blastp to ensure a lack of matches for IBP progenitors or ubiquitous sequences.
To further assess the identified putative IBPs, we used a series of published machine learning algorithms for classifying IBPs. All matches were assessed this way except in the case of the fish type II AFPs and the carrot (Daucus carota) AFP for which the match with the lowest e-value for each search organism was assessed instead. This was because these query IBPs had too many matches to assess given the limitations on the calculation time for some of the calculators used. The three web-accessible calculators we used for predicting AFPs through machine learning were: TargetFreeze (He et al., 2015), iAFP-Ense (Xiao et al., 2016) and CryoProtect (Pratiwi et al., 2017). For unknown reasons, not all sequences yielded outputs from the IBP calculators; 2.0% of sequences had no outputs from TargetFreeze (He et al., 2015) and 4.0% from CryoProtect (Pratiwi et al., 2017). Fish type II AFPs were further tested using the web-based disulfide bond predictor DiANNA 1.1 (Ferrè and Clote, 2005a,b, 2006), because fish type II AFPs have five disulfide bridges while C-type lectins have fewer (Graham et al., 2008). For all calculators, we also input the query IBPs to determine how much confidence we can have in each calculator's output. We also produced a histogram of the lengths of the match sequences inputted into the IBP calculators to provide insight into potential functions of the putative IBPs.
Investigating evolutionary origin of a putative IBP
To gain some insight into how these potential intertidal IBPs evolved, we evaluated the presence of genomic synteny for the best putative intertidal IBP for the fish type II AFP clade that met the criteria for all the above calculators: an unnamed protein product from Mytilus coruscus (NCBI accession no. CAC5422424.1). We located the coding region for the putative IBP in M. coruscus's genome, noting the contig the putative IBP gene is in and the four nearest protein coding genes (Table S3). We then performed tblastn searches (default parameters) for our putative IBP on the genomes of species of different degrees of relatedness to M. coruscus to locate orthologues (Table 2; Altschul et al., 1990). The contigs bearing these orthologues were then noted for each of these species as above (Table S3). We then performed tblastn searches on each genome for the four proteins surrounding the coding region for our primary protein of interest, comparing the arrangements of the coding regions for these proteins relative to M. coruscus to evaluate the presence of synteny. Genome snapshots (130,000 nt) surrounding the coding site for the potential orthologues of our putative IBP for each of the above species were then input into SimpleSynteny (Veltri et al., 2016) along with the sequences of our protein of interest and its four surrounding proteins to visualize the gene arrangement among species. To better understand trends in the gene mapping data, our protein of interest and its surrounding unknown protein products were aligned in MEGA (Kumar et al., 2018) using the MUSCLE algorithm (Edgar, 2004). A maximum likelihood tree was produced from the aligned sequences using 50 bootstrap replicates under the WAG model (Whelan and Goldman, 2001).
To determine whether the presence of IBP BLAST hits in search organisms is determined by habitat, phylum or the interaction between them, we used a logistic regression model. The sample sizes for terrestrial, estuarine and endoparasitic organisms were too small (n=7, 1 and 4, respectively) to include in this statistical analysis and we therefore omitted them. We also had to omit Annelida because of the small sample size (n=7) and Echinodermata because they are not found in freshwater habitats, which would impede the comparison across habitat types. To determine significant differences between groups, we used Tukey's honest significance test on the logistic regression model (Tukey, 1949). Statistical analysis was completed using R (http://www.R-project.org/) and the multcomp package (Hothorn et al., 2008), and alpha was set to 0.05.
Data collection and search for putative IBPs
The organism search list contained 150 species across the five (sub)phyla (Table 1; Table S2). Not all (sub)phyla were represented in all habitat types (Table 1). A total of 148 query IBP sequences were compiled with broad taxonomic representation reflecting the currently known diversity of IBP-producing taxa (Bar Dolev et al., 2016; Fig. 1; Table S1). Using blastp, we found that 42 of the query sequences had high homology with at least one protein sequence in 53 of the species in the search list (Fig. 1, Fig. 2; Fig. S1).
We were interested in whether intertidal species were more likely to contain putative IBPs, so we investigated the relationship between the probability of IBP homology and habitat type while controlling for (sub)phylum. The probability that a species contained a protein coding sequence that had high homology to a known IBP from the query list was not impacted by the (sub)phylum of the search organism (χ22,108=0.93, P=0.628; Fig. 2) nor was there an interaction between (sub)phylum and habitat (χ26,102=8.88, P=0.180). However, we found that habitat type was a strong predictor of IBP homology (χ23,110=22.46, P<0.001). More specifically, the proportion of intertidal invertebrates with protein sequence homology with known IBPs (55.3%) was significantly greater than that for freshwater (19.4%, z=2.93, P=0.016) and other marine species (5.0%, z=−2.93, P=0.016), but not subtidal species (48.0%, z=−0.56, P=0.939; Fig. 3). Subtidal invertebrates also had a higher likelihood of containing proteins with IBP homology than other marine species (z=2.60, P=0.042) but not freshwater species (z=2.22, P=0.108; Fig. 3). This probability did not significantly differ between freshwater and other marine invertebrates (z=−1.35, P=0.512; Fig. 3).
Assessing putative IBPs
The phylogeny of query IBPs grouped structurally similar IBPs into clades, with little evidence of phylogenetic signal; for example, tick AFGPs grouped with fish AFGPs rather than with IBPs from other arthropods, while type II AFPs from fish grouped in the middle of a largely arthropod IBP clade rather than with other fish IBPs (Fig. 1). Of the identified IBP clades, only three had significant homology with the invertebrates in our organism search list: Coleoptera AFPs, AFGPs and fish type II AFPs (Fig. 1). An AFP from a carrot (Daucus carota) and an ice-nucleating IBP from a bacterium (Pantoea agglomerans) also had strong but isolated homology with sequences from multiple search organisms (Fig. 1).
We wanted to investigate the above three clades further to ensure these trends were due to an IBP-specific search. To isolate shared sequence regions between IBPs, we obtained eight ancestral sequences from the Coleoptera AFP, AFGP and fish type II AFP clades: four from the Coleoptera AFP clade, two from the AFGP clade, and two from the fish type II AFP clade (Table 3). All ancestral sequences returned hits for IBPs in the non-redundant protein sequence database in NCBI (https://www.ncbi.nlm.nih.gov/) and, where applicable, did not have matches with sequences for progenitor proteins (Table 3), suggesting we successfully isolated these shared IBP-specific sequence regions. When searching for these ancestral sequences in the organism search list, two from the Coleoptera AFP clade (both from Dendroides canadensis) did not return hits, suggesting the initial search from these sequences was not specific for IBPs. For the other two coleopteran AFP query ancestral sequences, one returned matches in the same two species as the original queries, but the other ancestral sequence had matches in all but two of the original five species. In the case of the ancestral sequences of the AFGP queries, three of the original seven species were missing for the fish AFGPs and two of the 11 were missing for those of the ticks. In the case of the ancestral sequences for the fish type II AFPs, matches were found in all the same species as the original queries. With these exceptions, this analysis suggested that our search method was specific in finding putative IBPs in our search organisms.
We next aimed to determine whether the shared sequence regions of the matches for our above ancestral sequences in our putative IBPs were IBP specific rather than for IBP progenitors or for other non-IBPs common across a wide range of organisms. For the matches of the coleopteran AFP and the AFGP ancestral sequences, four and seven sequences were obtained, respectively (Table 3). For all but one of the sequences obtained through the matches for coleopteran AFP ancestral sequences, matches for IBPs were found and, in all cases, the narrow taxonomic distribution of these matches suggested that the sequence type is not ubiquitous and may be a derived IBP (Table 3). Sequences obtained from the matches for AFGP ancestral sequences were less consistent, with only three sequences returning matches for IBPs and three sequences returning matches across a broad taxonomic range, suggesting a ubiquitous sequence and an overall less specific search for IBPs (Table 3). Despite this, no hits for the progenitor trypsinogen-like proteases were obtained. The ancestral sequences were not obtained in the case of the matches for the fish type II AFP ancestral sequences; for reasons unknown, the phylogeny produced from these matches had multiple polytomies and could not be used to obtain ancestral sequences.
We next aimed to further assess ice-binding capabilities of the putative IBPs that we identified. Because only the top hits for each search organism were used for the fish type II AFPs and the carrot AFP, a total of 250 putative IBPs were examined using each of the three IBP calculators (He et al., 2015; Xiao et al., 2016; Pratiwi et al., 2017) and 86 of these sequences were also examined with a disulfide bridge calculator (Ferrè and Clote, 2005a,b, 2006). These 250 putative IBPs ranged from 79 to 5345 amino acids in length (Fig. S2). DiANNA 1.1 (Ferrè and Clote, 2005a,b, 2006) indicated that 69.8% of protein sequences with high homology to fish type II AFPs had five or more disulfide bridges and identified all query fish type II AFPs sequences as having five or more disulfide bridges. TargetFreeze (He et al., 2015) calculated 60.0% of the sequences to be IBPs, compared with 49.6% from iAFP-Ense (Xiao et al., 2016) and 65.2% from CryoProtect (Fig. 4; Pratiwi et al., 2017). This meant that while on average each calculator rejected 41.7% of the sequences, only 17.6% of the putative IBP sequences were not identified as IBPs by any calculator. When vetting the 42 query sequences with high homology to search organism sequences, TargetFreeze (He et al., 2015) accepted only 73.8% of the query sequences (Fig. 4), with all query AFGPs rejected. By contrast, iAFP-Ense (Xiao et al., 2016) accepted 90.5% of the query sequences and CryoProtect (Pratiwi et al., 2017) accepted 95.2% (Fig. 4). This means each calculator rejected an average of 13.5% of query sequences, but only one query IBP (2.4%), a thermal hysteresis protein from bittersweet nightshade (Solanum dulcamara; NCBI accession no. AAL26842.1) was rejected by all three IBP calculators. In many cases, including the AFGPs for TargetFreeze (He et al., 2015), rejection of a query sequence by the calculators did not equate to all respective hits being rejected as well (Table S4).
Investigating evolutionary origin of a putative IBP
To evaluate the evolutionary origin of a putative IBP from the hard-shelled mussel (M. coruscus), we evaluated the level of synteny in a group of search organisms with well-developed genomic resources and potential orthologues of the putative IBP (NCBI accession no. CAC5422424.1; Table 2). We selected the four nearest genes to the coding region of the M. coruscus putative IBP: two upstream and two downstream, referred to henceforth as gene or protein 1, 2 and 4, 5, respectively (NCBI accession nos CAC5422422.1, CAC5422423.1, CAC5422425.1, CAC5422426.1). BLAST of gene 2 against the non-redundant protein database of NCBI (https://www.ncbi.nlm.nih.gov/) found the strongest hit (other than various unnamed protein products from M. coruscus) to be a predicted collectin-12 protein from Mytilus edulis. Interestingly, gene 2 had high homology to the M. coruscus putative IBP, with 100% query coverage, 70% identity and an E-value of 2×10−91, suggesting that these two genes may be the result of a gene duplication event or, less likely, a technical artifact of the genome assembly process. No evidence for synteny across these five genes was found in any of the species, regardless of relatedness to M. coruscus (Fig. 5A,B). In nearly all species, the presumed orthologue for the putative IBP was isolated, with no orthology for the surrounding genes on the same contig, scaffold or even chromosome save gene 2, which would have potential orthologues of varying quality directly overlapping the orthologues of our putative IBP gene. The one exception was the great scallop (Pecten maximus), where gene 5 was found on the same chromosome as the orthologue for the putative IBP but located millions of base pairs away from it, suggesting that this relationship does not reflect true synteny at our level of interest.
In the Mediterranean mussel (Mytilus galloprovincialis), all top candidates for orthologues of the putative IBP were in the exact same locations as the potential orthologues for gene 2, but E-values were lower and percentage identities were greater for gene 2 compared with those for our putative IBP, suggesting the presence of a gene 2 orthologue, rather than one for the putative IBP. This overlap in orthologue sites for gene 2 and the putative IBP was also seen in the golden mussel (Limnoperna fortunei) and the sea slug Elysia chlorotica, but in the latter the potential orthologue for the putative IBP outscores that of gene 2. In all cases, BLAST output alignments had an overlap of varying scores between potential orthologue sites for the putative IBP and gene 2, matching the aforementioned high similarity between sequences (Fig. 5A). This similarity in sequences is reflected in their grouping and branch lengths, representing the number of substitutions, in the phylogeny produced from our protein of interest and the four surrounding proteins (Fig. 5C). In addition to this, the scores for the orthologues for both gene 2 and the putative IBP drop in power after the most closely related species M. galloprovincialis by well over 10 orders of magnitude.
Here, we provide evidence that IBPs evolve relatively easily in response to the risk of freezing. We found dozens of invertebrate species with sequences with high homology to known IBPs, supporting our hypothesis that IBPs occur across a much broader array of organisms than currently known. We predicted that the freezing risk in intertidal habitats would select for IBP presence and found much higher probabilities of putative IBP presence in intertidal species than in species found in habitats that have a lower risk of freezing. These findings strongly suggest that there are uncharacterized IBPs in intertidal invertebrates that have high homology to teleost type II AFPs and AFGPs, supporting our hypothesis that IBPs are selected for by intertidal habitats.
In silico considerations
This is not the first study to use molecular sequence data to predict the presence of IBPs (Krell et al., 2008), but this is the first to our knowledge to take this broad approach. Typically, IBPs are predicted from sequence data of specific species during genome annotation projects or transcriptomics research. For example, the genome project for the scallop Mizuhopecten yessoensis resulted in 15 predicted protein products annotated as ice-nucleating proteins alone (Wang et al., 2017). In these other studies, IBP presence was predicted by homology to identify an uncharacterized coding region or transcript, thus filling gaps in our knowledge for individual species. By contrast, in this study, we aimed to fill gaps in our knowledge of IBP evolution by taking a broad approach to identify putative IBPs and identify potential correlations with IBP abundance and specific habitat types. A major limitation of this study that is shared with genome and transcriptome studies is the inability to confirm the expression or ice-binding activity of these proteins. Sequence similarity to IBPs does not equate to ice-binding ability and despite our efforts to assess the putative IBPs found in this study, conclusions about the presence or absence of IBPs cannot be made for any of the species we used (Kandaswamy et al., 2011; Eslami et al., 2018; Nath and Subbiah, 2018; Sun et al., 2020; Usman et al., 2020). By extension, even if these putative IBPs are capable of binding to ice, we cannot verify whether these putative IBPs serve a cryoprotective function. For example, type IV AFPs from fish can bind to ice, but have been shown to serve a role in fish development rather than as a cryoprotectant (Gauthier et al., 2008; Xiao et al., 2014). An advantage of our study and its broad search list is the potential to avoid false negatives that might arise as a result of limited queries in traditional automated gene annotation processes. This could result in a broad underprediction of a given protein type, a phenomenon that is more common in the case of functionally rare and unique genes such as IBPs (Prosdocimi et al., 2012; Wilbrandt et al., 2019).
Despite the above limitations, validation of our search process suggests some degree of specificity for identifying IBPs rather than matches due to sequences unrelated to IBP activity, with some exceptions noted below. Our initial verification using a BLAST search of the queries and their ancestral sequences beyond our search organisms and against all NCBI's non-redundant database yielded results for IBPs, not their progenitor proteins. These query ancestral sequences also yielded hits in nearly all the same species as the initial IBPs save for a select group of coleopteran AFPs. We also attempted to verify our search method using the ancestral sequences of the matches, which suggested that our search method may not be specific in the case of some of the AFGPs as most of the sequences did not return matches for IBPs and returned matches across a wide taxonomic range. However, in all, this suggests that our search process was specific for finding derived IBPs and not general similarities in sequences that are coincidentally more common in intertidal invertebrates. Also, given the nature of how Expect thresholds are calculated and implemented in determining search results in BLAST, it is possible more potential IBPs exist but were rejected (González-Pech et al., 2019). In fact, other than being unable to isolate and characterize these proteins, all limitations of this study will likely lead to underestimation of true IBP frequency. For example, some intertidal invertebrates may have novel forms of IBPs, which we would have no way of searching for in this study.
Furthermore, many search organisms used in this study have wide geographic ranges and it may be that only poleward populations have selected for IBPs. Thus, if the specific specimens used for sequencing were from more equatorial populations, we may not detect putative IBPs that would otherwise be present in the species (Hayes et al., 1991). Similarly, if the sequencing was done on deep ocean rather than intertidal specimens of a species found in both habitats, selection for IBPs may not be observed. Expanding on this, information on some of the species used in this study is limited, leading to potential misclassification of habitat types. Many of the species used in this study occur across multiple habitats, but lesser-known species may be described as having only a single habitat as a result of limited resources upon creation of the species accounts we used for determination of habitat. For example, the well-studied Mediterranean mussel (M. galloprovincialis) occurs intertidally in certain parts of its range and subtidally in others (McDonald et al., 1991). A lesser studied species may not be sufficiently surveyed across its entire range and be misclassified in WoRMS (https://www.marinespecies.org/) or SeaLifeBase (https://www.sealifebase.ca/). This could explain the high prevalence of putative IBPs in subtidal species found in this study, as we cannot confirm they are never exposed to air and some of the species designated as subtidal may in fact be found in the intertidal. Also, the advent of shotgun sequencing means genomic resource availability is constantly increasing, expanding the search potential for IBPs (Giani et al., 2020). Similarly, there are a huge array of IBPs that have been characterized in the literature, but not yet sequenced (Madison et al., 1991; Duman et al., 2004). As reflected by the IBP sequence phylogeny (Fig. 1), IBP types do not have a common sequential or structural component that unites them all and it is probable that new structures of IBPs have yet to be discovered that would expand our search potential even further (Davies, 2014; Bar Dolev et al., 2016).
Because of this lack of shared sequence or structure across IBPs, there has been extensive work in the field of machine learning to identify IBPs from their amino acid sequence (e.g. Kandaswamy et al., 2011; He et al., 2015; Yang et al., 2015; Xiao et al., 2016; Pratiwi et al., 2017; Eslami et al., 2018; Khan et al., 2018; Nath and Subbiah, 2018; Usman and Lee, 2019; Sun et al., 2020; Usman et al., 2020; Wang et al., 2021). We used three IBP calculators in this study to further investigate our putative IBPs. Although most of the sequences identified by our BLAST searches as putative IBPs passed as IBPs according to at least one calculator, on average each calculator rejected 41.7% of the sequences. These calculators were created because IBPs are more similar to their progenitor non-IBPs than to each other, so the large fraction of proteins rejected by each calculator is unsurprising (Kandaswamy et al., 2011; Eslami et al., 2018; Nath and Subbiah, 2018; Sun et al., 2020; Usman et al., 2020). What is surprising, however, is the variability among calculator outputs. Despite each calculator rejecting an average of 41.7% of the putative IBPs, only 17.6% of the sequences were rejected by all calculators. Similarly, an average of 13.5% of query sequences were also rejected by each calculator, but only one was rejected by all three, suggesting that these calculators also struggle to predict IBPs individually, but we can have more confidence where the three overlap in their rejections. It also demonstrates the importance of training and testing datasets in creating machine learning-based IBP predictors, especially in the case of TargetFreeze (He et al., 2015), which rejected all query AFGPs, indicating a clear gap in the algorithm. By contrast, all calculators recognized the query carrot IBP but rejected nearly all its homologous sequences from the species search list. This may be an instance where the IBP calculators were powerful in their ability to differentiate IBPs from non-IBPs. However, it may be that some aspect of the carrot query IBP sequence is unique compared with that of other IBPs (Wang et al., 2020), and also that the calculators were trained with the sequence, meaning it could correctly identify it, but as it is unique in the database of IBPs, the calculators were not sufficiently trained in identifying other carrot-like IBPs, despite these IBP calculators being designed taking into account the impact of unbalanced data (Murphey and Guo, 2004; Usman et al., 2020). Expanded empirical studies of ice-binding activities will be necessary to resolve these uncertainties.
We also used DiANNA 1.1, the disulfide bridge calculator, to verify a subset of our hits for the fish type II AFPs (Ferrè and Clote, 2005a,b, 2006). DiANNA 1.1 is mostly intended for identifying the potential locations of disulfide bridges, rather than the amount, meaning it often overestimates the number of disulfide bridges (Ferrè and Clote, 2005a,b, 2006). Despite this, the calculator providing outputs for fewer than five disulfide bridges still acted as a sufficient criterion for rejection as in Graham et al. (2008). There are IBP calculators that exist that are precise in the identification of IBPs from C-type lectins, but these have prohibitive computational requirements (Kozuch et al., 2018). These highlighted shortcomings in the in silico research of IBPs emphasize the value of experimental verification of ice-binding activity.
In vivo considerations
The limited laboratory work that exists on IBPs in intertidal invertebrates also suggests they may be proteins with similarities to known AFGPs and fish type II AFPs in these species. The earliest instance of IBP identification in an intertidal invertebrate was an AFGP in the blue mussel (Mytilus edulis; Theede et al., 1976). Here, we found many intertidal species bearing strong homologous sequences to both teleost and tick AFGPs; however, M. edulis does not have a sequenced genome and was therefore absent from our search list, and so this could not be replicated in this study. Mytilus species that were included in our organism list did not have homologous sequences to AFGPs (save for M. coruscus, which had an unnamed protein product with homology to one of the tick AFGPs) but other molluscs had sequences with strong homology to the query AFGPs (Fig. 1). It is unknown how much homology, if any, the M. edulis AFGP has with the tick and teleost AFGPs and it should be noted that while observation of ice-binding activity has subsequently been repeated in M. edulis (Dubé, 2012), no characterization of the actual protein has been performed since the original study in 1976 (Theede et al., 1976; Duman, 2015). With respect to fish type II AFPs, actual isolation of a protein with high homology to this structure has not been completed in an intertidal invertebrate. However, a transcriptomic study comparing transcription before and after freezing in an intertidal barnacle (Semibalanus balanoides) found many transcripts automatically annotated as macrophage mannose receptors upregulated (Marshall et al., 2018 preprint). Mannose receptors are not associated with freeze tolerance, but other C-type lectins, specifically fish type II AFPs, are clearer contributors to freeze tolerance (Gronwald et al., 1998). It was hypothesized that these upregulated transcripts were misannotated and if this were the case it would corroborate the results of this study that found a strong signal for fish type II AFPs in intertidal invertebrates (Marshall et al., 2018 preprint). It should be noted, however, that S. balanoides was in our search organism list, but we did not find any strong homology to query IBPs. It should also be noted that most of the query IBPs used in this study primarily function to produce thermal hysteresis in freeze-avoidant species, where intertidal invertebrates are almost never freeze avoidant (Aarset, 1982). However, these putative IBPs may primarily act as ice recrystallization inhibitors in intertidal invertebrates, despite their similarity to IBPs used for freeze avoidance, as there is no correlation between thermal hysteresis and IRI ability in IBPs (Gruneberg et al., 2021). Additionally, based on the sequence length distribution of the putative IBPs, there are many that may function as ice nucleators (Fig. S2). This is because ice-nucleating IBPs are larger than other IBPs; for example, those found in bacteria are composed of over 1000 amino acids (Warren and Corotto, 1989), compared with around 100–400 amino acids for typical IBPs used for freeze avoidance or IRI (Worrall et al., 1998; Doucet et al., 2002).
There were also many genomic matches with a carrot (D. carota) IBP and bacterium (P. agglomerans) IBP. The carrot IBP primarily acts as an ice recrystallization inhibitor, which is advantageous to freeze-tolerant organisms, possibly explaining the intertidal signal for this protein (Knight and Duman, 1986; Worrall et al., 1998); however, the calculators suggest many of these hits may not be IBPs. The bacterial IBP was specifically one with ice-nucleating activity (Warren and Corotto, 1989). Ice-nucleating proteins are advantageous for freeze tolerance (Zachariassen and Hammel, 1976) and have been found in intertidal invertebrates before, specifically in an air-breathing gastropod (Melampus bidentatus), but it is unclear how homologous they would be to those from bacteria (Madison et al., 1991). The M. bidentatus ice-nucleating proteins were found to have similar amino acid proportions to bacterial ice-nucleating proteins, but the size of the protein was only a quarter of those found in bacteria and the sequence was not obtained (Madison et al., 1991). Given the size difference, it is unlikely the results of our study reflect the presence of a M. bidentatus-like IBP distributed across intertidal invertebrates. In the intertidal bivalve Geukensia demissa, freeze tolerance is accomplished through ice-nucleating bacteria, rather than through proteins produced by the animal itself (Loomis and Zinser, 2001). Whether a similar relationship is occurring in multiple other intertidal invertebrates is unknown, but considering how ubiquitous P. agglomerans is, and how frequently it acts as a symbiont, bacterial contamination of samples could partially account for the high signal for this IBP (Dutkiewicz et al., 2016).
While the Coleoptera AFP clade did not have a strong intertidal signal like the previously mentioned IBP groups, multiple query IBPs in this clade had homology for a protein labelled as an ‘insect AFP’ in a terrestrial crustacean (Trinorchestia longiramus). As with the other hits in this study, this is a predicted AFP from a genome annotation project, not a laboratory-characterized AFP (Patra et al., 2020). Given how closely insects and crustaceans are related compared with the other search phyla and the taxonomy of the query IBPs with strong signals, potential evolutionary homology could explain the acquisition of this crustacean's putative IBP. This may also be true for the strong homologies found for the tick AFGPs in some crustaceans in the search organism list, but none were automatically annotated as IBPs in these cases. Despite how closely related insects and ticks are to crustaceans, nothing from the query list is more closely related to crustaceans than other crustaceans. The query IBPs from a copepod (Stephos longipes) did not contain homologies to any sequences in the search organisms, although we initially expected this protein may return multiple hits in the crustaceans in our search list. These proteins are hypothesized to be acquired through lateral gene transfer from diatoms or snow moulds, both groups of IBPs that also did not yield hits in this study, which explains why no hits were found in these query IBPs despite being part of the search phyla (Kiko, 2010). Lateral gene transfer has been suggested for multiple other IBPs as well, with evidence for IBP acquisition through lateral gene transfer being seen in algae, diatoms and fungi (Sorhannus, 2011; Raymond, 2014; Arai et al., 2019; Raymond and Remias, 2019).
Type II AFPs in some fish have also been hypothesized to have been acquired through lateral gene transfer (Graham et al., 2012). Unlike previously mentioned examples of IBP lateral gene transfer, the fish type II AFPs remain confined within the same phylum, making it unlikely that lateral gene transfer explains the strong signal seen for fish type II AFPs seen in this study. This is corroborated by the fact that none of the hits found in this study were more than 60% identical to the respective query IBP sequences, despite the high homology suggested by hits surpassing the Expect threshold of 1×10−5. This suggests that all putative IBPs in the search organisms of this study were acquired convergently, including those for crustaceans highlighted in the previous paragraph. Type II AFPs evolved by gene duplication and neofunctionalization from C-type lectins in fish, and it is possible a similar process occurred in the C-type lectins of these intertidal taxa (Gronwald et al., 1998). The same can also be hypothesized for AFGPs, as they have evolved convergently within fish, from both trypsinogen-like proteases and non-sense DNA (Chen et al., 1997; Zhuang et al., 2019). A similar evolutionary pathway could explain the putative presence of AFGPs in our search organisms. Further research into the potential evolution of these IBPs could provide further understanding of the colonization of the intertidal zone in temperate and polar regions.
We investigated the potential evolutionary origin of these putative IBPs by selecting a strong IBP match in a search organism, M. coruscus, with many closely related species with genomic resources to be treated as a proof of principle. A basic search for synteny proved fruitless in this study, which can be used as support for horizontal gene transfer (Sevillya et al., 2020). However, for reasons mentioned above, we believe that this putative IBP evolved convergently and horizontal gene transfer could not be responsible for the acquisition of this protein. Despite this lack of synteny being found, our search methods revealed a high similarity between the potential IBP of M. coruscus and an unnamed protein product with a neighbouring coding region. Based on potential orthologues, we also found that neither of these two proteins is very conserved beyond M. galloprovincialis, which appeared to only have the neighbouring protein and not an orthologue for the potential IBP. Based on this, we suggest a duplication and neofunctionalization event occurred with this neighbour protein, resulting in an IBP in M. coruscus. This duplication and neofunctionalization would mirror the hypothesized evolutionary history for other known IBPs including fish type II AFPs (Liu et al., 2007) and fish type III AFPs (Deng et al., 2010), suggesting that evolutionary history repeated itself in intertidal invertebrates. This is supported by gene 2 having high similarity to a predicted collectin-12 from M. edulis, a C-type lectin. However, the function of gene 2 cannot be confirmed, only suggested through sequence similarity, and gene 2 and its orthologue in M. galloprovincialis may be putative IBPs themselves that evolved de novo, as seen in certain fish AFGPs (Zhuang et al., 2019), based on it not being conserved beyond the genus Mytilus. This would mean a duplication event occurred creating paralogues that both function as IBPs in M. coruscus; this may reflect the origin of the many AFP paralogs seen in some fish and insects (Swanson and Aquadro, 2002). The evolutionary origin of IBPs is still a developing field, with the evolution of most non-fish IBPs poorly studied (fish IBP evolution reviewed by Cheng and Zhuang, 2020), but there are also examples of IBPs obtained convergently in the case of AFGPs and type I AFPs from fish (Chen et al., 1997; Graham et al., 2013). Convergent evolution of similarly structured IBPs across phyla has not been explicitly described in the literature before, as most known instances of similar IBPs between phyla have been explained by horizontal gene transfer (Kiko, 2010; Sorhannus, 2011; Raymond, 2014; Arai et al., 2019; Raymond and Remias, 2019). This would make our proposed convergent evolution of this potential fish type II AFP-like IBP in M. coruscus unique. However, given the number of putative IBPs and their taxonomic distribution (Fig. 2), it is likely there are many other examples yet to be described. This combined with the multitude of confirmed IBPs suggests that convergent evolution of IBPs is common.
In this study, we demonstrate evidence for an enrichment of uncharacterized putative IBPs in intertidal invertebrates as compared with invertebrates living in other aquatic habitats, supporting the hypothesis that life in the intertidal zone might select for IBPs. In intertidal invertebrates, a strong signal for putative IBPs was found for type II AFPs from fishes and AFGPs from both fishes and ticks, reflecting existing data of AFGPs in intertidal mussels and evidence of fish type II AFPs in intertidal barnacles. We propose that these putative IBPs evolved convergently, potentially through a duplication and neofunctionalization event as we suggest for M. coruscus. Future studies will be necessary to confirm the expression and true ice-binding activity of these proteins, but we were able to demonstrate both through reverse BLAST searches and IBP calculators that our methods were specific in their approach, suggesting we detected IBPs and not simply proteins with high similarity to IBPs. Even with rejections considered from our alternative BLAST searches and IBP calculators, the trends seen in habitat-specific putative IBP presence holds true. We therefore conclude that IBPs readily evolve in response to intertidal environments, and this could help explain how intertidal organisms colonized temperate and polar regions.
We would like to thank Patricia Schulte and Jeffrey Richards for their input, which helped develop our methods and interpret our results. We thank two anonymous reviewers for their excellent suggestions, which significantly improved the manuscript. We used FigTree in creating one of our figures, created and made available to the public by Andrew Rambaut.
Conceptualization: B.J.M., K.E.M.; Methodology: B.J.M., K.E.M.; Formal analysis: I.C.H.B.; Investigation: I.C.H.B.; Data curation: I.C.H.B.; Writing - original draft: I.C.H.B.; Writing - review & editing: B.J.M., K.E.M.; Visualization: I.C.H.B.; Supervision: B.J.M., K.E.M.; Project administration: K.E.M.; Funding acquisition: K.E.M.
K.E.M. and B.J.M. are supported by individual Natural Sciences and Engineering Research Council of Canada Discovery grants. B.J.M is supported by a Scholar Award from Michael Smith Health Research BC and a Research Fellowship from the Alfred P Sloan Foundation.
Data are available from the Open Science Framework (OSF): doi:10.17605/OSF.IO/B7A92.
The authors declare no competing or financial interests.