Molecular evidence of intertidal habitats selecting for repeated ice-binding protein evolution in invertebrates

Abstract

Ice-binding proteins (IBPs) have evolved independently in multiple taxonomic groups to improve their survival of 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 ice-binding proteins 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 ice-binding protein was significantly greater in intertidal species as compared to 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, that there is an array of uncharacterized ice binding proteins and highlight the need for broader laboratory-based surveys of the diversity of ice binding activity across diverse taxonomic and ecological groups.Summary statementIntertidal invertebrates have a disproportionate number of putative ice-binding proteins relative to other habitats. These putative proteins are highly similar to antifreeze glycoproteins and type II antifreeze proteins from fish.

The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins

“…Although convergent evolution has been proposed to explain the presence of similar AFPs in distantly related fishes ( Chen et al 1997b ; Graham et al 2013 ; Zhuang et al 2019 ) and intertidal invertebrates ( Box et al 2022 ), the very high degree of similarity observed here between Cf- and NuAFPs ( fig. 6 ) seems to argue against this hypothesis.…”

“…The origins and convergent evolution of unrelated AFPs in diverse insect and fish taxa are of considerable interest from an evolutionary biology point of view ( Cheng 1998 ; Box et al 2022 ). In the present study, we addressed this question in a unique group of AFPs first reported in C. fumiferana almost four decades ago ( Hew et al 1983 ).…”

“…Known as AFPs or ice-binding proteins (IBPs), these molecules induce thermal hysteresis, a term that refers to the difference between freezing and melting points in the presence of AFPs ( Cheng 1998 ). AFPs have evolved independently in diverse organisms including fishes, insects, marine invertebrates, plants, fungi, and bacteria ( Duman and Serianni 2002 ; Box et al 2022 ). Among animals, insect AFPs are up to 100 times more active than those of fishes ( Scotter et al 2006 ), which have lower thermal hysteresis requirements than terrestrial arthropods (freezing point of sea water: −1.86°C; De Vries 1986 ).…”

“…Although these proteins tend to have some structural features in common across all taxa (e.g. flat ice-binding surfaces), most show no primary sequence homology (except some AFPs within Coleoptera; Cheng 1998 ) and are thus considered to have distinct evolutionary origins ( Box et al 2022 ). Among the best characterized insect AFPs are those of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a highly destructive defoliator of fir and spruce forests in Canada and the northeastern United States ( Johns et al 2019 ).…”

Ocean acidification increases susceptibility to sub-zero air temperatures in ecosystem engineers (Mytilus sp.): a limit to poleward range shifts

“…In intertidal bivalves, metabolites and anaerobic byproducts such as trimethylamine n-oxide (TMAO), betaine, taurine and strombine, likely to act as cryoprotectants, increasing freeze tolerance (Kennedy et al, 2020; Loomis et al, 1988). While under-explored, it also appears that many intertidal species may have an array of ice binding proteins that help manage ice growth and propagation (Box et al, 2022).…”