Phylogenetic analysis of the caspase family in bivalves: implications for programmed cell death, immune response and development

Abstract

Background Apoptosis is an important process for an organism’s innate immune system to respond to pathogens, while also allowing for cell differentiation and other essential life functions. Caspases are one of the key protease enzymes involved in the apoptotic process, however there is currently a very limited understanding of bivalve caspase diversity and function. Results In this work, we investigated the presence of caspase homologues using a combination of bioinformatics and phylogenetic analyses. We blasted the Crassostrea gigas genome for caspase homologues and identified 35 potential homologues in the addition to the already cloned 23 bivalve caspases. As such, we present information about the phylogenetic relationship of all identified bivalve caspases in relation to their homology to well-established vertebrate and invertebrate caspases. Our results reveal unexpected novelty and complexity in the bivalve caspase family. Notably, we were unable to identify direct homologues to the initiator caspase-9, a key-caspase in the vertebrate apoptotic pathway, inflammatory caspases (caspase-1, − 4 or − 5) or executioner caspases-3, − 6, − 7. We also explored the fact that bivalves appear to possess several unique homologues to the initiator caspase groups − 2 and − 8. Large expansions of caspase-3 like homologues (caspase-3A-C), caspase-3/7 group and caspase-3/7-like homologues were also identified, suggesting unusual roles of caspases with direct implications for our understanding of immune response in relation to common bivalve diseases. Furthermore, we assessed the gene expression of two initiator (Cg2A, Cg8B) and four executioner caspases (Cg3A, Cg3B, Cg3C, Cg3/7) in C. gigas late-larval development and during metamorphosis, indicating that caspase expression varies across the different developmental stages. Conclusion Our analysis provides the first overview of caspases across different bivalve species with essential new insights into caspase diversity, knowledge that can be used for further investigations into immune response to pathogens or regulation of developmental processes.

Evolution and Potential Function in Molluscs of Neuropeptide and Receptor Homologues of the Insect Allatostatins

“…This system provides an immediate and effective response and depends on haemocytes that circulate in the haemolymph and humoral factors like lysozymes, complementlike molecules, peptidoglycan-recognition proteins (PGRPs) amongst others (71,99,100). Recent studies have revealed that immune factors in bivalves and molluscs are highly diverse due to species-specific expansions [ (71,(101)(102)(103)(104)(105)(106), Peng et al, submitted]. The diversity of bivalves, their adaptation to highly diverse environments, the plethora of pathogenic microorganism to which they are exposed, and their very different susceptibilities makes them excellent model systems to understand how environmental adaptation has shaped the immune system.…”

Hormonal Regulation of Programmed Cell Death in Sea Urchin Metamorphosis

“…In indirectly developing mollusks, metamorphosis, and settlement is characterized by substantial tissue remodeling. For example, veliger larvae of bivalves, scaphopods and gastropods lose their velar lobes during this process and build the adult ganglionic nervous system (Vogeler et al, 2021). Meanwhile, the central component of the larval nervous system, the apical organ, degenerates likely through apoptosis (Kiss, 2010;Heyland et al, 2011).…”

“…Like vertebrates, mollusks use both intrinsic and extrinsic apoptotic mechanisms and the presence of perforin in several bivalves may suggest the existence of a perforin/granzyme apoptotic pathway as well (Romero et al, 2015). These pathways also include caspases that are homologous to vertebrate caspases such as, CASP1, CASP2, CASP3, CASP6, CASP8, and a combination caspase-3/7 (Vogeler et al, 2021). Another similarity between vertebrate and mollusk apoptotic networks is the common convergence of the execution pathway, as initiated by the cleavage of CASP3 (Romero et al, 2015).…”

“…These pro-inflammatory cytokines then burst from the dying cell (Hanson, 2016). While little is known about the existence of pyroptosis outside of vertebrates, there is some evidence of a pyroptosis induction pathway in bivalves that is regulated by caspase-3 and gasdermin E-like proteins (Vogeler et al, 2021). Ferroptosis is another non-apoptotic form of programmed cell death which is executed by excessive production of reactive oxygen species (Hanson, 2016).…”

Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution

“…Protein recycling pathways, chaperone proteins, and apoptotic inhibitors can be employed to maintain cellular function during infection by inducing high levels of oxidative stress to remove intracellular pathogens ( Sunila and LaBanca 2003 ; Donaghy et al 2009 ; Hughes et al 2010 ; Zhang et al 2011 ; Brulle et al 2012 ; McDowell et al 2014 ; Smits et al 2020 ). This is reflected in the high diversity of inhibitor of apoptosis proteins (IAPs) shared by bivalves ( Song et al 2021 ; Vogeler et al 2021 ). The largest IAP gene family we identified was OG17.…”