Using machine learning to predict protein–protein interactions between a zombie ant fungus and its carpenter ant host

Abstract

Parasitic fungi produce proteins that modulate virulence, alter host physiology, and trigger host responses. These proteins, classified as a type of “effector,” often act via protein–protein interactions (PPIs). The fungal parasite Ophiocordyceps camponoti-floridani (zombie ant fungus) manipulates Camponotus floridanus (carpenter ant) behavior to promote transmission. The most striking aspect of this behavioral change is a summit disease phenotype where infected hosts ascend and attach to an elevated position. Plausibly, interspecific PPIs drive aspects of Ophiocordyceps infection and host manipulation. Machine learning PPI predictions offer high-throughput methods to produce mechanistic hypotheses on how this behavioral manipulation occurs. Using D-SCRIPT to predict host–parasite PPIs, we found ca. 6000 interactions involving 2083 host proteins and 129 parasite proteins, which are encoded by genes upregulated during manipulated behavior. We identified multiple overrepresentations of functional annotations among these proteins. The strongest signals in the host highlighted neuromodulatory G-protein coupled receptors and oxidation–reduction processes. We also detected Camponotus structural and gene-regulatory proteins. In the parasite, we found enrichment of Ophiocordyceps proteases and frequent involvement of novel small secreted proteins with unknown functions. From these results, we provide new hypotheses on potential parasite effectors and host targets underlying zombie ant behavioral manipulation.

Multiomic interpretation of fungus-infected ant metabolomes during manipulated summit disease

“…The monoamine neurotransmitters dopamine, serotonin, and octopamine (analogous to vertebrate norepinephrine) have been implicated in modulating locomotor, foraging, learning, social, reproductive, and aggressive behaviors in many insects, and have been tested in social insects, including ants 48 – 52 . Additionally, direct host-parasite interactions have been hypothesized to occur by Ophiocordyceps proteins binding Camponotus neuroreceptors for biogenic amines and other neurotransmitters 25 . Serotonin, octopamine, and melanin derived from L-3,4-dihydroxyphenylalanine (L-DOPA), or tyrosine and dopamine, have roles in insect immunity as well 53 , 54 .…”

“…In support of this scenario, we found reduced abundances of metabolite precursors (immediate or two biosynthetic steps removed) coupled with transcriptomic data indicating increased (dopamine and serotonin) or unchanged (octopamine) synthetic enzyme gene expression. Corroborating a possible disruption of neuronal signaling, computationally predicted protein–protein binding interactions between the host and parasite have highlighted ant dopamine, serotonin, and octopamine G-protein coupled receptors as putative targets of secreted parasite proteins 25 .…”

“…In the myrmecophilous Ophiocordyceps , investigations of phenotypes, genomes, transcriptomes, and metabolomes continue to bring various mechanistic hypotheses of behavioral manipulation into focus. The range of hypotheses comprise fungal neuromodulators and effector proteins, host circadian rhythms and phototropism, insect hormones, fungal neuroprotectants, and ant muscular hyperactivity 6 , 7 , 14 , 19 – 25 . Previous metabolomic studies, centered on the Ophiocordyceps kimflemingiae zombie ant fungus and its host Camponotus castaneus , have identified various metabolites associated with manipulation.…”

What does your gut tell you? Influences of a zombie-making and generalist fungal entomopathogen on carpenter ant micro- and mycobiota

“…These GPCRs were annotated to have functions involved in the perception of light and smell, and the binding of biogenic amines such as dopamine. Most of the pathogen-related behavioral changes modulated by these GPCRs are likely due to the predicted binding of Ophiocordyceps secreted proteins that are upregulated during manipulated summiting (20). However, other GPCRs might be interacting with (altered levels of) microbial peptides secreted by the microbiome.…”

Pathogen-Mediated Alterations of Insect Chemical Communication: From Pheromones to Behavior

“…Numerous fungal molecules have been proposed to interact with ant molecular pathways, resulting in behavioral changes such as modified locomotion, feeding, light-sensing, circadian rhythms, and muscular hyperactivity [26][27][28][29][30][31][32]. The use of machine learning to predict host-parasite protein-protein interaction (PPIs) is an emerging approach aimed at generating fresh insights into the mechanisms behind these behavioral alterations, as recently shown by Will and colleagues [33]. In this study, PPIs involving fungal S8 proteases, oxidation-reduction processes, gene regulation, GPCRs, and cuticular proteins have surfaced as promising candidates for functional validation, providing new insights into co-evolved adaptations that underlie these modified behaviors.…”