Ecology drives the observed spectrum of hydrophobin protein diversity across kingdom fungi

Authors: Lovett, Brian; KASSON, MATTHEW - West Virginia University; GANDIER, JULIE-ANNE - Aalborg University

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 8/19/2022
Publication Date: 8/19/2022
Citation: Lovett, B.R., Kasson, M.T., Gandier, J. 2022. Ecology drives the observed spectrum of hydrophobin protein diversity across kingdom fungi. bioRxiv. https://doi.org/10.1101/2022.08.19.504535.
DOI: https://doi.org/10.1101/2022.08.19.504535

Interpretive Summary: Fungi are a broad group of organisms that enjoy an enormous diversity of lifestyles and forms. This wide range of lifestyles is enabled by a concert of proteins, but one family of proteins called hydrophobins is of unique importance to fungi. Hydrophobins are small, secreted proteins which can remarkably self-assemble into thin films, typically where air and water meet. These films alter surfaces allowing fungi to grow and spread effectively. Despite being essential to many fungi, hydrophobins can be very different from one another, which has limited study of them across multiple fungi. In this paper, we developed a method to survey a broad range of fungi and identify hydrophobins. We further grouped these various hydrophobins, and assigned them into related classes. This work revealed specific types of hydrophobins are present in certain groups of fungi. We found that fungal ecology is related to the observed profile of hydrophobins from particular fungi. Our results provide an expansive modern view of the hydrophobin family, extending the current understanding of this group. We identified a number of unexpected findings, including hydrophobins from new groups of fungi and hydrophobins that may function inside cells. These results will be a touchstone for future breakthroughs in the field and generate a number of exciting hypotheses for further study. Hydrophobins are essential for many fungi, and so furthering our understanding of this protein family will certainly support ongoing efforts to apply or mitigate fungi in agricultural settings.

Technical Abstract: Hydrophobins mediate the interactions between fungi and the elements of their ecosystem via assembly at interfaces serving a wide range of diverse functions. As such, these proteins can be seen as a means by which fungi not only adapt to a pre-existing environment, but also actively participate in the construction of their own ecological niches. Through this lens, we provide an expansive hydrophobin survey across the ecological breadth of Kingdom Fungi and advance the view that hydrophobins are best defined as a generic molecular structure with shared core structural features that accommodate a remarkable diversity of amino acid sequences. We examine the relationship between hydrophobin sequences, fungus phylogeny, and associated ecology from 45 fungal proteomes predicted from genomes spanning eight phyla and more than 25 orders. To capture the full spectrum of the hydrophobin amino acid sequence space mapped by our study, we describe the family as a continuum of overlapping hidden Markov models (HMMs), each HMM representing clusters of sequence similarity spanning existing hydrophobin classes. Overall, our approach uncovered ecology as a major driver of hydrophobin diversification, further expanded the known hydrophobins beyond Dikarya, and uncovered evidence extending the possibilities for their function from exclusively extracellular to include intracellular. In addition, we identified novel core groups of cysteine-rich proteins whose conservation across fungi suggest they play key ecological roles. Together, our work offers an ontological framework that captures the diversity of hydrophobin amino acid sequences and highlights the need to revisit challenging fundamental questions regarding hydrophobins to achieve a mechanistic understanding of their function as emerging from assembly within an ecosystem.