Abstract

Secreted proteins are translocated across membranes through multiple routes. In eukaryotes, secreted proteins with N-terminal signal sequences can use either the signal recognition particle (SRP) or the alternative Sec63 translocon to cross the endoplasmic reticulum membrane. Large-scale experiments on the substrates of these pathways are primarily from the model yeast Saccharomyces cerevisiae, but less is known about conservation of translocation pathways. Here we take a computational approach to analyse secretion signals across the fungi. Computational predictions by the Phobius model robustly separate known SRP-dependent from Sec63-dependent proteins in S. cerevisiae. Prior work suggested that this separation is driven by the compound hydropathy of the signal peptide’s hydrophobic helix, i.e., its length multiplied by maximum hydropathy. Instead, we find that the length of the hydrophobic helix is the major discriminator in native proteins: 8-13 amino acids for Sec63-dependent proteins and 16-27 amino acids for SRP-dependent proteins. Secreted proteins in diverse fungal species also separate into distinct populations by Phobius predictions and by the length of the hydrophobic helix. Our analysis across fungi shows that distinct functional groups of proteins, including fungal cell wall proteins and extracellular proteins, have cleaved signal peptides with short hydrophobic helices, similarly to Sec63-dependent proteins in S. cerevisiae. Our results suggest that the Sec63 translocon is critical for cell wall biogenesis and protein secretion in fungi, including secretion of major virulence factors in fungal pathogens of plants and animals.