The rhomboid gene was discovered in Drosophila, where it encodes a seven transmembrane protein that is the signal-generating component of epidermal growth factor (EGF) receptor signaling during development. Although metazoan developmental regulators are rarely conserved outside the animal kingdom, rhomboid proteins are conserved in all kingdoms of life, but the significance of this remains unclear. Recent biochemical reconstitution and high-resolution crystal structures have provided proof that rhomboid proteins function as novel intramembrane proteases, with a serine proteaselike catalytic apparatus embedded within the membrane bilayer, buried in a hydrophilic cavity formed by a protein ring. A thorough consideration of all known examples of rhomboid function suggests that, despite biochemical similarity in mechanism and specificity, rhomboid proteins function in diverse processes including quorum sensing in bacteria, mitochondrial membrane fusion, apoptosis, and stem cell differentiation in eukaryotes; rhomboid proteins are also now starting to be linked to human disease, including early-onset blindness, diabetes, and parasitic diseases. Regulating cell signaling is at the heart of rhomboid protein function in many, but not all, of these processes. Further study of these novel enzymes promises to reveal the evolutionary path of rhomboid protein function, which could provide insights into the forces that drive the molecular evolution of regulatory mechanisms.Developmental biology has progressed from descriptive observation to mechanistic analysis in the latter half of the 20th century (Wolpert 1998). Powerful genetic tools applied to model organisms have led to an intricate and beautiful picture of how genes build complex organisms. Parallel analyses in diverse animals and sequencing of their genomes revealed that a relatively small number of master genes and core regulatory pathways are used repeatedly in different contexts to build complex patterns, and these factors are conserved among animals.In addition to revealing some of the underlying logic of how organisms are constructed, these approaches were powerful in identifying the factors that mediate this intricate level of organization. But little is still known about how these key regulators exert their functions biochemically, which is central to understanding core biological processes that drive development at the molecular level.Most developmental regulators are conserved in the animal kingdom but are not found in other kingdoms, including plants, perhaps because plants and animals evolved multicellular development after splitting from a common ancestor (Meyerowitz 2002). But in recent years a small number of factors have been discovered that are conserved across kingdoms, raising the exciting possibility that they are key regulators that evolved very early. One such class of regulatory proteins are intramembrane proteases.Intramembrane proteolysis, the cleavage of membrane proteins within their membrane spanning segments, has recently been discovered to...