Ubiquitin signaling: extreme conservation as a source of diversity

Abstract

Around 2 × 103-2.5 × 103 million years ago, a unicellular organism with radically novel features, ancestor of all eukaryotes, dwelt the earth. This organism, commonly referred as the last eukaryotic common ancestor, contained in its proteome the same functionally capable ubiquitin molecule that all eukaryotic species contain today. The fact that ubiquitin protein has virtually not changed during all eukaryotic evolution contrasts with the high expansion of the ubiquitin system, constituted by hundreds of enzymes, ubiquitin-interacting proteins, protein complexes, and cofactors. Interestingly, the simplest genetic arrangement encoding a fully-equipped ubiquitin signaling system is constituted by five genes organized in an operon-like cluster, and is found in archaea. How did ubiquitin achieve the status of central element in eukaryotic physiology? We analyze here the features of the ubiquitin molecule and the network that it conforms, and propose notions to explain the complexity of the ubiquitin signaling system in eukaryotic cells.

Figure 1

Schematic representation of ubiquitin evolution from an ancestral beta-grasp fold gene. (A) Beta-grasp fold is found in multiple protein families in prokaryotes and eukaryotes. Arrows show functional diversification at the levels of: beta-grasp fold ancestor, sulphur transfer precursor and ubiquitin-type families, and boxes contain groups of proteins, as reported in (3). (B) An evolutionary tree including branches of main groups is shown, and the origin of eukaryotes is hypothetically linked to the origin of ubiquitin.

Figure 2

Hypothetical evolution of the Ubiquitin-Proteasome System from an operon-like cluster. (A) Schematic representation of an operon-like cluster, based on C. subterraneum (11), in which the minimal representation of the factors required for ubiquitin-signaling is found in this type of genetic arrangement. (B) Representation of an expanded UPS, as found in eukaryotes, which includes groups of factors involved in UPS and their interactions. Central arrows indicate distinct behaviors in UPS evolution: while ubiquitin was conserved, the rest of ubiquitin signaling genes underwent an expansive process. (C) Percentage of ubiquitin and UPS related genes (including ubiquitin-like related factors) with respect to all annotated open reading frames in the genomes of: C. subterraneum (as a hypothetical model of eukaryote ancestor), the protist N. gruberi, the yeast S. cerevisiae and H. sapiens. A dramatic increase in the abundance of UPS genes is observed in eukaryotes.

Figure 3

Strict conservation of functional traits of ubiquitin through evolution. Multiple alignment of eukaryotic ubiquitin protein sequences is shown. Proteins are grouped by eukaryotic kingdoms. On the top of the alignment, amino acids composing ubiquitin interactive surfaces (isoleucine 44 and aspartate 58 patches) are shown in blue and violet, respectively. The first aligned sequence, from H. sapiens, contains in bold the N-terminal methionine, the seven lysine residues and the glycine-glycine C-terminal motif involved in ubiquitin conjugation. At the bottom, Clustal similarity symbols are included. Within the alignment, positions that show no variation are shown in black. Amino acid variations are highlighted in colors.

Figure 4

Hypothesis of a massive gain of function of ubiquitin in early eukaryotes. A schematic representation of the hypothetical behavior of ubiquitin evolutionary rate and ubiquitin physiological roles during time is shown. Ubiquitin evolved from ancestral forms of beta-grasp folded proteins (see also Figure 1), and its evolutionary rate decreased to a minimum, coincident with the origin of eukaryotes. Concomitantly, ubiquitin physiological roles increased massively, which resulted in a dramatic increase of ubiquitin signaling related genes in eukaryotic genomes.