Involvement of E3 Ligases and Deubiquitinases in the Control of HIF-α Subunit Abundance

Abstract

The ubiquitin and hypoxia-inducible factor (HIF) pathways are cellular processes involved in the regulation of a variety of cellular functions. Enzymes called ubiquitin E3 ligases perform protein ubiquitylation. The action of these enzymes can be counteracted by another group of enzymes called deubiquitinases (DUBs), which remove ubiquitin from target proteins. The balanced action of these enzymes allows cells to adapt their protein content to a variety of cellular and environmental stress factors, including hypoxia. While hypoxia appears to be a powerful regulator of the ubiquitylation process, much less is known about the impact of DUBs on the HIF system and hypoxia-regulated DUBs. Moreover, hypoxia and DUBs play crucial roles in many diseases, such as cancer. Hence, DUBs are considered to be promising targets for cancer cell-specific treatment. Here, we review the current knowledge about the role DUBs play in the control of HIFs, the regulation of DUBs by hypoxia, and their implication in cancer progression.

Keywords: DUBs; E3 ligases; HIF; Hypoxia; cancer; ubiquitylation.

Figure 1

Scheme of protein substrate ubiquitylation. This pathway requires ubiquitin (Ub) and the availability of Ub-activating (E1), Ub-conjugating (E2), and Ub-ligating (E3) enzymes. Two major classes of Ub-ligating enzymes, really interesting new gene (RING)- and homologous to the E6-AP carboxyl terminus (HECT)-domain-containing E3 ligases, are presented.

Figure 2

Schematic representation of different types of protein substrate Ub modifications together with their roles in cell functioning.

Figure 3

Cellular role of deubiquitinating enzymes (DUBs). (A) Processing of ubiquitin precursors. Ubiquitin is encoded by four genes: UBA52, RPS27, UBB, and UBC. In the case of UBA52 and RPS27, ubiquitin is produced as a precursor, where a single ubiquitin is attached to ribosomal proteins L40 or S27a. The UBC and UBB genes express precursors comprised of 3–10 single ubiquitins attached “head to tail”. The production of free ubiquitin out of the precursor forms is one of the main roles of DUBs. (B) Removal of degradative or nondegradative marks from protein substrates, therefore rescuing substrates from degradation or modulating ubiquitylation signaling. (C) Editing of ubiquitin chains by changing one type of ubiquitin signal to another (e.g., transformation of polyubiquitin tag to monoubiquitin tag). (D) Recycling that ensures ubiquitin re-enters the ubiquitin pool by preventing ubiquitin degradation in the proteasome or lysosome together with its substrate.

Figure 4

E3 Ub-ligating and deubiquitinating enzymes (DUBs) involved in hypoxia-inducible factor (HIF)-α stability and signaling. DUBs and E3 Ub ligases involved in the oxygen-dependent regulation of HIF-1α and HIF-2α degradation are depicted in red. DUBs and ubiquitin E3 ligases involved in oxygen-independent regulation of HIF degradation are depicted in black. DUBs involved in the regulation of HIF mRNA stability and/or expression are depicted in blue. Non-enzymatic and/or indirect regulations are indicated in italics.

Figure 5

Involvement of E3 ligases and DUBs in the oxygen-dependent regulation of HIF. HIF-α subunits are hydroxylated in an O₂-, Fe²⁺-, 2-oxoglutarate (2-OG)-, and ascorbate-dependent reaction. Hydroxylated HIF-α subunits are then recognized by von Hippel-Lindau (VHL), ubiquitylated, and degraded by the proteasome. VHL itself can be degraded by the E3 ligase SMURF1 (SMAD ubiquitination regulatory factor-1), which can be opposed by USP9X. VHL-mediated ubiquitylation can be antagonized by the DUBs USP20, USP8, MCPIP1, and UCHL1. E3 ligases are depicted in bold.

Figure 6

Schematic representation of HIF prolyl hydroxylases (PHDs) and factor-inhibiting HIF (FIH)) interplaying with E3 ligases and DUBs and their impact on HIF cellular abundance. Seven in absentia homologs ½ (SIAH1/2) and speckle-type POZ protein (SPOP) promote ubiquitylation of PHD1 and PHD3. So far, no E3 ligase is known for PHD2. Ankyrin repeat and SOCS box protein 4 (ASB4) and Otubain-1 (OTUB1) are hydroxylated by FIH.

Figure 7

Involvement of E3 ligases and DUBs in the oxygen-independent regulation of HIF. E3 ligases are depicted in bold. The dotted line indicates known direct interactions between an E3 ligase and DUB.

Figure 8

Regulation of DUBs by hypoxia. Hypoxia can cause either a decrease in the level of certain DUBs (depicted in red) or an increase in the level of other DUBs (depicted in blue).