Ubiquitin
The Many Roles of Ubiquitin
Different types of UB modifications are capable of transmitting unique signals. Ubiquitinylation can be used to modify a protein’s activity, to change its subcellular location, or to alter protein-protein interactions. The addition of a single UB molecule (mono-ubiquitinylation) is a reversible modification used to alter the function and localisation of key proteins in several processes, including transcription, histone function, and membrane trafficking. The addition of poly-UB chains linked via Lys(6) or Lys(63) residues may also modulate a protein’s function or location; in particular, Lys(63) poly-UB-linked proteins are known to be involved in processes such as signalling DNA repair and DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation. The structural differences achieved by attaching different types of UB modifications may account for their unique differences in signalling capabilities. The type of UB modification attached to a target protein is determined through the E2 and E3 enzymes. Often processes are controlled by a combination of UB-associated methods; for instance, frequent targets of ubiquitinylation are transcription factors, whose function is modulated both by UB-induced degradation, as well as by UB-controlled nuclear-cytoplasmic trafficking of transcription factors and modified substrates.
A few of the processes that non-proteolytic ubiquitinylation is involved in are listed below:
Protein processing
Lys(6) poly-UB chains can be recognised by the 26S proteasome as processing signals, rather than degradation signals. For example, Lys(6) poly-ubiquitinylation of the breast and ovarian cancer tumour suppressor BRCA1 will be edited and de-ubiquitinylated by the 26S proteasome (stabilised) rather than degraded.
Cell signalling
Ubiquitinylation can reversibly alter the way a protein is recognised by a cell, much in the same way as occurs with modifications by phosphorylation. These modifications can affect a variety of different signalling systems. For example, Lys(63) poly-UB-linked chains can signal activation of the IkBa kinase (IKK) in the inflammatory signalling pathway. IKK activation causes the degradation of IkBa, which leads to the activation and translocation of the transcription factor NFkB to the nucleus, where it activates the genes required to mount an inflammatory response.
Transcription regulation
Histone modifications are key determinants in gene expression, in part through providing interaction surfaces for proteins that impact on chromatin accessibility. These modifications include acetylation, methylation, phosphorylation and ubiquitinylation, and they often work synergistically. Modifications on different histones, or at different positions within a histone, can have opposite effects. The mono-ubiquitinylation of histone H2B is required for gene activation, possibly by the recruitment of an acetyltransferase complex. Ubiquitinylated H2B is also required for histone H3 methylation at positions Lys(4) and Lys(79), which in turn is necessary for histone activation and subsequent gene expression.
X inactivation
The ubiquitinylation of histone H2A has an opposite effect to that of H2B, namely gene silencing. Histone H2A ubiquitinylation is an abundant modification (5-15% of total H2A) in higher eukaryotes, and occurs on the inactive X chromosome in female mammals. H2A ubiquitinylation is associated with the recruitment of Polycomb repressor complex 1 (PRC1) of the Polycomb group (PcG) proteins, which are memory factors involved in chromatin-related heritable gene silencing. Two of the core PRC1 proteins, PSC and dRING, have a RING finger domain that is characteristic of UB and of certain E3 ligases. It is unclear whether H2A ubiquitinylation also plays a part in the methylation of histone H3 at position Lys(27), which is central to PcG-dependent silencing.
DNA damage tolerance
Lys(63) poly-UB-modifications are known to be involved in the tolerance of DNA damage. These modifications occur on the DNA polymerase processing factor PCNA (proliferating cell nuclear antigen), which trimerises to encircle the template DNA strand during replication to serve as a scaffold for accessory factors. The access of accessory proteins to PCNA is partly determined by the type of PCNA UB-modification, which in turn determines the fate of the DNA lesion. Mono-ubiquitinylation of PCNA can lead to the recruitment of a trans-lesion polymerise that instigates an error-prone method of DNA lesion bypass, whereas poly-Lys(63) ubiquitinylation of PCNA leads to an error-free process that may involve a poly-UB-dependent switch of the DNA template strand.
Membrane trafficking
Many signalling receptors and adaptor proteins require mono-ubiquitinylation to recruit proteins of the endocytic and exocytic pathways, and for sorting cargo for vesicular trafficking. For instance, mono-ubiquitinylation acts as a signal for receptor endocytosis and for targeting to the lysosomes, where non-UB-mediated proteolysis occurs. Genetic defects that act to disrupt UB-controlled sorting of cargo for trafficking are often linked to aberrations in cell growth, and may result in oncogenic transformation. For example, c-Cbl is an E3 ligase that attaches UB to tyrosine-phosphorylated receptors for the epidermal growth factor (EGF), thereby accelerating their internalisation in tiny membranous sacs called endosomes - these endosomes are either delivered to the lysosome for degradation, or recycled back to the cell membrane. Cancer-causing c-Cbl mutants have been found to either block receptor internalisation or enhance recycling of active receptors. On the negative side, UB is involved in enabling viruses such as HIV and Ebola to make their way to the cell surface after replicating inside the cell.