3.3 | Ubiquitin-like microproteins
Several groups recently reported the discovery of ubiquitin-like
microproteins. In one example, the ubiquitin pseudogene UBBP4 was
reported to be translated. Interestingly, UBBP4 encodes three
ubiquitin variants within two independent open reading frames, and mass
spectrometric evidence uniquely identifying all three have been
previously obtained. The UBBP4 ubiquitin-like proteins exhibit
high sequence similarity to canonical ubiquitin, with 1 (variant
Ubbp4A1), 4 (Ubbp4B1 or
UbKEKS), or 8 amino acid substitutions
(Ubbp4A2). Ubbp4A2 and
UbKEKS retain a functional C-terminal diglycine motif
and can be covalently conjugated to high molecular weight cellular
proteins, while UbbpA1 was predominantly observed as a
monomer. Despite being ~700-fold less abundant than
canonical ubiquitin, UbKEKS modifies a specific subset
of cellular proteins including lamins, and, rather than promoting
proteasomal degradation, may be important for regulating target protein
localization and/or function.
In 2020 the TINCR RNA, which was previously classified as
noncoding, was shown to encode an 87-amino acid microprotein with 85%
sequence homology to ubiquitin. The microprotein translated fromTINCR RNA, termed pTINCR or TUBL, was predicted to adopt a
ubiquitin-like fold (Figure 4D). This prediction was confirmed in a
recent crystal structure of pTINCR, which revealed an overall
ubiquitin-like fold with a positively charged N-terminal domain
hypothesized to enable interaction with other biomolecules (Figure 4E).
Due to the lack of a C-terminal diglycine motif, pTINCR is a type II
ubiquitin-like protein that associates with ubiquitin-binding proteins
rather than being covalently attached to proteins. pTINCR is expressed
in skin, and mice lacking pTINCR exhibit a mild delay in wound healing.
Importantly, two reports have identified pTINCR as a tumor suppressor in
cutaneous squamous cell carcinoma and other epithelial cancers. pTINCR
is upregulated after DNA damage-induced p53 activation, and it is
frequently lost or mutated in squamous cell carcinoma. It normally
promotes differentiation of keratinocytes and other epithelial cell
types via its interaction with SUMOylated Cdc42. Consequently, mouse
embryonic stem cell-derived teratomas overexpressing pTINCR exhibit
decreased growth and increased keratin deposition consistent with
involvement in differentiation of skin cells. Along the same lines,
pTINCR overexpression inhibits the proliferation of squamous cell
carcinoma cells in culture and in xenografts. Additionally, mice
heterozygous for Xpc that lack pTINCR are DNA damage
repair-deficient and exhibit increased formation of invasive skin
papillomas and squamous cell carcinomas relative to Xpcheterozygous/pTINCR wild-type mice upon UV exposure. Overall, pTINCR is
a type II ubiquitin-like microprotein that is required for keratinocyte
differentiation and acts as a tumor suppressor in squamous cell
carcinoma.