Proteomics-Based Trapping to Study Substrates of Histone Deacetylase 6 Catalytic Domain 1

Histone
deacetylase 6 (HDAC6) is linked with various cellular functions,
such as gene expression and protein degradation, as well as many diseases,
including breast cancers and Alzheimer’s disease. HDAC6 removes
the acetyl group of acetyllysine from histones to regulate gene expression
in the nucleus. However, with predominant localization in the cytoplasm,
various cytoplasmic substrates of HDAC6 have also been identified.
HDAC6 is unique among the other 11 metal-dependent HDAC family members
due to the presence of two independent and active deacetylase domains.
Recently, an inactive mutant of HDAC6 has been used as a trap to discover
substrates of the second catalytic domain (CD2). Here, substrates
of the first catalytic domain (CD1) of HDAC6 were explored using trapping
mutants and proteomics analysis, with 21 putative substrates identified.
Among them, the E3 ubiquitin ligase HUWE1 was validated as a novel
HDAC6 substrate. Specifically, E3 ligase HUWE1 was deacetylated by
HDAC6 CD1 to elevate degradation activity. HDAC6 CD1 also regulated
the protein levels of E3 ligase UBR5. These studies document the interplay
between protein deacetylation and degradation by HDAC6 CD1, which
is consistent with a model where HDAC6 CD1-mediated deacetylation
influences protein degradation via E3 ligases.