Heather P. Ostendorff

The histone deacetylase inhibitor valproic acid selectively induces proteasomal degradation of HDAC2

Histone‐modifying enzymes play essential roles in physiological and aberrant gene regulation. Since histone deacetylases (HDACs) are promising targets of cancer therapy, it is important to understand the mechanisms of HDAC regulation. Selective modulators of HDAC isoenzymes could serve as efficient and well‐tolerated drugs. We show that HDAC2 undergoes basal turnover by the ubiquitin–proteasome pathway. Valproic acid (VPA), in addition to selectively inhibiting the catalytic activity of class I HDACs, induces proteasomal degradation of HDAC2, in contrast to other inhibitors such as trichostatin A (TSA). Basal and VPA‐induced HDAC2 turnover critically depend on the E2 ubiquitin conjugase Ubc8 and the E3 ubiquitin ligase RLIM. Ubc8 gene expression is induced by both VPA and TSA, whereas only TSA simultaneously reduces RLIM protein levels and therefore fails to induce HDAC2 degradation. Thus, poly‐ubiquitination and proteasomal degradation provide an isoenzyme‐selective mechanism for downregulation of HDAC2.

Ubiquitination-dependent cofactor exchange on LIM homeodomain transcription factors

The interactions of distinct cofactor complexes with transcription factors are decisive determinants for the regulation of gene expression. Depending on the bound cofactor, transcription factors can have either repressing or transactivating activities. To allow a switch between these different states, regulated cofactor exchange has been proposed; however, little is known about the molecular mechanisms that are involved in this process. LIM homeodomain (LIM-HD) transcription factors associate with RLIM (RING finger LIM domain-binding protein) and with CLIM (cofactor of LIM-HD proteins; also known as NLI, Ldb and Chip) cofactors. The co-repressor RLIM inhibits the function of LIM-HD transcription factors, whereas interaction with CLIM proteins is important for the exertion of the biological activity conferred by LIM-HD transcription-factors. Here we identify RLIM as a ubiquitin protein ligase that is able to target CLIM cofactors for degradation through the 26S proteasome pathway. Furthermore, we demonstrate a ubiquitination-dependent association of RLIM with LIM-HD proteins in the presence of CLIM cofactors. Our data provide a mechanistic basis for cofactor exchange on DNA-bound transcription factors, and probably represent a general mechanism of transcriptional regulation.

Orchestrating nuclear functions: ubiquitin sets the rhythm

The nucleus of the eukaryotic cell must carry out many functions simultaneously. These tasks include ensuring that the cell is continuously supplied with an appropriate, changing set of proteins on its way through cell divisions and differentiation. During these processes, the integrity of the genetic material must be maintained against a constant onslaught of damaging physiological and environmental factors. Fulfilling these complex tasks requires the dynamic integration and synchronization of different nuclear functions. Protein modification by ubiquitin is proving to be a crucial tool for nuclear functioning, and is emerging as a decisive mechanism that enables the concerted regulation of nuclear pathways.

Multiple functions of LIM domain-binding CLIM/NLI/Ldb cofactors during zebrafish development

The crucial involvement of CLIM/NLI/Ldb cofactors for the exertion of the biological activity of LIM homeodomain transcription factors (LIM-HD) has been demonstrated. In this paper we show that CLIM cofactors are widely expressed during zebrafish development with high protein levels in specific neuronal cell types where LIM-HD proteins of the Isl class are synthesized. The overexpression of a dominant-negative CLIM molecule (DN-CLIM) that contains the LIM interaction domain (LID) during early developmental stages of zebrafish embryos results in an impairment of eye and midbrain-hindbrain boundary (MHB) development and disturbances in the formation of the anterior midline. On a cellular level we show that the outgrowth of peripheral but not central axons from Rohon Beard (RB) and trigeminal sensory neurons is inhibited by DN-CLIM overexpression. We demonstrate a further critical role of CLIM cofactors for axonal outgrowth of motor neurons. Additionally, DN-CLIM overexpression causes an increase of Isl-protein expression levels in specific neuronal cell types, likely due to a protection of the DN-CLIM/LIM-HD complex from proteasomal degradation. Our results demonstrate multiple roles of the CLIM cofactor family for the development of entire organs, axonal outgrowth of specific neurons and protein expression levels.

Proteasomal selection of multiprotein complexes recruited by LIM homeodomain transcription factors

Complexes composed of multiple proteins regulate most cellular functions. However, our knowledge about the molecular mechanisms governing the assembly and dynamics of these complexes in cells remains limited. The in vivo activity of LIM homeodomain (LIM-HD) proteins, a class of transcription factors that regulates neuronal development, depends on the high-affinity association of their LIM domains with cofactor of LIM homeodomain proteins (LIM-HDs) (CLIM, also known as Ldb or NLI). CLIM cofactors recruit single-stranded DNA-binding protein 1 (SSDP1, also known as SSBP3), and this interaction is important for the activation of the LIM-HD/CLIM protein complex in vivo. Here, we identify a cascade of specific protein interactions that protect LIM-HD multiprotein complexes from proteasomal degradation. In this cascade, CLIM stabilizes LIM-HDs, and SSDP1 stabilizes CLIM. Furthermore, we show that stabilizing cofactors prevent binding of ubiquitin ligases to multiple protein interaction domains in LIM-HD recruited protein complexes. Together, our results indicate a combinatorial code that selects specific multiprotein complexes via proteasomal degradation in cells with broad implications for the assembly and specificity of multiprotein complexes.

Dynamic expression of LIM cofactors in the developing mouse neural tube

The developmental regulation of LIM homeodomain transcription factors (LIM‐HD) by the LIM domain‐binding cofactors CLIM/Ldb/NLI and RLIM has been demonstrated. Whereas CLIM cofactors are thought to be required for at least some of the in vivo functions of LIM‐HD proteins, the ubiquitin ligase RLIM functions as a negative regulator by its ability to target CLIM cofactors for proteasomal degradation. In this report, we have investigated and compared the protein expression of both factors in the developing mouse neural tube. We co‐localize both proteins in many tissues and, although widely expressed, we detect high levels of both cofactors in specific neural tube regions, e.g., in the ventral neural tube, where motor neurons reside. The mostly ubiquitous distribution of RLIM‐ and CLIM‐encoding mRNA differs from the more specific expression of both cofactors at the protein level, indicating post‐transcriptional regulation. Furthermore, we show that both cofactors not only co‐localize with each other but also with Isl and Lhx3 LIM‐HD proteins in developing ventral neural tube neurons. Our results demonstrate the dynamic expression of cofactors participating in the regulation of LIM‐HD proteins during the development of the neural tube in mice and suggest additional post‐transcriptional regulation in the nuclear LIM‐HD protein network. Developmental Dynamics 235:786–791, 2006.

Expression of the zebrafish recognition molecule F3/F11/contactin in a subset of differentiating neurons is regulated by cofactors associated with LIM domains

We have identified a zebrafish homolog of the F3/F11/contactin (F3) recognition molecule. The gene shares 55% amino acid identity with F3 molecules in other vertebrates. Expression of F3 mRNA is first detectable at 16 h post-fertilization (hpf) in trigeminal and Rohon-Beard neurons. At 18-24 hpf, additional weaker expression is present in discrete cell clusters in the hindbrain, in the anterior lateral line/acoustic ganglion and in spinal motor neurons. Transcription factors of the LIM homeodomain class (LIM-HD) and their associated cofactors CLIM/NLI/Ldb (CLIM) have been implicated in the development of peripheral axons of trigeminal and Rohon-Beard neurons. We demonstrate that ectopic overexpression of a dominant-negative CLIM molecule early during zebrafish development strongly reduces expression of F3 mRNA in these neurons indicating regulation of F3 by the LIM-HD protein network. These results and the spatiotemporal correlation of F3 expression with axonal differentiation in a subset of primary neurons suggest an important role of F3 for axon growth.

Expression of the zebrafish recognition molecule F3/F11/contactin in a subset of differentiating neurons is regulated by cofactors associated with LIM domains.

We have identified a zebrafish homolog of the F3/F11/contactin (F3) recognition molecule. The gene shares 55% amino acid identity with F3 molecules in other vertebrates. Expression of F3 mRNA is first detectable at 16 h post-fertilization (hpf) in trigeminal and Rohon-Beard neurons. At 18-24 hpf, additional weaker expression is present in discrete cell clusters in the hindbrain, in the anterior lateral line/acoustic ganglion and in spinal motor neurons. Transcription factors of the LIM homeodomain class (LIM-HD) and their associated cofactors CLIM/NLI/Ldb (CLIM) have been implicated in the development of peripheral axons of trigeminal and Rohon-Beard neurons. We demonstrate that ectopic overexpression of a dominant-negative CLIM molecule early during zebrafish development strongly reduces expression of F3 mRNA in these neurons indicating regulation of F3 by the LIM-HD protein network. These results and the spatiotemporal correlation of F3 expression with axonal differentiation in a subset of primary neurons suggest an important role of F3 for axon growth.