Control of cyclin C levels during development of Dictyostelium

Loss of Cln3 function in the social amoeba Dictyostelium discoideum causes pleiotropic effects that are rescued by human CLN3

The neuronal ceroid lipofuscinoses (NCL) are a group of inherited, severe neurodegenerative disorders also known as Batten disease. Juvenile NCL (JNCL) is caused by recessive loss-of-function mutations in CLN3, which encodes a transmembrane protein that regulates endocytic pathway trafficking, though its primary function is not yet known. The social amoeba Dictyostelium discoideum is increasingly utilized for neurological disease research and is particularly suited for investigation of protein function in trafficking. Therefore, here we establish new overexpression and knockout Dictyostelium cell lines for JNCL research. Dictyostelium Cln3 fused to GFP localized to the contractile vacuole system and to compartments of the endocytic pathway. cln3⁻ cells displayed increased rates of proliferation and an associated reduction in the extracellular levels and cleavage of the autocrine proliferation repressor, AprA. Mid- and late development of cln3⁻ cells was precocious and cln3⁻ slugs displayed increased migration. Expression of either Dictyostelium Cln3 or human CLN3 in cln3⁻ cells suppressed the precocious development and aberrant slug migration, which were also suppressed by calcium chelation. Taken together, our results show that Cln3 is a pleiotropic protein that negatively regulates proliferation and development in Dictyostelium. This new model system, which allows for the study of Cln3 function in both single cells and a multicellular organism, together with the observation that expression of human CLN3 restores abnormalities in Dictyostelium cln3⁻ cells, strongly supports the use of this new model for JNCL research.

The cyclin-dependent kinase family in the social amoebozoan Dictyostelium discoideum

Cyclin-dependent kinases (Cdk) are a family of serine/threonine protein kinases that regulate eukaryotic cell cycle progression. Their ability to modulate the cell cycle has made them an attractive target for anti-cancer therapies. Cdk protein function has been studied in a variety of Eukaryotes ranging from yeast to humans. In the social amoebozoan Dictyostelium discoideum, several homologues of mammalian Cdks have been identified and characterized. The life cycle of this model organism is comprised of a feeding stage where single cells grow and divide mitotically as they feed on their bacterial food source and a multicellular developmental stage that is induced by starvation. Thus it is a valuable system for studying a variety of cellular and developmental processes. In this review I summarize the current knowledge of the Cdk protein family in Dictyostelium by highlighting the research efforts focused on the characterization of Cdk1, Cdk5, and Cdk8 in this model Eukaryote. Accumulated evidence indicates that each protein performs distinct functions during the Dictyostelium life cycle with Cdk1 being required for growth and Cdk5 and Cdk8 being required for processes that occur during development. Recent studies have shown that Dictyostelium Cdk5 shares attributes with mammalian Cdk5 and that the mammalian Cdk inhibitor roscovitine can be used to inhibit Cdk5 activity in Dictyostelium. Together, these results show that Dictyostelium can be used as a model system for studying Cdk protein function.

Dynamic acetylation of lysine-4-trimethylated histone H3 and H3 variant biology in a simple multicellular eukaryote

Dynamic acetylation of all lysine-4-trimethylated histone H3 is a complex phenomenon involved in Immediate-early gene induction in metazoan eukaryotes. Higher eukaryotes express repeated copies of three closely related H3 variants, inaccessible to genetic analysis. We demonstrate conservation of these phenomena in Dictyostelium which has three single-copy H3 variant genes. Although dynamic acetylation is targeted to two H3 variants which are K4-trimethylated, K9-acetylation is preferentially targeted to one. In cells lacking Set1 methyltransferase and any detectable K4-trimethylation, dynamic acetylation is lost demonstrating a direct link between the two. Gene replacement to express mutated H3 variants reveals a novel interaction between K4-trimethylation on different variants. Cells expressing only one variant show defects in growth, and in induction of a UV-inducible gene, demonstrating the functional importance of variant expression. These studies confirm that dynamic acetylation targeted to H3K4me3 arose early in evolution and reveal a very high level of specificity of histone variant utilization in a simple multicellular eukaryote.

3.6-KB mouse cyclin C promoter fragment is predominantly active in the testis

Cyclin C is a highly conserved protein that regulates cell-cycle, messenger RNA transcription and cell adhesion. Recently published studies demonstrate that this protein is an essential player during early embryonic development of multicellular eukaryotes as well. In order to understand better its complex function at the level of tissues or organs, spatial expression characteristics of cyclin C and regulatory components of its expression are needed to be determined. In vitro studies on human cells suggested that approximately the first 3 kilobases of the cyclin C promoter might contain all the regulatory elements that might mimic transcription of cyclin C. To test the hypothesis, we generated reporter transgenic lines where the first 3.6-kilobase region of mouse cyclin C promoter fragment drives the transcription of a marker gene. Messenger RNA levels of the marker gene and cyclin C isoforms were measured in nine organs with reverse transcription coupled quantitative realtime polymerase chain reaction and their expression patterns were compared. The marker gene is predominantly transcribed in testes and does not follow the transcriptional regulation of the examined cyclin C isoforms. Thus, the isolated promoter fragment alone is not sufficient for the complete physiological modulation of cyclin C RNA levels, however, it is capable of enhancing testicular transcription which can be exploited in future applications.

Dysregulation of CDK8 and Cyclin C in tumorigenesis

Appropriately controlled gene expression is fundamental for normal growth and survival of all living organisms. In eukaryotes, the transcription of protein-coding mRNAs is dependent on RNA polymerase II (Pol II). The multi-subunit transcription cofactor Mediator complex is proposed to regulate most, if not all, of the Pol II-dependent transcription. Here we focus our discussion on two subunits of the Mediator complex, cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC), because they are either mutated or amplified in a variety of human cancers. CDK8 functions as an oncoprotein in melanoma and colorectal cancers, thus there are considerable interests in developing drugs specifically targeting the CDK8 kinase activity. However, to evaluate the feasibility of targeting CDK8 for cancer therapy and to understand how their dysregulation contributes to tumorigenesis, it is essential to elucidate the in vivo function and regulation of CDK8-CycC, which are still poorly understood in multi-cellular organisms. We summarize the evidence linking their dysregulation to various cancers and present our bioinformatics and computational analyses on the structure and evolution of CDK8. We also discuss the implications of these observations in tumorigenesis. Because most of the Mediator subunits, including CDK8 and CycC, are highly conserved during eukaryotic evolution, we expect that investigations using model organisms such as Drosophila will provide important insights into the function and regulation of CDK8 and CycC in different cellular and developmental contexts.

Mediator complex proteins are required for diverse developmental processes

The Mediator complex serves a crucial function in gene regulation, forming a link between gene-specific transcription factors and RNA polymerase II. Most protein-coding genes therefore require Mediator complex activity for transcriptional regulation. Given the essential functions performed by Mediator complex proteins in gene regulation, it is not surprising that mutations in Mediator complex genes disrupt animal and plant development. What is more intriguing is that the phenotypes of individual Mediator complex mutants are distinct from each other, demonstrating that certain developmental processes have a greater requirement for specific Mediator complex genes. Additionally, the range of developmental processes that are altered in Mediator complex mutants is broad, affecting a variety of cell types and physiological systems. Gene expression defects in Mediator complex mutants reveal distinct roles for individual Mediator proteins in transcriptional regulation, suggesting that the deletion of one Mediator complex protein does not interfere with transcription in general, but instead alters the expression of specific target genes. Mediator complex proteins may have diverse roles in different organisms as well, as mutants in the same Mediator gene in different species can display dissimilar phenotypes.

Targets downstream of Cdk8 in Dictyostelium development

Background

Cdk8 is a component of the mediator complex which facilitates transcription by RNA polymerase II and has been shown to play an important role in development of Dictyostelium discoideum. This eukaryote feeds as single cells but starvation triggers the formation of a multicellular organism in response to extracellular pulses of cAMP and the eventual generation of spores. Strains in which the gene encoding Cdk8 have been disrupted fail to form multicellular aggregates unless supplied with exogenous pulses of cAMP and later in development, cdk8^- cells show a defect in spore production.

Results

Microarray analysis revealed that the cdk8^- strain previously described (cdk8^-_HL) contained genome duplications. Regeneration of the strain in a background lacking detectable gene duplication generated strains (cdk8^-₂) with identical defects in growth and early development, but a milder defect in spore generation, suggesting that the severity of this defect depends on the genetic background. The failure of cdk8^- cells to aggregate unless rescued by exogenous pulses of cAMP is consistent with a failure to express the catalytic subunit of protein kinase A. However, overexpression of the gene encoding this protein was not sufficient to rescue the defect, suggesting that this is not the only important target for Cdk8 at this stage of development. Proteomic analysis revealed two potential targets for Cdk8 regulation, one regulated post-transcriptionally (4-hydroxyphenylpyruvate dioxygenase (HPD)) and one transcriptionally (short chain dehydrogenase/reductase (SDR1)).

Conclusions

This analysis has confirmed the importance of Cdk8 at multiple stages of Dictyostelium development, although the severity of the defect in spore production depends on the genetic background. Potential targets of Cdk8-mediated gene regulation have been identified in Dictyostelium which will allow the mechanism of Cdk8 action and its role in development to be determined.