Caister Academic Press

Dictyostelium Transcriptional Activators

The CRISPR/Cas System: Emerging Technology and Application
Edited by: Muhammad Jamal
A useful and timely review of the applications of the CRISPR/Cas system across diverse fields and a discussion of novel avenues of research.
Dictyostelium Transcriptional Activators are discussed in relation to Dictyostelium Genomics and the published sequence of the Dictyostelium genome.

Dictyostelium Transcriptional Activators

Dictyostelium Transcriptional Activators and a short description of their functions.
Information from Shaulsky and Huang in Dictyostelium Genomics

Zinc fingers

Zinc fingers bind DNA through loops (fingers) that are formed when non-contiguous histidine and/or cysteine residues become associated by coordinating a Zinc ion. In addition to numerous activators that fulfill these criteria, the Zinc finger group includes two specific subgroups:

A. GATA activators.
The Dictyostelium genome contains 19 GATA activators, including stkA and comH.

B. Steroid receptors.
These activators are usually inactive in the cell. They are activated by direct binding to a small ligand, such as a steroid hormone. The steroid receptor Zinc fingers have only cysteines and no histidine residues in their Zinc binding sites. This gene family is not found in the Dictyostelium genome.

Signal Transducers and Activators of Transcription (STAT)

STAT proteins activate transcription in response to extracellular signals. Signal-mediated activation of membrane receptor-kinases leads to auto-phosphorylation of the receptor on tyrosine residues. The phosphorylated tyrosine is recognized by the SH2 domain of STAT, which then becomes activated via phosphorylation by JAK protein kinases. The modified STATs dimerize and translocate into the nucleus, where they activate transcription.
There are 7 families of mammalian STATs, all of which share an N-terminal domain involved in dimerization, a coiled-coil domain involved in protein-protein interactions, a DNA-binding domain, and a C-terminal SH2 domain.
There are 3 STATs in the Dictyostelium genome, dstA, dstB and dstC. They encode the Transcriptional Activators STATa, STATb and STATc, respectively. Dictyostelium is the simplest organism known to utilize STATs, although the STATs are probably activated differently than in other organisms because Dictyostelium does not have classical receptor-tyrosine kinases.

Helix-turn-helix (HTH)

HTH activators are a large family of DNA-binding proteins that includes bacterial and bacteriophage regulators of transcription and of plasmid copy-number.
The Dictyostelium genome contains 13 putative homeobox Transcriptional Activators.

bZIP Transcriptional Activators

bZIP activators function as obligate dimers. They are characterized by a leucine zipper, which is a stretch of amino acids where every 7th residue is a leucine. The zipper forms an amphypathic alpha helix, which is responsible for dimerization with other bZIPs. Upon interaction, the leucine residues of the two bZIPs interdigitate through hydrophobic interactions such that the two helices wrap around each other to form a coiled-coil. A basic domain near the leucine zipper provides the DNA binding activity. bZIPs bind as dimers to short inverted repeat DNA sequences. They may form homodimers and heterodimers.
There are 19 bZIPs in the Dictyostelium genome.

MADS-box Transcriptional Activators

MADS-box Transcriptional Activators also function as dimers. The MADS-box family includes the serum response factor SRF and floral-regulatory activators such as agamus. The MADS box is the DNA binding domain.
There are 4 MADS-box Transcriptional Activators in the Dictyostelium genome, including srfA

Myb Transcriptional Activators

This family contains a unique DNA binding domain which specifically recognizes the sequence 5' (C/T)AAC(G/T)G 3'. There are 36 putative MYBs in the Dictyostelium genome.

Basic Helix-Loop-Helix (bHLH) activators

Proteins of this family are characterized by two amphypathic helices connected by a loop of 12-28 amino acids. The helices present a hydrophobic aspect and a charged aspect, a configuration that allows protein-protein interactions. A basic domain near the HLH motif interacts with DNA. There are no obvious bHLH transcriptional activators in the Dictyostelium genome.

CBF/NF-Y Transcriptional Activators

Proteins of this family are also known as histone-like Transcriptional Activators. In general, their function is to bind the 5' CCAAT 3' sequence found in most eukaryotic promoters (CAAT box). These activators bind DNA as heterodimers, made by the proteins CBF-A and CBF-B. Both subunits are required for DNA binding, but they can bind each other in the absence of DNA. The Dictyostelium genome contains one putative CBF-A gene and one putative CBF-B gene.

Other activators

There are 1-3 putative members of most other major groups of Transcriptional Activators.

SNF5 Transcriptional Activators. Proteins of this family are similar to an essential component of the yeast SWI/SNF complex, which is an ATP-dependent chromatin-remodeling factor.

E2F/DP Transcriptional Activators. An E2F activator can bind DNA as a homodimer or as a heterodimer with a TDP transcription activator. The E2F DNA binding fold resembles the winged-helix DNA binding motif. In mammals it is required for proper cell-cycle progression. It binds the sequence 5' (C/G)GCGC(G/C) 3'.

WRKY Transcriptional Activators are prevalent in plants. They contain a 60 - amino acid domain that is defined by the N-terminal sequence WRKYGQK. The domain binds the DNA sequence 5' (T)(T)TGAC(C/T) 3', also known as the 'W box'.

Zinc-cluster Transcriptional Activators are known mainly in fungi. The most famous member is the yeast GAL4 transcription activator. Zinc-cluster activators contain a cysteine-rich domain that forms a binuclear Zinc cluster, where two Zinc ions are bound by six cysteine residues.

Fork Head Transcriptional Activators. These activators are found in flies, mammals and yeast but seem to be absent in Dictyostelium. They form a family of Transcriptional Activators that bind DNA through a unique DNA-binding domain of about 100 amino acids (also known as the winged-helix domain). Fork Head Transcriptional Activators bind B-DNA as monomers. There are no obvious members of this gene family in the Dictyostelium genome.

Unique Transcriptional Activators. The function of 30-50% of the genes in any sequenced genome is unknown. There is a growing notion that some of them may be species-specific Transcriptional Activators that would not be recognized as such in searches based on sequence comparisons. There are three examples of such unusual Transcriptional Activators in Dictyostelium.

A. GBF was purified as a protein capable of binding the G-box regulatory DNA sequence of several developmentally induced genes. The protein is very basic and contains two putative Zinc fingers. gbfA-null cells develop into loose aggregates but then arrest, probably due to their inability to induce post-aggregative gene expression.

B. CRTF was purified as a protein capable of binding the carA promoter. The protein contains a Zinc finger-like motif that is required for DNA binding. crtF-null cells fail to develop under standard conditions and fail to sporulate under conditions that bypass the early cAMP-signaling mechanism.

C. CbfA is a Dictyostelium protein that binds the regulatory DNA element of the retrotransposon TRE5-A. It appears to regulate the expression of other developmental genes and is required for proper developmental progression. Despite its name, it is not similar to either the A or the B subunits of the CAAT-box binding factor CBF.

Missing activators

Some of the glaring omissions are the bHLH, steroid receptors, and forkhead Transcriptional Activators. Also missing are transcription regulators carrying a BAH (Bromo-Adjacent Homology) domain, a protein-protein interaction domain mostly involved in silencing or negative regulation of transcription.

Further reading