Molecular characterization of a zebrafish TCF ETS-domain transcription factor

Genome-Wide Analysis and the Expression Pattern of the MADS-Box Gene Family in Bletilla striata

Bletilla striata (Thunb. ex A. Murray) Rchb. f., a species of the perennial herb Orchidaceae, has potent anti-inflammatory and antiviral biological activities. MADS-box transcription factors play critical roles in the various developmental processes of plants. Although this gene family has been extensively investigated in many species, it has not been analyzed for B. striata. In total, 45 MADS-box genes were identified from B. striata in this study, which were classified into five subfamilies (Mδ, MIKC, Mα, Mβ, and Mγ). Meanwhile, the highly correlated protein domains, motif compositions, and exon-intron structures of BsMADSs were investigated according to local B. striata databases. Chromosome distribution and synteny analyses revealed that segmental duplication and homologous exchange were the main BsMADSs expansion mechanisms. Further, RT-qPCR analysis revealed that BsMADSs had different expression patterns in response to various stress treatments. Our results provide a potential theoretical basis for further investigation of the functions of MADS genes during the growth of B. striata.

Genomic and biochemical insights into the specificity of ETS transcription factors

ETS proteins are a group of evolutionarily related, DNA-binding transcriptional factors. These proteins direct gene expression in diverse normal and disease states by binding to specific promoters and enhancers and facilitating assembly of other components of the transcriptional machinery. The highly conserved DNA-binding ETS domain defines the family and is responsible for specific recognition of a common sequence motif, 5'-GGA(A/T)-3'. Attaining specificity for biological regulation in such a family is thus a conundrum. We present the current knowledge of routes to functional diversity and DNA binding specificity, including divergent properties of the conserved ETS and PNT domains, the involvement of flanking structured and unstructured regions appended to these dynamic domains, posttranslational modifications, and protein partnerships with other DNA-binding proteins and coregulators. The review emphasizes recent advances from biochemical and biophysical approaches, as well as insights from genomic studies that detect ETS-factor occupancy in living cells.

Complexity in transcription control at the activation domain-mediator interface

Transcript elongation by polymerase II paused at the Egr1 promoter is activated by mitogen-activated protein kinase phosphorylation of the ternary complex factor (TCF) ELK1 bound at multiple upstream sites and subsequent phospho-ELK1 interaction with mediator through the MED23 subunit. Consequently, Med23 knockout (KO) nearly eliminates Egr1 (early growth response factor 1) transcription in embryonic stem (ES) cells, leaving a paused polymerase at the promoter. Med23 KO did not, however, eliminate Egr1 transcription in fibroblasts. Chromatin immunoprecipitation analysis and direct visualization of fluorescently labeled TCF derivatives and mediator subunits revealed that three closely related TCFs bound to the same control regions. The relative amounts of these TCFs, which responded differently to the loss of MED23, differed in ES cells and fibroblasts. Transcriptome analysis suggests that most genes expressed in both cell types, such as Egr1, are regulated by alternative transcription factors in the two cell types that respond differently to the same signal transduction pathways.

Ets ternary complex transcription factors

The three ternary complex factors (TCFs) Elk-1, Net and Sap-1 form a subfamily of the E twenty-six (Ets) domain transcription factors. Their characteristic property is the ability to form a ternary nucleoprotein complex with the serum response factor (SRF) over the serum response element (SRE) of the c-fos promoter. The molecular mechanisms that underlie the function and regulation of these factors have been extensively studied and the TCFs are a paradigm for the study of transcriptional regulation in response to extracellular signalling through the mitogen-activated protein (MAP) kinase pathway. As final effectors of multiple signalling pathways and components of protein complexes on immediate early promoters, they represent key elements in the complex and dynamic regulation of gene expression. This review summarises the molecular, structural and biochemical studies that have led to the understanding of the functional domains of the TCFs, ternary complex formation, transcriptional regulation, protein partners and target genes in cell lines. Finally, the emerging studies of the biological roles of the TCFs in vivo will be discussed.

Ternary complex factors: prime nuclear targets for mitogen-activated protein kinases

Ternary complex factors (TCFs), a subgroup of the ETS protein family, were first described in the context of c-fos gene regulation. Subsequently, their early identification as nuclear targets for mitogen-activated protein kinases served to exemplify the fundamental links in eukaryotic cells between growth factor-mediated signalling pathways and gene control. This article provides an overview of recent work on ternary complex factors, addressing their expression and molecular structure, as well as how selective interactions with members of other protein families serve to up-1 regulate or restrict their activity. Although only one genetic study on ternary complex factors has been published to date, unravelling of the underlying molecular events provides a basis for tentative predictions about their biological roles in mammalian organisms.

Identification of two new cytochrome P450 genes and their 5'-flanking regions from the housefly, Musca domestica

Two new cytochrome P450 cDNAs, named CYP28B1 and CYP4G13v2, and their 5'-flanking regions were cloned and sequenced from a housefly strain, ALHF. The cDNA sequences of CYP28B1 and CYP4G13v2 have open reading frames of 1449 and 1653 nucleotides encoding proteins of 483 and 551 amino acid residues, respectively. Sequence analysis shows that both CYP28B1 and CYP4G13v2 putative P450 proteins contain: (1) a highly hydrophobic N terminus; (2) a P450 protein signature motif, FXXGXRXCXG, known as the important ligand for heme binding; (3) a motif, YXXAXXXEXXR, which is a conserved P450 sequence coinciding with Helix K; and (4) a typical aromatic sequence, A(1)XXPXXA(2)XPXBA(3), which is conserved within most P450s. The 5'-flanking regions of CYP28B1 (>2kb) and CYP4G13v2 (>1 kb) were isolated from adaptor-ligated ALHF genomic DNA libraries. The transcription start points of CYP28B1 and CYP4G13v2 were mapped to 176 and 163 nucleotides upstream of the ATG translation start codon within the conserved arthropod promoter elements of TCATT and ACAGT, respectively. Possible regulatory binding sites for general transcription factors, Sp1 and AP1, were mapped in the 5' promoter regions of CYP28B1 whereas TFIID and Oct-1 were mapped in CYP4G13v2. Five conserved cis-acting elements for tissue- or cell-specific transcription regulatory factors were identified in the promoter regions of both P450 genes. A structure of five 153-nucleotide (nt) highly identical repeats and two partial repeat sequences were found in the promoter region of CYP28B1. The homologous (90% identity) sequences of the 153-nt repeat were also found in the promoter region of CYP4G13v2. The homologous sequences of the repeat in other insect P450 gene promoter regions are discussed.

Integrin beta 1 signaling is necessary for transforming growth factor-beta activation of p38MAPK and epithelial plasticity

Transforming growth factor-beta (TGF-beta) can induce epithelial to mesenchymal transdifferentiation (EMT) in mammary epithelial cells. TGF-beta-mediated EMT involves the stimulation of a number of signaling pathways by the sequential binding of the type II and type I serine/threonine kinase receptors, respectively. Integrins comprise a family of heterodimeric extracellular matrix receptors that mediate cell adhesion and intracellular signaling, hence making them crucial for EMT progression. In light of substantial evidence indicating TGF-beta regulation of various beta(1) integrins and their extracellular matrix ligands, we examined the cross-talk between the TGF-beta and integrin signal transduction pathways. Using an inducible system for the expression of a cytoplasmically truncated dominant negative TGF-beta type II receptor, we blocked TGF-beta-mediated growth inhibition, transcriptional activation, and EMT progression. Dominant negative TGF-beta type II receptor expression inhibited TGF-beta signaling to the SMAD and AKT pathways, but did not block TGF-beta-mediated p38MAPK activation. Interestingly, blocking integrin beta(1) function inhibited TGF-beta-mediated p38MAPK activation and EMT progression. Limiting p38MAPK activity through the expression of a dominant negative-p38MAPK also blocked TGF-beta-mediated EMT. In summary, TGF-beta-mediated p38MAPK activation is dependent on functional integrin beta(1), and p38MAPK activity is required but is not sufficient to induce EMT.

Tissue-specific expression of the Ets gene Xsap-1 during Xenopus laevis development

We report the cloning of Xenopus laevis Xsap-1 cDNA, encoding a member of the ternary complex factor subfamily of ETS transcription factors. The expression pattern of Xsap-1 was examined during Xenopus embryogenesis using whole-mount in situ hybridization. Spatial expression of Xsap-1 mRNA is first detected at the animal pole at the mid-blastula stage. During neurulation Xsap-1 is expressed in cells participating in neural tube formation, in the sensorial layer of the epidermal ectoderm, and in an anterior region of the ventral mesoderm. Later, Xsap-1 expression is observed in the eye, ear vesicle, branchial arches, heart, pronephros, in the somites, and the developing nervous system, such as fore-, mid-, and hindbrain as well as in the cranial ganglion X.

Transcriptional regulation of hemopoiesis

The regulation of blood cell formation, or hemopoiesis, is central to the replenishment of mature effector cells of innate and acquired immune responses. These cells fulfil specific roles in the host defense against invading pathogens, and in the maintenance of homeostasis. The development of hemopoietic cells is under stringent control from extracellular and intracellular stimuli that result in the activation of specific downstream signaling cascades. Ultimately, all signal transduction pathways converge at the level of gene expression where positive and negative modulators of transcription interact to delineate the pattern of gene expression and the overall cellular hemopoietic response. Transcription factors, therefore, represent a nodal point of hemopoietic control through the integration of the various signaling pathways and subsequent modulation of the transcriptional machinery. Transcription factors can act both positively and negatively to regulate the expression of a wide range of hemopoiesis-relevant genes including growth factors and their receptors, other transcription factors, as well as various molecules important for the function of developing cells. The expression of these genes is dependent on the complex interactions between transcription factors, co-regulatory molecules, and specific binding sequences on the DNA. Recent advances in various vertebrate and invertebrate systems emphasize the importance of transcription factors for hemopoiesis control and the evolutionary conservation of several of such mechanisms. In this review we outline some of the key issues frequently identified in studies of the transcriptional regulation of hemopoietic gene expression. In teleosts, we expect that the characterization of several of these transcription factors and their regulatory mechanisms will complement recent advances in a number of fish systems where identification of cytokine and other hemopoiesis-relevant factors are currently under investigation.

DNA binding specificity studies of four ETS proteins support an indirect read-out mechanism of protein-DNA recognition

Members of the ETS family of transcription factors are involved in several developmental and physiological processes, and, when overexpressed or misexpressed, can contribute to a variety of cancers. Each family member has a conserved DNA-binding domain that recognizes DNA sequences containing a G-G-A trinucleotide. Discrimination between potential ETS-binding sites appears to be governed by both the nucleotides flanking the G-G-A sequence and protein-protein interactions. We have used an adaptation of the "length-encoded multiplex" approach (Desjarlais, J. R., and Berg, J. M. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 11099-11103) to define DNA binding specificities for four ETS proteins: Fli-1, SAP-1, PU.1, and TEL. Our results support a model in which cooperative effects among neighboring bases flanking the central G-G-A site contribute to the formation of stable ETS/DNA complexes. These results are consistent with a mechanism for specific DNA binding that is partially governed by an indirect read-out of the DNA sequence, in which a sequence-specific DNA conformation is sensed or induced.