The CCR4-NOT complex is a highly conserved, multifunctional machinery controlling mRNA metabolism. Its components have been implicated in several aspects of mRNA and protein expression, including transcription initiation, elongation, mRNA degradation, ubiquitination, and protein modification. In this review, we will focus on the role of the CCR4-NOT complex in mRNA degradation. The complex contains two types of deadenylase enzymes, one belonging to the DEDD-type family and one belonging to the EEP-type family, which shorten the poly(A) tails of mRNA. We will review the present state of structure-function analyses into the CCR4-NOT deadenylases and summarize current understanding of their roles in mRNA degradation. We will also review structural and functional work on the Tob/BTG family of proteins, which are known to interact with the CCR4-NOT complex and which have been reported to suppress deadenylase activity in vitro.
Animals ; Humans ; Multiprotein Complexes ; chemistry ; genetics ; metabolism ; Protein Conformation ; RNA, Messenger ; genetics ; metabolism ; Transcription Factors ; chemistry ; genetics ; metabolism

Saussurea medusa is a rare traditional Chinese medicinal herb. Besides anti-inflammatory and analgesic activities, it has effects of disinhibiting cold, dispelling dampness and promoting blood circulation. Flavonoids are the main medicinal compounds in S. medusa. Contents of flavonoids and expression of flavonoids biosynthesis related genes in white and red (induced by low temperature, high sucrose and high light) callus were analyzed. The results showed that the total flavone in red line was 3.60 times higher compared to white line. The accumulation of rutin in red line (0.25% of dry weight) was 2.40 times higher compared to white line. Anthocyanins were abundant in red line, with the contents of cyanidin 3-O-glucosidechloride and cyanidin 3-O-succinyl glycoside 0.12% and 0.19% of dry weight respectively. CHS, F3'H, FNS, FLS, DFR and ANS genes were highly expressed in red line compared to white line. Expression of three transcription factors (MYB, bHLH and WD40) in red line was significantly higher than that in white line, especially the expression of MYB (19.70 times higher compared to white line). These results indicated that high expression levels of transcription factors induced high expression of structural genes in red line, thereby enhancing the flavonoids biosynthesis. The expression of bHLH and WD40 was similar, whereas it was significantly different from that of MYB, indicating that bHLH and WD40 could form a binary complex to regulate expression of structural genes and flavonoids biosynthesis.
Anthocyanins ; chemistry ; Cell Line ; Flavonoids ; chemistry ; Glucosides ; chemistry ; Plant Proteins ; genetics ; metabolism ; Plants, Medicinal ; chemistry ; Saussurea ; chemistry ; genetics ; Transcription Factors ; genetics ; metabolism

Animals ; Chromosomal Proteins, Non-Histone ; chemistry ; genetics ; metabolism ; Humans ; Models, Molecular ; Mutation ; Transcription Factors ; chemistry ; genetics ; metabolism

Transcription factor is one of the key factors in the regulation of gene expression at the transcriptional level. It plays an important role in plant growth, active components biosynthesis and response to environmental change. This paper summarized the structure and classification of bHLH transcription factors and elaborated the research progress of bHLH transcription factors which regulate the active components in plants, such as flavonoids, alkaloids, and terpenoids. In addition, the possibility of increasing the concentration of active substances by bHLH in medicinal plants was assessed. The paper emphasized great significance of model plants and multidisciplinary research fields including modern genomics, transcriptomics, metabolomics and bioinformatics, providing the contribution to improve the discovery and function characterization of bHLH transcription factors. Accelerating the research in the mechanism of bHLH transcription factors on the regulation of active components biosynthesis will promote the development of breeding and variety improvement of Chinese medicinal materials, also ease the pressure of resources exhaustion of traditional Chinese medicine home and abroad.
Alkaloids ; biosynthesis ; Basic Helix-Loop-Helix Transcription Factors ; chemistry ; classification ; genetics ; metabolism ; Flavonoids ; biosynthesis ; Plants, Medicinal ; genetics ; metabolism ; Terpenes ; metabolism

In this new era of the genome, the complete sequences of various organisms (from the simplest to the most complex such as human) are now available, which provides new opportunities to study biology and to develop therapeutic strategies. But the paucity of research tools that manipulate specific genes in vivo represents a major limitation of functional genomic studies. In nature, the expression of genes is regulated at the transcriptional level primarily by proteins that bind to nucleic acids. Many of these proteins, which are termed transcription factors, are typically consist of two essential yet separable modules: DNA-binding domain (DBD) and effector domain (ED). Attempts to control the gene expression by artificial transcription factors are based on the application of this rule. Among the many naturally occurring DNA-binding domains, the Cys2-His2 zinc-finger domain has demonstrated the greatest potential for the design of novel sequence-specific DNA-binding proteins. Each zinc finger domain, which comprises about 30 amino acids that adopt a compact structure by chelating a zinc ion, typically functions by binding 3 base pairs of DNA sequence. Several zinc fingers linked together would bind proportionally longer DNA sequences. Ideally, these artificial DNA binding proteins could be designed to specifically target and regulate one single gene within a genome as complex as that found in human. Such proteins would be powerful tools in basic and applied research.
DNA ; chemistry ; genetics ; metabolism ; DNA-Binding Proteins ; metabolism ; Gene Expression Regulation ; Humans ; Transcription Factors ; chemistry ; genetics ; metabolism ; Zinc Fingers ; genetics ; physiology

This article reviewed key genes that involved in fatty acid synthesis and triacylglycerol assembly pathway. The transcription factors which play important roles in seed development and oil content were also reviewed. We summarized the achievement in modifying fatty acid composition and increase oil content in plant by gene engineering using these genes.
Fatty Acids ; biosynthesis ; genetics ; Genetic Engineering ; methods ; Plant Oils ; chemistry ; Plants, Genetically Modified ; genetics ; metabolism ; Seeds ; genetics ; metabolism ; Transcription Factors ; genetics ; Triglycerides ; analysis ; biosynthesis ; genetics

Hypoxia-inducible factor (HIF-1) is an oxygen-dependent transcriptional activator, which plays crucial roles in the angiogenesis of tumors and mammalian development. HIF-1 consists of a constitutively expressed HIF-1beta subunit and one of three subunits (HIF-1alpha, HIF-2alpha or HIF-3alpha). The stability and activity of HIF-1alpha are regulated by various post-translational modifications, hydroxylation, acetylation, and phosphorylation. Therefore, HIF-1alpha interacts with several protein factors including PHD, pVHL, ARD-1, and p300/CBP. Under normoxia, the HIF-1alpha subunit is rapidly degraded via the von Hippel-Lindau tumor suppressor gene product (pVHL)- mediated ubiquitin-proteasome pathway. The association of pVHL and HIF-1alpha under normoxic conditions is triggered by the hydroxylation of prolines and the acetylation of lysine within a polypeptide segment known as the oxygen-dependent degradation (ODD) domain. On the contrary, in the hypoxia condition, HIF-1alpha subunit becomes stable and interacts with coactivators such as p300/CBP to modulate its transcriptional activity. Eventually, HIF-1 acts as a master regulator of numerous hypoxia-inducible genes under hypoxic conditions. The target genes of HIF-1 are especially related to angiogenesis, cell proliferation/survival, and glucose/iron metabolism. Moreover, it was reported that the activation of HIF-1alpha is closely associated with a variety of tumors and oncogenic pathways. Hence, the blocking of HIF-1a itself or HIF-1alpha interacting proteins inhibit tumor growth. Based on these findings, HIF-1 can be a prime target for anticancer therapies. This review summarizes the molecular mechanism of HIF-1a stability, the biological functions of HIF-1 and its potential applications of cancer therapies.
Alternative Splicing ; Gene Expression Regulation ; Gene Therapy ; Growth Substances/metabolism ; Humans ; Protein Isoforms/chemistry/genetics/*metabolism ; Protein Subunits/genetics/metabolism ; Research Support, Non-U.S. Gov't ; Signal Transduction/physiology ; Transcription Factors/chemistry/genetics/*metabolism ; Transcription, Genetic

BACKGROUNDT cell factor-4 (TCF-4) plays an important role in development and carcinogenesis. Recently, the role of TCF-4 has been described in colon cancer and other cancers. However, whether TCF-4 plays a similar role in lung cancer is unknown. To answer this question, we studied the expression of TCF-4 protein and mRNA in non-small-cell lung cancer (NSCLC) and the relation of TCF-4 expression pattern to histological type and cell differentiation.

METHODSTissue samples from sixty cases of pathologically diagnosed NSCLC and eight normal tissue samples were obtained between September 2001 and March 2003. Immunohistochemistry was used to investigate the distribution of TCF-4 protein. The staining patterns of the tumors were divided into 4 categories: nuclear staining alone or nuclear staining greater than cytoplasmic staining; cytoplasmic staining or cytoplasmic staining greater than nuclear staining; equal nuclear and cytoplasmic staining; no nuclear staining or cytoplasmic staining. The integrated optical density (OD) values of all sections were analyzed by UIC MetaMorph image analysis software. The expression of TCF-4 mRNA was detected by one-step reverse transcription-polymerase chain reaction (RT-PCR). The integrated density values of the PCR products were analyzed semi-quantitatively.

RESULTSImmunohistochemistry showed that there was no expression of TCF-4 in normal tissue. However, TCF-4 was expressed in 86.7% (52/60) of NSCLC samples, mainly in the nuclei of tumor cells. Furthermore, there was a significant difference in TCF-4 localization patterns between squamous cell carcinomas and adenocarcinomas (P < 0.05). The integrated OD values of TCF-4 expression was significantly higher in tumors with moderate-poor cell differentiation than in well differentiated tumors (51.63 +/- 6.67 vs 46.13 +/- 12.31, P < 0.01). There was no TCF-4 mRNA expression in normal tissue. However, 63.9% (23/36) of carcinoma samples expressed TCF-4 mRNA. TCF-4 mRNA expression was significantly higher in tumors with moderate-poor cell differentiation than in well differentiated tumors (P < 0.05). There were no significant differences in mRNA expression in comparison with histological type.

CONCLUSIONSThe sub-cellular distribution of TCF-4 may correlate with NSCLC histological type. High expression of TCF-4 mRNA and protein may be associated with the degree of cell differentiation in NSCLC.

Carcinoma, Non-Small-Cell Lung ; chemistry ; Cytoskeletal Proteins ; metabolism ; Female ; Humans ; Immunohistochemistry ; Lung Neoplasms ; chemistry ; Male ; Middle Aged ; RNA, Messenger ; analysis ; TCF Transcription Factors ; Trans-Activators ; metabolism ; Transcription Factor 7-Like 2 Protein ; Transcription Factors ; analysis ; genetics ; beta Catenin

mPem, a homeobox gene, is expressed in a time and stage specific manner during murine ontogeny. Pem transcripts are abundant in 7- and 8-day mouse embryos, but decrease precipitously thereafter. On Day 9 they become abundant in placenta and yolk sac, persisting there until parturition. Although Pem transcripts are not detectable in most of adult tissues, they are present in reproductive system such as testis, epididymis and ovary. This indicates a important role for Pem during embryogenesis and reproductive development. To study the function of mPem protein, we used a GAL4 based yeast two-hybrid assay to screen a 7-day mouse embryo library with full-length of mPem. 3 proteins were found interacting with mPem protein. One of theses is Mdfic. We confirmed the interaction between mPem and Mdfic in yeast and in vitro. Mdfic, MyoD family inhibitor domain containing, encodes the myoD family inhibitor domain (I-mfa domain). The interaction between mPem and Mdfic suggested they maybe form the transcriptional regulator complex to regulate embryo differentiation.
Animals ; Embryo, Mammalian ; Embryonic Development ; Female ; Genes, Homeobox ; genetics ; Homeodomain Proteins ; chemistry ; metabolism ; Mice ; Pregnancy ; Protein Binding ; Transcription Factors ; chemistry ; metabolism ; Two-Hybrid System Techniques

The core promoter is an important yet often overlooked component in the regulation of transcription by RNA polymerase II. In fact, the core promoter is the ultimate target of action of all of the factors and coregulators that control the transcriptional activity of every gene. In this review, I describe our current knowledge of a downstream core promoter element termed the DPE, which is a TFIID recognition site that is conserved from Drosophila to humans. The DPE is located from +28 to +32 relative to the +1 transcription start site, and is mainly present in core promoters that lack a TATA box motif. Moreover, in Drosophila, the DPE appears to be about as common as the TATA box. There are distinct mechanisms of basal transcription from DPE- versus TATA-dependent core promoters. For instance, NC2/Dr1-Drap1 is a repressor of TATA-dependent transcription and an activator of DPE-dependent transcription. In addition, DPE-specific and TATA-specific transcriptional enhancers have been identified. These findings further indicate that the core promoter is an active participant in the regulation of eukaryotic gene expression.
Animals ; Base Sequence ; DNA-Binding Proteins/metabolism ; Enhancer Elements (Genetics) ; Feedback, Biochemical ; Gene Expression Regulation ; Human ; Models, Genetic ; *Promoter Regions (Genetics) ; RNA Polymerase II/*metabolism ; Transcription Factors/chemistry/genetics/*metabolism ; *Transcription, Genetic