The current knowledge on how transcription factors (TFs), the ultimate targets and executors of cellular signalling pathways, are regulated by protein–protein interactions remains limited. Here, we performed proteomics analyses of soluble and chromatin-associated complexes of 56 TFs, including the targets of many signalling pathways involved in development and cancer, and 37 members of the Forkhead box (FOX) TF family. Using tandem affinity purification followed by mass spectrometry (TAP/MS), we performed 214 purifications and identified 2,156 high-confident protein–protein interactions. We found that most TFs form very distinct protein complexes on and off chromatin. Using this data set, we categorized the transcription-related or unrelated regulators for general or specific TFs. Our study offers a valuable resource of protein–protein interaction networks for a large number of TFs and underscores the general principle that TFs form distinct location-specific protein complexes that are associated with the different regulation and diverse functions of these TFs.

CD5 and CD6, two type I cell surface antigens predominantly expressed by T cells and a subset of B cells, have been shown to function as accessory molecules capable of modulating T cell activation. Here we report the cloning of a cDNA encoding Sp␣, a secreted protein that is highly homologous to CD5 and CD6. Sp␣ has the same domain organization as the extracellular region of CD5 and CD6 and is composed of three SRCR (scavenger receptor cysteine rich) domains. Chromosomal mapping by fluorescence in situ hybridization and radiation hybrid panel analysis indicated that the gene encoding Sp␣ is located on the long arm of human chromosome 1 at q21-q23 within contig WC1.17. RNA transcripts encoding Sp␣ were found in human bone marrow, spleen, lymph node, thymus, and fetal liver but not in non-lymphoid tissues. Cell binding studies with an Sp␣ immunoglobulin (Sp␣-mIg) fusion protein indicated that Sp␣ is capable of binding to peripheral monocytes but not to T or B cells. Sp␣-mIg was also found to bind to the monocyte precursor cell lines K-562 and weakly to THP-1 but not to U937. Sp␣-mIg also bound to the B cell line Raji and weakly to the T cell line HUT-78. These findings indicate that Sp␣, a novel secreted protein produced in lymphoid tissues, may regulate monocyte activation, function, and/or survival.Leukocyte function is regulated by a discrete number of cell surface and secreted antigens that govern leukocyte activation, proliferation, survival, cell adhesion and migration, and effector function. Among the proteins that have been shown to regulate leukocyte function are members of the SRCR 1 family. This family of proteins can be divided into two groups based upon the number of cysteine residues per SRCR domain, intron-exon organization, and domain organization (1). Group B includes the cell surface proteins CD5 (2) and CD6 (3), which are predominantly expressed by thymocytes, mature T cells, and a subset of B cells, WC1 (4, 5), which is expressed by ␥␦ T cells in cattle, and M130 (6), which is expressed by activated monocytes. Of these, only CD5 and CD6 have been studied extensively. Monoclonal antibody (mAb) cross-linking studies suggest that both CD5 and CD6 can function as accessory molecules capable of modulating T cell activation (7,8). The role of CD5 and CD6 in the regulation of T cell function is further supported by the finding that following T cell activation, Tyr residues in the cytoplasmic domain of these two proteins are transiently phosphorylated. This provides a molecular mechanism whereby the cytoplasmic domains of both CD5 and CD6 can interact with intracellular SH2 containing proteins involved in signal transduction (9). Furthermore, phenotypic analysis of a CD5-deficient murine strain showed that its T cells are hyper-responsive to stimulation (10, 11), suggesting that CD5 expression is required for the normal regulation of T cell receptor (TCR)-mediated T cell activation.CD5 and CD6 are structurally the most closely related members of the group B SRCR family of proteins (1). They are both ty...

Proteins are carriers of biological functions and the effects of atmospheric-pressure non-thermal plasmas on proteins are important to applications such as sterilization and plasma-induced apoptosis of cancer cells. Herein, we report our detailed investigation of the effects of helium-oxygen non-thermal dielectric barrier discharge (DBD) plasmas on the inactivation of lactate dehydrogenase (LDH) enzyme solutions. Circular dichroism (CD) and dynamic light scattering (DLS) indicate that the loss of activity stems from plasma-induced modification of the secondary molecular structure as well as polymerization of the peptide chains. Raising the treatment intensity leads to a reduced alpha-helix content, increase in the percentage of the beta-sheet regions and random sequence, as well as gradually decreasing LDH activity. However, the structure of the LDH plasma-treated for 300 seconds exhibits a recovery trend after storage for 24 h and its activity also increases slightly. By comparing direct and indirect plasma treatments, plasma-induced LDH inactivation can be attributed to reactive species (RS) in the plasma, especially ones with a long lifetime including hydrogen peroxide, ozone, and nitrate ion which play the major role in the alteration of the macromolecular structure and molecular diameter in lieu of heat, UV radiation, and charged particles.

Folate-mediated one-carbon metabolism (FOCM) comprises a network of interconnected folate-dependent metabolic pathways responsible for serine and glycine interconversion, de novo purine synthesis, de novo thymidylate synthesis and homocysteine remethylation to methionine. These pathways are compartmentalized in the cytosol, nucleus and mitochondria. Individual enzymes within the FOCM network compete for folate cofactors because intracellular folate concentrations are limiting. Although there are feedback mechanisms that regulate the partitioning of folate cofactors among the folate-dependent pathways, less recognized is the impact of cell cycle regulation on FOCM. This review summarizes the evidence for temporal regulation of expression, activity and cellular localization of enzymes and pathways in the FOCM network in mammalian cells through the cell cycle. This article is categorized under: Biological Mechanisms > Metabolism Physiology > Mammalian Physiology in Health and Disease.

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.

This study was undertaken to investigate the prevalence of Salmonella, Listeria monocytogenes, Staphylococcus aureus, Vibrio parahaemolyticus, and Escherichia coli O157:H7 in Chinese food products. The prevalence of these pathogens was 3.46%, 5.79%, 7%, 0.24%, and 0%, respectively. Raw meats were mainly contaminated with Salmonella (39/365, 10.7%), L. monocytogenes (26/365, 7.1%), and S. aureus (40/365, 11%), while cooked food products were mainly contaminated with L. monocytogenes (45/384, 11.7%) followed by S. aureus (12/384, 3.1%), and raw milk was mainly contaminated with S. aureus (34/209, 16.3%) and Salmonella (4/209, 1.9%). Antimicrobial resistance was evaluated in Salmonella, L. monocytogenes, and S. aureus. Antimicrobial resistance for L. monocytogenes was most frequently observed for cefotaxime (51/72, 70.8%) followed by furazolidone (40/72, 55.6%). Multiple resistance (resistance to >or=2 antibiotics) was observed for 63.9% (46/72) of L. monocytogenes isolates. Resistance of Salmonella was most frequently observed to amoxicillin (11.6%), ticarcilline (11.6%), cephalothin (11.6%), and cefuroxime (11.6%). Multiple resistance was observed for 16.3% (7/43) of the Salmonella isolates. Staphylococcus aureus was resistant to penicillin (93.1%) followed by tetracycline and oxacillin COAG (49.4% and 37.9%, respectively). About 79% (69/87) of S. aureus isolated demonstrated multiple resistance. The data showed that raw meat, cooked food products, and raw milk were most commonly contaminated with foodborne pathogens and many pathogens were resistant to different antibiotics. The study provided useful information for assessment of the possible risk posed to Chinese consumers, which has significant public health impact in China.

Background: Long non-coding RNAs (lncRNAs) are emerging as key players in gene expression that govern cell developmental processes, and thus contributing to diseases, especially cancers. Many studies have suggested that aberrant expression of lncRNAs is responsible for drug resistance, a substantial obstacle for cancer therapy. Drug resistance not only results from individual variations in patients, but also from genetic and epigenetic differences in tumors. It is reported that drug resistance is tightly modulated by lncRNAs which change the stability and translation of mRNAs encoding factors involved in cell survival, proliferation, and drug metabolism. In this review, we summarize recent advances in research on lncRNAs associated with drug resistance and underlying molecular or cellular mechanisms, which may contribute helpful approaches for the development of new therapeutic strategies to overcome treatment failure.

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