Upstream Binding Protein Research Articles

Autoantibodies and their clinical characteristics in systemic sclerosis

Systemic sclerosis (SSc) is a connective tissue disorder characterized by microvascular damage and excessive fibrosis of the skin and internal organs with autoimmune background. One representative feature of the immunological abnormalities in SSc patients is the presence of antinuclear antibodies (ANA). More than 90% of patients with SSc are positive for ANA. Although a role of ANA in the pathogenesis in SSc remains unclear, the particular ANA are often indicative of clinical feature, disease course, and overall severity. Therefore, subgrouping patients based on the type of autoantibodies present can be useful in diagnosis and management. Anticentromere antibody (ACA), anti-DNA topoisomerase I antibody (Ab), and anti-RNA polymerase Ab are the representative autoAbs found in patients with SSc. Other serum ANA found in SSc include anti-Th/To Ab, anti-U3RNP Ab, anit-human upstream-binding protein (hUBF) Ab, anti-centriole Ab, anti-U1RNP Ab, anti-Ku Ab, and anti-PM-Scl Ab. It is documented that the prevalence of SSc-related Abs and clinical characteristics of patients with SSc are influenced by ethnicity. Identifying several SSc-related Abs requires a complicated technique that include immunoprecipitation assay. Establishment of a system routinely available to screen ANA specificities such as enzyme-linked immunosorbent assay is needed.

Far upstream element binding protein 1: a commander of transcription, translation and beyond

The far upstream binding protein 1 (FBP1) was first identified as a DNA-binding protein that regulates c-Myc gene transcription through binding to the far upstream element (FUSE) in the promoter region 1.5 kb upstream of the transcription start site. FBP1 collaborates with TFIIH and additional transcription factors for optimal transcription of the c-Myc gene. In recent years, mounting evidence suggests that FBP1 acts as an RNA-binding protein and regulates mRNA translation or stability of genes, such as GAP43, p27(Kip) and nucleophosmin. During retroviral infection, FBP1 binds to and mediates replication of RNA from Hepatitis C and Enterovirus 71. As a nuclear protein, FBP1 may translocate to the cytoplasm in apoptotic cells. The interaction of FBP1 with p38/JTV-1 results in FBP1 ubiquitination and degradation by the proteasomes. Transcriptional and post-transcriptional regulations by FBP1 contribute to cell proliferation, migration or cell death. FBP1 association with carcinogenesis has been reported in c-Myc dependent or independent manner. This review summarizes biochemical features of FBP1, its mechanism of action, FBP family members and the involvement of FBP1 in carcinogenesis.

Upstream binding protein 1 (UBP1)

Upstream binding protein 1 (UBP1)

2‐D DIGE profiling of hepatocellular carcinoma tissues identified isoforms of far upstream binding protein (FUBP) as novel candidates in liver carcinogenesis

Hepatocellular carcinoma (HCC) is a major cause of cancer worldwide and is often characterized by aggressive tumour behaviour and poor prognosis. One of the major etiologies is hepatitis B or C virus (HBV or HCV) infections. In order to better comprehend the molecular mechanisms involved in HCC progression, we performed a systematic analysis on moderately and poorly differentiated human HCC tissues using 2-D DIGE coupled to MALDI-TOF/TOF MS. A total of 52 and 26 proteins were found to be dysregulated in moderately and poorly differentiated HCC tissues, respectively. For the first time, the over-expression of a novel protein family, far upstream binding proteins (FUBPs) was identified in both stages of HCC and confirmed by western blots. FUBPs are of particular interest due to their transcriptional activity on the oncogene, c-myc. It has generally been accepted that c-myc plays an important role in HCC progression but its exact activators remain poorly understood. Interestingly, we also observed elevated c-myc levels in the tissues used in this study by western blot analysis. We therefore propose that the FUBP family of proteins may be one of the possible upstream players that are involved in modulating the c-myc levels in HCC tumorigenesis.

Validation of Far Upstream Binding Protein (FUBP) Isoforms in Human Hepatocellular Carcinoma Samples Using MRM Initiated Detection and Sequencing (MIDAS) Approach

The over-expression of a novel protein family, far upstream binding proteins (FUBPs) was identified in human hepatocellular carcinoma (HCC) for the first time. They were obtained first by using two dimensional-difference gel electrophoresis (2D-DIGE.) coupled with mass spectrometry (MS). A complementary approach using a four-plex isobaric tagging off-line two dimensional liquid chromatography tandem mass spectrometry (4-plex iTRAQ off-line 2-D LC/MS/MS) was also conducted and these same FUBP isoforms were found to be regulated. Confirmation of these protein isoforms was first performed using western blots but this approach was dependent on the availability of antibodies against FUBP. Thus an alternative and faster approach using MIDAS methodology was also implemented to validate these protein isoforms. We report here that MIDAS could distinguish successfully the two FUBP isoforms in HCC, and at the same time provide quantification data which can be compared with all the quantification techniques employed here.

2-D DIGE Profiling of Hepatocellular Carcinoma Tissues Identified Isoforms of Far Upstream Binding Protein (FUBP) as Novel Candidates in Liver Carcinogenesis

2-D DIGE Profiling of Hepatocellular Carcinoma Tissues Identified Isoforms of Far Upstream Binding Protein (FUBP) as Novel Candidates in Liver Carcinogenesis

Dissection of the essential steps for condensin accumulation at kinetochores and rDNAs during fission yeast mitosis

The condensin complex has a fundamental role in chromosome dynamics. In this study, we report that accumulation of Schizosaccharomyces pombe condensin at mitotic kinetochores and ribosomal DNAs (rDNAs) occurs in multiple steps and is necessary for normal segregation of the sister kinetochores and rDNAs. Nuclear entry of condensin at the onset of mitosis requires Cut15/importin α and Cdc2 phosphorylation. Ark1/aurora and Cut17/Bir1/survivin are needed to dock the condensin at both the kinetochores and rDNAs. Furthermore, proteins that are necessary to form the chromatin architecture of the kinetochores (Mis6, Cnp1, and Mis13) and rDNAs (Nuc1 and Acr1) are required for condensin to accumulate specifically at these sites. Acr1 (accumulation of condensin at rDNA 1) is an rDNA upstream sequence binding protein that physically interacts with Rrn5, Rrn11, Rrn7, and Spp27 and is required for the proper accumulation of Nuc1 at rDNAs. The mechanism of condensin accumulation at the kinetochores may be conserved, as human condensin II fails to accumulate at kinetochores in hMis6 RNA interference–treated cells.

DNA Micro-Array Gene Expression Profiling of Angiogenesis in Collagen Gel Culture

We examined angiogenesis-related gene expression profiles using collagen gel culture and a DNA chip. After isolation of total RNA from cultures before and after capillary tube formation, a mouse whole-genome array study was performed. Seventy-three out of over 35,000 transcripts were expressed after capillary tube formation. The majority of genes did not show any significant differences between before and after capillary tube formation. However, there were 7 upregulated genes; tumor necrosis factor alpha-induced protein (Tnfαip) 2, vascular endothelial growth factor b (Vegfb), corticotropin releasing hormone receptor (Crhr) 2, vascular endothelial growth factor C (Vegfc), fi broblast growth factor (Fgf) 6, protein O-fucosyltransferase (Pofut) 1, hypoxia inducible factor 1 alpha subunit (Hif-1a). Eleven down-regulated genes were identified; ras homolog gene family member B (RhoB), Fgf-2, Thrombospondin (Thbs) 1, Angiogenin (Ang) 3, guanine nucleotide binding protein alpha (Gna) 13, tumor necrosis factor receptor superfamily member 12a (Tnfrsf12a), plasminogen (Plg), Elk3, upstream binding protein (Ubp) 1, integrin alpha V (Itgav), mitogen activated protein kinase (Mapk) 14. These up- and down-regulated genes identified in this study offer the strategies which improve the myocardial substrate during and following a myocardial infarction, such as the regrowth of functional blood vessels to the ischemic myocardium.

General expression vectors for Staphylococcus carnosus enabled efficient production of the outer membrane protein A of Klebsiella pneumoniae.

General expression vectors, designed for intracellular expression or secretion of recombinant proteins in the non-pathogenic Staphylococcus carnosus, were constructed. Both vector systems encode two different affinity tags, an upstream albumin binding protein and a downstream hexahistidyl peptide, and are furnished with cleavage sites for two site-specific proteases for optional affinity tag removal. To evaluate the novel vectors, the gene encoding the outer membrane protein A (OmpA) of Klebsiella pneumoniae was introduced into the vectors. Efficient production was demonstrated in both systems, although, as expected for OmpA fusions, somewhat better intracellularly, and the fusion proteins could be recovered as full-length products by affinity chromatography.

General expression vectors for Staphylococcus carnosus enabled efficient production of the outer membrane protein A of Klebsiella pneumoniae

General expression vectors, designed for intracellular expression or secretion of recombinant proteins in the non-pathogenic Staphylococcus carnosus, were constructed. Both vector systems encode two different affinity tags, an upstream albumin binding protein and a downstream hexahistidyl peptide, and are furnished with cleavage sites for two site-specific proteases for optional affinity tag removal. To evaluate the novel vectors, the gene encoding the outer membrane protein A (OmpA) of Klebsiella pneumoniae was introduced into the vectors. Efficient production was demonstrated in both systems, although, as expected for OmpA fusions, somewhat better intracellularly, and the fusion proteins could be recovered as full-length products by affinity chromatography.

Recombination Hot Spot of Hepatitis B Virus Genome Binds to Members of the HMG Domain Protein Family and the Y Box Binding Protein Family; Implication of These Proteins in Genomic Instability

Objective: Previously we hypothesized that the occurrence of hepatocellular carcinoma (HCC) is enhanced by genomic instability induced by the integrated hepatitis B virus (HBV) DNA. Using an in vitro recombination assay, we showed that a subgenomic fragment of HBV DNA designated 15AB (nt1855–1914) is indispensable for in vitro recombination, and also showed the existence of 15AB binding protein. On the assumption that the 15AB binding protein may be a candidate cellular recombinogenic protein which accelerates genomic instability and hepatocarcinogenesis, we tried to isolate it by southwestern screening. Results and Conclusion: We obtained several positive clones including mouse upstream binding factor (UBF) and DNA binding protein A (dbpA). UBF belongs to an HMG domain protein family and dbpA belongs to a Y box binding protein family. 15AB binding seemed to be mediated by the conserved DNA binding domains in these families, because other members in the families such as HMG1 and YB-1 also bound to 15AB. We report them here because several documents have already suggested the possible association of these families and DNA recombination.