Current Protein and Peptide Science - Volume 7, Issue 2, 2006

Azo dyes, which are characterized by one or more azo bonds, are a predominant class of colorants used in tattooing, cosmetics, foods, and consumer products. These dyes are mainly metabolized by bacteria to colorless aromatic amines, some of which are carcinogenic, by azoreductases that catalyze a NAD(P)H-dependent reduction. The resulting amines are further degraded aerobically by bacteria. Some bacteria have the ability to degrade azo dyes both aerobically and anaerobically. Plant-degrading white rot fungi can break down azo dyes by utilizing a number of oxidases and peroxidases as well. In yeast, a ferric reductase system participates in the extracellular reduction of azo dyes. Recently, two types of azoreductases have been discovered in bacteria. The first class of azoreductases is monomeric flavin-free enzymes containing a putative NAD(P)H binding motif at their N-termini; the second class is polymeric flavin dependent enzymes which are studied more extensively. Azoreductases from bacteria represent novel families of enzymes with little similarity to other reductases. Dissociation and reconstitution of the flavin dependent azoreductases demonstrate that the non-covalent bound flavin prosthetic group is required for the enzymatic functions. In this review, structures and carcinogenicity of azo colorants, protein structure, enzymatic function, and substrate specificity, as well as application of the azo dyes and azoreductases will be discussed.

Insulin-resistance is a major problem associated with diabetes and that is increasing rapidly worldwide. Insulin is a peptide hormone secreted by the β-cells of the pancreatic islets of Langerhans in response to increased circulating levels of glucose and amino acids and it is essential for appropriate tissue development, growth, and maintenance of wholebody glucose homeostasis by regulating carbohydrate, lipid and protein metabolism. Insulin resistance is a defect in signal transduction. The signaling mechanisms involved in the various biologic responses to insulin remain somewhat elusive. This review focuses on the structure and activity of insulin receptor, inheritance of insulin resistance, insulin receptor and alleles, enzyme activity in insulin resistance, insulin receptor in phosphorylation and relating substrate. We have discussed insulin receptor substrate-family (IRS) related to insulin resistance, detail downstream signaling effects, GLUT4 vesicle translocation and related events, cytokine-mediated insulin resistance, and feedback control mechanisms. This review also focuses on insulin resistance in obesity-linked metabolic syndrome, insulin resistance related to plasma membrane disturbances and insulin resistance for exercise and cellular integrity. Finally, we can conclude that insulin resistance is really a complex phenomenon in which several genetic defects combine with environmental stresses.

EBNA 3C is one of only nine proteins expressed by the tumourigenic γ-herpesvirus Epstein-Barr virus (EBV) during the infection and immortalization of human B lymphocytes. In fact, the expression of EBNA 3C has been shown to be essential for the B-cell transformation process to take place. The mechanism by which EBNA 3C contributes to viral pathogenicity has therefore been the subject of intensive research over many years. The first clues on the function of EBNA 3C came from analysis of the primary amino acid sequence of EBNA 3C which identified a number of domains commonly found in transcriptional regulatory proteins. These domains include a proline-rich and a glutamine-proline-rich domain and a putative bZIP domain located in the N-terminus of the protein. EBNA 3C has subsequently been shown to function as a regulator of both viral and cellular transcription and to have potent effects on normal cell-cycle regulatory pathways. This review will discuss our current knowledge of the functions of EBNA 3C, the roles played by the different domains of EBNA 3C in these functions, and summarize some recent work from our laboratory that provides the first structural and functional analysis of the putative bZIP domain of EBNA 3C.

In the past two decades a large initiative has been put forth to understand the biological and pathogenic properties of the human T-cell lymphotropic virus type 1 (HTLV-1); this has ultimately led to the development of various experimental vaccination and therapeutic strategies to combat HTLV-1 infection. The focus of this work is to outline key targets for the design of therapeutics for HTLV-1, such as fusion mediated by the envelope glycoprotein, and to discuss reports of novel vaccines or therapeutics. These strategies include peptide, recombinant protein, DNA, and viral vectors. The final focus of this review is to acquaint the reader with vaccine approaches developed in our laboratory over the last decade. These strategies include the development of envelope glycoprotein derived B-cell epitopes for the induction of neutralizing antibodies, as well as a strategy to generate a multivalent cytotoxic T-lymphocyte (CTL) response against the HTLV-1 Tax antigen.

By utilizing recently developed full-length cDNA technologies, large-scale cDNA sequencing was carried out by several cDNA projects. Now full-length cDNA resources cover the major part of the protein-coding human genes. Comprehensive analyses of the collected full-length cDNA data revealed not only the complete sequences of thousands of novel gene transcripts but also novel alternatively spliced isoforms of hitherto identified genes. However, it was not as easy as expected to deduce their encoded amino acid sequences based solely on the full-length cDNA sequences. It was neither always the case that the longest open reading frame corresponded to the real protein coding region nor that the first ATG was the translation initiator codon. Also, proteome-wide mass-spectrometry analysis has shown that there is an unexpectedly large population of small proteins, encoded by so-called upstream open reading frames, within the cell. Since sound manual annotations by experts were still indispensable to address these problems, an international meeting to make transcriptome-wide functional annotations of cDNAs was held, namely the H-invitational. In this meeting, functional annotations were made both manually and computationally for most of the pre-existing full-length cDNAs collected from world-wide cDNA projects. The achieved integrated information for each of the cDNAs was published as a database. It was also shown that the full-length cDNA data were useful for identifying alternative splicing variants, exact transcriptional start sites of the mRNAs and the adjacent promoter regions. Rapidly accumulating genome data as well as versatile use of the transcriptome information will shortly lay a firm foundation for proteome-level understanding of human gene networks.

The application of recombinant immunotoxin and radioimmunoconjugate in Cancer therapy has revived the "magic bullet" concept predicted a century ago. Many of the recombinant antibodies have received FDA approval for various indication of cancer in recent years and numerous others are in clinical trials.

The ubiquitin-mediated protein degradation pathway exerts a wide spectrum of effects and modulates a variety of biological processes including cell cycle progression, transcriptional regulation, signal transduction, antigen presentation, apoptosis (or programmed cell death), oncogenesis, preimplantation, and DNA repair. Recently, the importance of deubiquitination mechanism has been emerged as an essential regulatory step to control these cellular mechanisms for homeostasis. Even though a number of deubiquitinating enzymes have recently been isolated, relatively little is known about their substrates and biological functions. Identified from yeast to human, deubiquitinating (DUB) enzymes are classified into the ubiquitin C-terminal hydrolase (UCH), the ubiquitin-specific processing proteases (UBP or USP), Jab1/Pad1/MPN domain containing metallo-enzymes (JAMM), Otu domain ubiquitin-aldehyde binding proteins (OTU), and Ataxin-3/Josephin domain containing proteins (Ataxin-3/Josephin). Several members of a novel DUB subfamily induced by cytokines in murine lymphocytes have recently been identified. In addition, human DUB enzyme DUB-3, highly homologous to USP17 and induced by cytokines interleukin (IL)-4 and IL-6, has been recently isolated and showed that it has significant homology to the known murine DUB subfamily members. Interestingly, both murine DUB and human USP17 subfamily members are localized and clustered on murine chromosome 7 and on human chromosomes 4 and 8, respectively. This review introduces the reader to provide a great understanding of cytokine-inducible DUB enzymes in both mouse and human, and new insights into DUB subfamily members.