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Abstract: Psoriasis is a chronic inflammatory skin disease with unknown aetiology. Infiltration of inflammatory cells as the initial event in the development of new psoriatic plaques together with the defined inflamed areas of such lesions argues for an immunological disease with a local production of a causal antigen. The auto-antigen Pso p27 is a protein expressed in the skin lesions. We recently demonstrated that Pso p27 is homologous to the core amino acid sequences of squamous cell carcinoma antigens 1 and 2 (SCCA1/2) and it is apparently generated from SCCA molecules by digestion with highly specific endoproteases. In this communication we demonstrate the generation of Pso p27 from SCCA1 with extracts from psoriatic scale and even more remarkably, the generation of Pso p27 from SCCA1 in the presence of mast cell associated chymase. These findings open up for new therapeutic strategies in psoriasis and probably also in other autoimmune diseases as Pso p27 epitopes have been detected in diseased tissues from patients with various chronic inflammatory diseases. [Copyright &y& Elsevier]

Abstract: The present work aims at identifying enzymatic activities that may contribute to the post-mortem autolysis of the ventral muscle, known as belly bursting, in herring (Clupea harengus). Gelatinolytic proteases extracted from several herring tissues and also from a sardine (Sardina pilchardus) tissue were partially characterised using gelatin zymography, inhibitor analysis, immunodetection with anti-trypsin antibody and MALDI-TOF/TOF peptide sequencing. The results indicate the presence of gelatinolytic trypsin-like serine proteases and metalloproteases in several samples including the ventral muscle of herring. MS/MS analysis gave partial sequences of peptides from some of the proteases, and these were identified as elastase, trypsin and aspartyl aminopeptidase. It is likely that belly bursting in herring is caused by leakage of enzyme-rich fluids from the intestine and/or pyloric caeca which may also contain exogenous proteases from the digestive systems of the prey. [Copyright &y& Elsevier]

We tested the hypothesis that exercise training would attenuate metabolic impairment in a model of severe cancer cachexia. We used multiple in vivo and in vitro methods to explore the mechanisms underlying the beneficial effects induced by exercise training in tumor-bearing rats. Exercise training improved running capacity, prolonged lifespan, reduced oxidative stress, and normalized muscle mass and contractile function in tumor-bearing rats. An unbiased proteomic screening revealed COP9 signalosome complex subunit 2 (COPS2) as one of the most downregulated proteins in skeletal muscle at the early stage of cancer cachexia. Exercise training normalized muscle COPS2 protein expression in tumor-bearing rats and mice. Lung cancer patients with low endurance capacity had low muscle COPS2 protein expression as compared to age-matched control subjects. To test whether decrease in COPS2 protein levels could aggravate or be an intrinsic compensatory mechanism to protect myotubes from cancer effects, we performed experiments in vitro using primary myotubes. COPS2 knockdown in human myotubes affected multiple cellular pathways, including regulation of actin cytoskeleton. Incubation of cancer-conditioned media in mouse myotubes decreased F-actin expression, which was partially restored by COPS2 knockdown. Direct repeat 4 (DR4) response elements have been shown to positively regulate gene expression. COPS2 overexpression decreased the DR4 activity in mouse myoblasts, and COPS2 knockdown inhibited the effects of cancer-conditioned media on DR4 activity. These studies demonstrated that exercise training may be an important adjuvant therapy to counteract cancer cachexia and uncovered novel mechanisms involving COPS2 to regulate myotube homeostasis in cancer cachexia. • Exercise training prolongs lifespan, reduces oxidative stress, and improves skeletal muscle function in tumor-bearing rats. • Muscle COP9 signalosome complex subunit 2 (COPS2) protein is downregulated in cancer cachexia. • Exercise training restores COPS2 protein expression to control levels. • Cancer-conditioned media decreased F-actin expression in myotubes, which is partially restored by COPS2 knockdown. • COPS2 overexpression decreases DR4 activity and COPS2 knockdown inhibits cancer-conditioned media effects on DR4 activity. [ABSTRACT FROM AUTHOR]

[Display omitted] • Proteins were extracted from brewers' spent grain (BSG) by alkaline method. • HCl and citric acid (CA) were used as protein precipitants. • CA led to lower protein content and higher carbohydrate and fat content. • The saturated/unsaturated fatty acids ratio was increased by using CA. • CA weakened emulsifying properties while enhancing foaming properties of proteins. Brewer's spent grain (BSG) is an abundant agro-industrial residue and a sustainable low-cost source for extracting proteins. The composition and functionality of BSG protein concentrates are affected by extraction conditions. This study examined the use of citric acid (CA) and HCl to precipitate BSG proteins. The resultant protein concentrates were compared in terms of their composition and functional properties. The BSG protein concentrate precipitated by CA had 10% lower protein content, 5.8% higher carbohydrate, and 5.4% higher lipid content than the sample precipitated by HCl. Hydrophilic/hydrophobic protein and saturated/unsaturated fatty acid ratios increased by 16.9% and 26.5% respectively, in the sample precipitated by CA. The formation of CA-cross-linkages was verified using shotgun proteomics and Fourier transform infrared spectroscopy. Precipitation by CA adversely affected protein solubility and emulsifying properties, while improving foaming properties. This study provides insights into the role of precipitants in modulating the properties of protein concentrates. [ABSTRACT FROM AUTHOR]

Abstract: In human cell nuclei, UNG2 is the major uracil-DNA glycosylase initiating DNA base excision repair of uracil. In activated B cells it has an additional role in facilitating mutagenic processing of AID-induced uracil at Ig loci and UNG-deficient patients develop hyper-IgM syndrome characterized by impaired class-switch recombination and disturbed somatic hypermutation. How UNG2 is recruited to either error-free or mutagenic uracil processing remains obscure, but likely involves regulated interactions with other proteins. The UNG2 N-terminal domain contains binding motifs for both proliferating cell nuclear antigen (PCNA) and replication protein A (RPA), but the relative contribution of these interactions to genomic uracil processing is not understood. Interestingly, a heterozygous germline single-nucleotide variant leading to Arg88Cys (R88C) substitution in the RPA-interaction motif of UNG2 has been observed in humans, but with unknown functional relevance. Here we demonstrate that UNG2-R88C protein is expressed from the variant allele in a lymphoblastoid cell line derived from a heterozygous germ line carrier. Enzyme activity as well as localization in replication foci of UNG2-R88C was similar to that of WT. However, binding to RPA was essentially abolished by the R88C substitution, whereas binding to PCNA was unaffected. Moreover, we show that disruption of the PCNA-binding motif impaired recruitment of UNG2 to S-phase replication foci, demonstrating that PCNA is a major factor for recruitment of UNG2 to unperturbed replication forks. Conversely, in cells treated with hydroxyurea, RPA mediated recruitment of UNG2 to stalled replication forks independently of functional PCNA binding. Modulation of PCNA- versus RPA-binding may thus constitute a functional switch for UNG2 in cells subsequent to genotoxic stress and potentially also during the processing of uracil at the immunoglobulin locus in antigen-stimulated B cells. [Copyright &y& Elsevier]

Abstract: Uracil in DNA is repaired by base excision repair (BER) initiated by a DNA glycosylase, followed by strand incision, trimming of ends, gap filling and ligation. Uracil in DNA comes in two distinct forms; U:A pairs, typically resulting from replication errors, and mutagenic U:G mismatches, arising from cytosine deamination. To identify proteins critical to the rate of repair of these lesions, we quantified overall repair of U:A pairs, U:G mismatches and repair intermediates (abasic sites and nicked abasic sites) in vitro. For this purpose we used circular DNA substrates and nuclear extracts of eight human cell lines with wide variation in the content of BER proteins. We identified the initiating uracil–DNA glycosylase UNG2 as the major overall rate-limiting factor. UNG2 is apparently the sole glycosylase initiating BER of U:A pairs and generally initiated repair of almost 90% of the U:G mismatches. Surprisingly, TDG contributed at least as much as single-strand selective monofunctional uracil–DNA glycosylase 1 (SMUG1) to BER of U:G mismatches. Furthermore, in a cell line that expressed unusually high amounts of TDG, this glycosylase contributed to initiation of as much as ∼30% of U:G repair. Repair of U:G mismatches was generally faster than that of U:A pairs, which agrees with the known substrate preference of UNG-type glycosylases. Unexpectedly, repair of abasic sites opposite G was also generally faster than when opposite A, and this could not be explained by the properties of the purified APE1 protein. It may rather reflect differences in substrate recognition or repair by different complex(es). Lig III is apparently a minor rate-regulator for U:G repair. APE1, Pol β, Pol δ, PCNA, XRCC1 and Lig I did not seem to be rate-limiting for overall repair of any of the substrates. These results identify damaged base removal as the major rate-limiting step in BER of uracil in human cells. [Copyright &y& Elsevier]

Highlights: [•] We analyzed error sources in genomic uracil assays. [•] We present a method that ameliorates possible technical shortcomings. [•] Nucleotides co-eluted in DNA isolation step, causing overestimation. [•] In vitro cytosine deamination to uracil caused overestimation. [•] We report 400–600 uracils per genome in repair-proficient cells. [ABSTRACT FROM AUTHOR]

The transcription factor interferon regulatory factor-3 (IRF3) regulates expression of type I interferon-β and plays an important role in antiviral immunity. Despite the biological importance of IRF3, its in vivo phosphorylation pattern has not been reported. In this study, we have identified residues in IRF3 that are phosphorylated in vivo after infection with Sendai virus. We found that Sendai virus induced phosphorylation of the C-terminal residues Thr390 and Ser396, in addition to either Ser385 or Ser386. Moreover, Ser173 and Ser175 were constitutively phosphorylated. Ser396 has previously been suggested to be the major target of the IRF3-activating kinase TBK1 (TANK-binding kinase- 1), whereas Thr390 has not previously been implicated in IRF3 regulation. Mutagenesis studies indicated that phosphorylation of Thr390 promotes Ser396 phosphorylation and binding to the coactivator cAMP-response element-binding protein. Taken together, our results show that IRF3 is subject to multiple interdependent phosphorylations, and we identify Thr390 as a novel in vivo phosphorylation site that modulates the phosphorylation status of TBK1-targeted Ser396. [ABSTRACT FROM AUTHOR]

The Escherichia coli AlkB protein and human homologs hABH2 and hABH3 are 2-oxoglutarate (2OG)/Fe(II)-dependent DNA/RNA demethylases that repair 1-methyladenine and 3-methylcytosine residues. Surprisingly, hABH1, which displays the strongest homology to AlkB, failed to show repair activity in two independent studies. Here, we show that hABH1 is a mitochondrial protein, as demonstrated using fluorescent fusion protein expression, immunocytochemistry, and Western blot analysis. A fraction is apparently nuclear and this fraction increases strongly if the fluorescent tag is placed at the N-terminal end of the protein, thus interfering with mitochondrial targeting. Molecular modeling of hABH1 based upon the sequence and known structures of AlkB and hABH3 suggested an active site almost identical to these enzymes. hABH1 decarboxylates 2OG in the absence of a prime substrate, and the activity is stimulated by methylated nucleotides. Employing three different methods we demonstrate that hABH1 demethylates 3-methyl-cytosine in single-stranded DNA and RNA in vitro. Site-specific mutagenesis confirmed that the putative Fe(II) and 2OG binding residues are essential for activity. In conclusion, hABH1 is a functional mitochondrial AlkB homolog that repairs 3-methyl-cytosine in single-stranded DNA and RNA. [ABSTRACT FROM AUTHOR]