Protein Tagging, Destruction and Infection.

Cells possess protein quality control mechanisms to maintain proper cellular homeostasis. In eukaryotes, the roles of the ubiquitination and proteasome-mediated degradation of cellular proteins is well established. Recent studies have elucidated protein tagging mechanisms in prokaryotes, involving transfer messenger RNA (tmRNA) and pupylation. In this review, newer insights and bioinformatics analysis of two distinct bacterial protein tagging machineries are discussed. The machinery for tmRNAmediated tagging is present in several eubacterial representatives, e.g. Escherichia coli, Mycobacterium tuberculosis, Bacillus subtilis etc., but not in two archaeal representatives, such as Thermoplasma acidophilum and Sulfolobus solfataricus. On the other hand, the machinery involving tagging with the prokaryotic ubiquitin-like protein (Pup) is absent in most bacteria but is encoded in some eubacterial representatives, e.g. Mycobacterium tuberculosis and Mycobacterium leprae. Furthermore, molecular details on the relationship between protein tagging and enzymes involved in protein degradation in bacteria during infection are emerging. Several pathogenic bacteria that do not express the major ATP-dependent proteases, Lon and Caseinolytic protease (ClpP), are avirulent. Also, some ATP-independent peptidases, such as PepA and PepN, modulate the infection process. The roles of bacterial proteins involved in tagging and degradation during infection are discussed. These aspects add a new dimension to better understanding of the peculiarities of host-pathogen interactions.

Cereblon and its downstream substrates as molecular targets of immunomodulatory drugs.

Thalidomide was first developed as a sedative around 60 years ago, but exhibited teratogenicity, leading to serious defects such as limb deformities. Nevertheless, thalidomide is now recognized as a therapeutic drug for the treatment of Hansen's disease and myeloma. Immunomodulatory drugs (IMiDs), a new class of anti-cancer drug derived from thalidomide, have also been developed and exert potent anti-cancer effects. Although the molecular mechanism of thalidomide and IMiDs remained unclear for a long time, cereblon, a substrate receptor of the CRL4 E3 ubiquitin ligase was identified as a primary direct target by a new affinity technique. A growing body of evidence suggests that the effect of IMiDs on myeloma and other cancer cells is mediated by CRBN. Each IMiD binds to CRBN and alters the substrate specificity of the CRBN E3 ubiquitin ligase complex, resulting in breakdown of intrinsic downstream proteins such as Ikaros and Aiolos. Here we give an overview of the current understanding of mechanism of action of IMiDs via CRBN and prospects for the development of new drugs that degrade protein of interest.

Local antimicrobial, protease and cytokine defense systems in psoriatic skin.

BACKGROUND: Psoriasis vulgaris is an inflammatory skin condition characterized by dramatic biochemical and immunological changes. AIMS: The aim of the study was to evaluate antimicrobial response, tissue degeneration reactions and distribution of inflammatory cytokines in untreated psoriatic skin as well as the correlations between these factors and influence on the course of the disease. METHODS: We evaluated skin samples obtained from routine punch biopsies in 40 patients with psoriasis vulgaris. All tissue specimens were examined by hematoxylin and eosin staining and immunohistochemistry for human beta defensin 2 (HBD-2), matrix metalloproteinase 2 (MMP-2), tumor necrosis factor-alpha (TNF-alpha), interleukin 6 (IL-6) and IL-8. The staining intensity was semi-quantitatively graded. RESULTS: Numerous keratinocytes, fibroblasts and macrophages expressed HBD-2 while the number of MMP-2-positive macrophages, fibroblasts and epitheliocytes varied. TNF-alpha-positive cells varied from a few to numerous in each microscopic field. IL-6-positive cells varied from a few to abundant and IL-8-positive cells from numerous to abundant in each field. LIMITATIONS: This study had a rather small patient number. CONCLUSIONS: Psoriatic skin shows a strong correlative increase in skin antimicrobial proteins and enzymes mediating tissue degeneration suggesting that the skin maintains compensatory mechanisms during persistent remodeling. While individual notable decrease in antimicrobial proteins was observed in some tissue samples, generally the increased human beta defensin associated with psoriasis is likely to be due to an altered immune status. TNF-alpha, IL-6 and IL-8 are common cytokines expressed in psoriatic skin plaques to maintain the inflammatory cycle. HBD-2, MMP-2 and TNF-alpha positively correlate with the severity of psoriasis. Meanwhile, the expression of IL-8 significantly decreases with clinically more severe psoriasis, perhaps making these factors candidate prognostic factors for psoriatic inflammation.

The thalidomide-binding domain of cereblon defines the CULT domain family and is a new member of the ß-tent fold.

Despite having caused one of the greatest medical catastrophies of the last century through its teratogenic side-effects, thalidomide continues to be an important agent in the treatment of leprosy and cancer. The protein cereblon, which forms an E3 ubiquitin ligase compex together with damaged DNA-binding protein 1 (DDB1) and cullin 4A, has been recently indentified as a primary target of thalidomide and its C-terminal part as responsible for binding thalidomide within a domain carrying several invariant cysteine and tryptophan residues. This domain, which we name CULT (cereblon domain of unknown activity, binding cellular ligands and thalidomide), is also found in a family of secreted proteins from animals and in a family of bacterial proteins occurring primarily in δ-proteobacteria. Its nearest relatives are yippee, a highly conserved eukaryotic protein of unknown function, and Mis18, a protein involved in the priming of centromeres for recruitment of CENP-A. Searches for distant homologs point to an evolutionary relationship of CULT, yippee, and Mis18 to proteins sharing a common fold, which consists of two four-stranded ß-meanders packing at a roughly right angle and coordinating a zinc ion at their apex. A ß-hairpin inserted into the first ß-meander extends across the bottom of the structure towards the C-terminal edge of the second ß-meander, with which it forms a cradle-shaped binding site that is topologically conserved in all members of this fold. We name this the ß-tent fold for the striking arrangement of its constituent ß-sheets. The fold has internal pseudosymmetry, raising the possibility that it arose by duplication of a subdomain-sized fragment.

Deciphering the mystery of thalidomide teratogenicity.

Thalidomide was originally developed in 1954 as a sedative that was commonly used to ameliorate morning sickness. However, thalidomide exposure during the first trimester of pregnancy caused multiple birth defects (e.g. phocomelia and amelia), affecting ≈ 10,000 children worldwide in the late 1950s and early 1960s. Thalidomide is now recognized as a clinically effective, albeit strictly restricted, drug for the treatment of leprosy and multiple myeloma. Investigators have studied thalidomide teratogenicity for half a century, proposing over 30 hypotheses to account for its actions. Among these, the anti-angiogenesis and oxidative stress models have gained widespread support. Nonetheless, the precise molecular mechanisms and direct targets of thalidomide have not heretofore been elucidated. We developed ferrite-glycidyl methacrylate beads that enable magnetic separation and efficient purification of ligand-binding molecules; the beads were recently employed to identify cereblon as a primary target of thalidomide. Cereblon forms an E3 ubiquitin ligase complex with DDB1, Cul4A, and Roc1, which is important for the expression of fibroblast growth factor 8, an essential regulator of limb development. Expression of a drug binding-deficient mutant of cereblon suppressed thalidomide-induced effects in zebrafish and chicks. This suggests that thalidomide downregulates fibroblast growth factor 8 expression and induces limb malformation by binding to wild-type cereblon, inhibiting the function of the associated E3 ubiquitin ligase. The present review summarizes the teratogenicity of thalidomide, including existing models for its mode of action, and discusses the identification of cereblon as a key molecule for deciphering the longstanding mystery of thalidomide teratogenicity.

Teratogenic effects of thalidomide: molecular mechanisms.

Fifty years ago, prescription of the sedative thalidomide caused a worldwide epidemic of multiple birth defects. The drug is now used in the treatment of leprosy and multiple myeloma. However, its use is limited due to its potent teratogenic activity. The mechanism by which thalidomide causes limb malformations and other developmental defects is a long-standing question. Multiple hypotheses exist to explain the molecular mechanism of thalidomide action. Among them, theories involving oxidative stress and anti-angiogenesis have been widely supported. Nevertheless, until recently, the direct target of thalidomide remained elusive. We identified a thalidomide-binding protein, cereblon (CRBN), as a primary target for thalidomide teratogenicity. Our data suggest that thalidomide initiates its teratogenic effects by binding to CRBN and inhibiting its ubiquitin ligase activity. In this review, we summarize the biology of thalidomide, focusing on the molecular mechanisms of its teratogenic effects. In addition, we discuss the questions still to be addressed.

Rhomboid homologs in mycobacteria: insights from phylogeny and genomic analysis.

BACKGROUND: Rhomboids are ubiquitous proteins with diverse functions in all life kingdoms, and are emerging as important factors in the biology of some pathogenic apicomplexa and Providencia stuartii. Although prokaryotic genomes contain one rhomboid, actinobacteria can have two or more copies whose sequences have not been analyzed for the presence putative rhomboid catalytic signatures. We report detailed phylogenetic and genomic analyses devoted to prokaryotic rhomboids of an important genus, Mycobacterium. RESULTS: Many mycobacterial genomes contained two phylogenetically distinct active rhomboids orthologous to Rv0110 (rhomboid protease 1) and Rv1337 (rhomboid protease 2) of Mycobacterium tuberculosis H37Rv, which were acquired independently. There was a genome-wide conservation and organization of the orthologs of Rv1337 arranged in proximity with glutamate racemase (mur1), while the orthologs of Rv0110 appeared evolutionary unstable and were lost in Mycobacterium leprae and the Mycobacterium avium complex. The orthologs of Rv0110 clustered with eukaryotic rhomboids and contained eukaryotic motifs, suggesting a possible common lineage. A novel nonsense mutation at the Trp73 codon split the rhomboid of Mycobacterium avium subsp. Paratuberculosis into two hypothetical proteins (MAP2425c and MAP2426c) that are identical to MAV_1554 of Mycobacterium avium. Mycobacterial rhomboids contain putative rhomboid catalytic signatures, with the protease active site stabilized by Phenylalanine. The topology and transmembrane helices of the Rv0110 orthologs were similar to those of eukaryotic secretase rhomboids, while those of Rv1337 orthologs were unique. Transcription assays indicated that both mycobacterial rhomboids are possibly expressed. CONCLUSIONS: Mycobacterial rhomboids are active rhomboid proteases with different evolutionary history. The Rv0110 (rhomboid protease 1) orthologs represent prokaryotic rhomboids whose progenitor may be the ancestors of eukaryotic rhomboids. The Rv1337 (rhomboid protease 2) orthologs appear more stable and are conserved nearly in all mycobacteria, possibly alluding to their importance in mycobacteria. MAP2425c and MAP2426c provide the first evidence for a split homologous rhomboid, contrasting whole orthologs of genetically related species. Although valuable insights to the roles of rhomboids are provided, the data herein only lays a foundation for future investigations for the roles of rhomboids in mycobacteria.

Identification of a primary target of thalidomide teratogenicity.

Half a century ago, thalidomide was widely prescribed to pregnant women as a sedative but was found to be teratogenic, causing multiple birth defects. Today, thalidomide is still used in the treatment of leprosy and multiple myeloma, although how it causes limb malformation and other developmental defects is unknown. Here, we identified cereblon (CRBN) as a thalidomide-binding protein. CRBN forms an E3 ubiquitin ligase complex with damaged DNA binding protein 1 (DDB1) and Cul4A that is important for limb outgrowth and expression of the fibroblast growth factor Fgf8 in zebrafish and chicks. Thalidomide initiates its teratogenic effects by binding to CRBN and inhibiting the associated ubiquitin ligase activity. This study reveals a basis for thalidomide teratogenicity and may contribute to the development of new thalidomide derivatives without teratogenic activity.

Saccharomyces cerevisiae CCMI 885 secretes peptides that inhibit the growth of some non-Saccharomyces wine-related strains.

The nature of the toxic compounds produced by Saccharomyces cerevisiae CCMI 885 that induce the early death of Hanseniaspora guilliermondii during mixed fermentations, as well as their ability to inhibit the growth of other non-Saccharomyces wine-related strains, was investigated. The killing effect of mixed supernatants towards H. guilliermondii was inactivated by protease treatments, thus revealing the proteinaceous nature of the toxic compounds. Analysis of the protein pattern of mixed supernatants on Tricine SDS-PAGE showed that this S. cerevisiae strain secretes peptides (<10 kDa), which were detected only when death of H. guilliermondii was already established. Death-inducing supernatants were ultrafiltrated by 10 and 2 kDa membranes, respectively, and the inhibitory effect of those permeates were tested in H. guilliermondii cultures. Results indicated that the (2-10) kDa protein fraction of those supernatants seemed to contain antimicrobial peptides active against H. guilliermondii. Thus, the (2-10) kDa protein fraction was concentrated and its inhibitory effect tested against strains of Kluyveromyces marxianus, Kluyveromyces thermotolerans, Torulaspora delbrueckii and H. guilliermondii. Under the growth conditions used for these tests, the (2-10) kDa protein fraction of S. cerevisiae CCMI 885 supernatants exhibited a fungistatic effect against all the strains and a fungicidal effect against K. marxianus.

Comparative genomics of mycobacterial proteases.

Although proteases are recognized as important virulent factors in pathogenic microorganisms, little information is available so far regarding the potential role of these enzymes in diseases caused by mycobacteria. Here we use bioinformatic tools to compare the protease-coding genes present in the genome of Mycobacterium leprae, Mycobacterium tuberculosis, Mycobacterium bovis and Mycobacterium avium paratuberculosis. This analysis allowed a review of the nomenclature of the protease family present in mycobacteria. A special attention was devoted to the 'decaying genome' of M. leprae where a relatively high level of conservation of protease-coding genes was observed when compared to other genes families. A total of 39 genes out of the 49 found in M. bovis were identified in M. leprae. Of relevance, a core of well-conserved 38 protease genes shared by the four species was defined. This set of proteases is probably essential for survival in the host and disease outcome and may constitute novel targets for drug development leading to a more effective control of mycobacterial diseases.

Expression analysis of proteases of Mycobacterium leprae in human skin lesions.

Proteases are commonly involved in bacterial pathogenesis and their inhibition has represented a successful therapeutic approach to treat infectious diseases. However, there is little information on the role of proteases in the pathogenesis of Mycobacteria. Five of these genes, three coding for putative secreted proteases, were selected in the present study to investigate their expression in Mycobacterium leprae isolated from skin biopsies of multibacillary leprosy patients. Via nested-PCR, it was demonstrated that mycP1 or ML0041, htrA2 or ML0176, htrA4 or ML2659, gcp or ML0379 and clpC or ML0235 are transcribed in vivo during the course of human infection. Moreover, the expression of Gcp in leprosy lesions was further confirmed by immunohistochemistry using a specific hyperimmune serum. This observation reinforces the potential role of mycobacterial proteases in the context of leprosy pathogenesis.

Protease (PrA and PrB) and prolyl and arginyl aminopeptidase activities from Debaryomyces hansenii as a function of growth phase and nutrient sources.

The effects of nutrient sources and growth phase of Debaryomyces hansenii on the protease (PrA and PrB) and aminopeptidase (prolyl-[PAP] and arginyl-[AAP] aminopeptidases) activities were investigated. These activities were also monitored during growth on a whole sarcoplasmic muscle protein extract (WSPE) and on an equivalent medium but free of compounds under 10 kDa (SPE>10 kDa). The levels of specific protease and aminopeptidase activities were higher when cells were grown in urea and dipeptides than when grown in either ammonium or free amino acids as nitrogen sources. The level of each aminopeptidase (PAP or AAP) activity was preferentially induced by its own substrate (ProLeu or LysAla), suggesting a role in the utilization of exogenous peptides. Higher specific activities for all proteolytic enzymes were detected when using acetate as carbon source. The time course experiments carried out on urea or sarcoplasmic protein-containing media revealed an increase in all activities during transition and advanced stages of stationary phase of growth. In muscle protein extracts, the absence of low molecular mass nutrients (SPE>10 kDa) initially induced the production of PrA, PrB, and AAP activities, possibly involved in the breakdown of muscle oligopeptides.

Protease, peptidase and esterase activities by lactobacilli and yeast isolates from Feta cheese brine.

AIMS: The study of peptidase, esterase and caseinolytic activity of Lactobacillus paracasei subsp. paracasei, Debaryomyces hansenii and Sacchromyces cerevisiae isolates from Feta cheese brine. METHODS AND RESULTS: Cell-free extracts from four strains of Lact. paracasei subsp. paracasei, four strains of D. hansenii and three strains of S. cerevisiae, isolated from Feta cheese brine were tested for their proteolytic and esterase enzyme activities. Lactobacillus paracasei subsp. paracasei strains had intracellular aminopeptidase, dipeptidyl aminopeptidase, dipeptidase, endopeptidase and carboxypeptidase activities. Esterases were detected in three of four strains of lactobacilli and their activities were smaller with higher molecular weight fatty acids. The strains of yeasts did not exhibit endopeptidase as well as dipeptidase activities except on Pro-Leu. Their intracellular proteolytic activity was higher than that of lactobacilli. Esterases from yeasts preferentially degraded short chain fatty acids. Lactobacilli degraded preferentially beta-casein. Caseinolytic activity of yeasts was higher than that of lactobacilli. CONCLUSIONS: The results suggest that Lact. paracasei subsp. paracasei and yeasts may contribute to the development of flavour in Feta cheese. SIGNIFICANCE AND IMPACT OF THE STUDY: Selected strains could be used as adjunct starters to make high quality Feta cheese.

Characterisation of yeast flora isolated from an artisanal Portuguese ewes' cheese.

The evolution of the yeast flora was studied for an artisanal semi-hard ewes' cheese made from raw milk. Mean log10 yeast counts per gram of cheese body ranged from 2.7 to 6.4, with the higher counts observed after a ripening period of 30 days. The yeast population decreased thereafter and, at the end of curing process, reached values similar to those of the beginning. A total of 344 yeasts strains were randomly isolated from the curd and cheese body during the 60 days long ripening period. Esterase activity was common to almost all isolates (98%) while proteolysis was observed in 12% of the total yeast population. The proportion of strains with positive glucose fermentation increased from 21% in the curd to 75% at the end of the ripening period. A total of 150 isolates representative of the physiological characteristics tested were examined with the API ID 32C system showing different degrees of quality of identification. Only 15% of the strains (23 isolates) were excellently identified being assigned to the species Candida zeylanoides. The most frequent species appeared to be Debaryomyces hansenii (anamorph Candida famata) and Candida intermedia. These two species amounted to 9% of the yeasts in the curd increasing to 86% at the end of the ripening period.

Behavior of Brevibacterium linens and Debaryomyces hansenii as ripening flora in controlled production of soft smear cheese from reconstituted milk: protein degradation.

Model smear soft cheeses, prepared with Debaryomyces hansenii and Brevibacterium linens as ripening starters, were ripened under aseptic conditions. Results of the cheese-making trials, in triplicate, were similar and showed similar patterns of protein degradation. In all of the trials, the acid-soluble nitrogen and nonprotein nitrogen (NPN) indexes and NH3 concentrations of the rind were low until d 10. The acid-soluble nitrogen and NPN of the rind then increased to 100 and 18% of total nitrogen, respectively, at d 76. The NH3 concentrations remained low until d 24 and increased until d 70, reaching about 1.8 g of NH3/kg of DM, and then remained constant. The acid-soluble nitrogen and NPN indexes and NH3 concentrations in the inner cheese mass were lower than in the rind. They showed the same evolution, reaching about 18% for acid-soluble nitrogen, 10% for NPN, and 1.5 g of NH3/kg of DM. It was shown that the inner cheese pH and populations of D. hansenii and B. linens have an effect on proteolysis. Viable cell counts of D. hansenii and B. linens were correlated with the environmental conditions and with proteolytic products. The determining role of carbon source and NH3 diffusions on the cheese ripening process were confirmed.