Immunomodulatory proteins of orthopoxviruses

The review considers recent data on the structural-functional organization of the genome of orthopoxviruses pathogenic for humans, including the variola, monkeypox, cowpox, and vaccinia viruses. Emphasis was placed on the structure of molecular virulence factors that suppress the inflammatory reactions, immune response, and interferon effects induced by virus infection.     

Immunomodulatory activity of extracellular heat shock proteins and their autoantibodies

HSP are groups of stress‐inducible proteins which contribute to quality control by assisting the correct folding of both nascent and denatured proteins, and promoting the degradation of unrecoverable denatured proteins. HSP also help to maintain cellular homeostasis and protect from cell death through a mechanism called thermotolerance. Cells subjected to mild stress induce HSP which then protect them against subsequent stress. However, in cells subjected to severe stress, HSP promote apoptosis. Besides these intracellular events, HSP also exist in extracellular fluids, and have been shown to contribute to immunomodulation. In innate immunity extracellular HSP, like various microbial substances, induce various proinflammatory cytokines. In acquired immunity they interact with antigenic polypeptides and assist in antigen presentation. The extracellular HSP are so‐called adjuvant. Release of HSP from cells is triggered by stress and trauma, and is thus regarded as an immunological “danger signal”. In addition, anti‐HSP autoantibodies are frequently found in patients with autoimmune diseases and inflammatory disorders, and these autoantibodies can modulate the “danger signal” triggered by extracellular HSP.     

Validating subcellular localization prediction tools with mycobacterial proteins

Background  

The computational prediction of mycobacterial proteins' subcellular localization is of key importance for proteome annotation and for the identification of new drug targets and vaccine candidates. Several subcellular localization classifiers have been developed over the past few years, which have comprised both general localization and feature-based classifiers. Here, we have validated the ability of different bioinformatics approaches, through the use of SignalP 2.0, TatP 1.0, LipoP 1.0, Phobius, PA-SUB 2.5, PSORTb v.2.0.4 and Gpos-PLoc, to predict secreted bacterial proteins. These computational tools were compared in terms of sensitivity, specificity and Matthew's correlation coefficient (MCC) using a set of mycobacterial proteins having less than 40% identity, none of which are included in the training data sets of the validated tools and whose subcellular localization have been experimentally confirmed. These proteins belong to the TBpred training data set, a computational tool specifically designed to predict mycobacterial proteins.     

Exogenous secretory proteins do not inhibit carbamylcholine-stimulated release of pulse-labelled secretory proteins from rat pancreatic tissue slices

Experiments were conducted to test the concept that the results of secretion studies employing pancreatic tissue slices are significantly biased by the distribution of exocrine secretory proteins between the tissue and the incubation medium. The findings demonstrate (1) that the kinetics of release of pulse-labelled secretory proteins from cholinergically-stimulated tissue slices are independent of the concentration of exogenous exocrine secretory proteins and (2) that if there are bidirectional fluxes of secretory proteins across the cell membrane of pancreatic exocrine cells, these fluxes do not account for the fractional release of pulse-labelled secretory proteins.     

SecA-mediated targeting and translocation of secretory proteins

More than 30 years of research have revealed that the dynamic nanomotor SecA is a central player in bacterial protein secretion. SecA associates with the SecYEG channel and transports polypeptides post-translationally to the trans side of the cytoplasmic membrane. It comprises a helicase-like ATPase core coupled to two domains that provide specificity for preprotein translocation. Apart from SecYEG, SecA associates with multiple ligands like ribosomes, nucleotides, lipids, chaperones and preproteins. It exerts its essential contribution in two phases. First, SecA, alone or in concert with chaperones, helps mediate the targeting of the secretory proteins from the ribosome to the membrane. Next, at the membrane it converts chemical energy to mechanical work and translocates preproteins through the SecYEG channel. SecA is a highly dynamic enzyme, it exploits disorder–order kinetics, swiveling and dissociation of domains and dimer to monomer transformations that are tightly coupled with its catalytic function. Preprotein signal sequences and mature domains exploit these dynamics to manipulate the nanomotor and thus achieve their export at the expense of metabolic energy. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.     

Recombinant mycobacterial proteins future directions to improve protective efficacy

A large number of subunit vaccine candidates have recently been developed as alternatives to Mycobacterium bovis Bacillus Calmette-Guerin (BCG), which gives unpredictable and highly variable protection against tuberculosis. Immunological potential of various recombinant proteins against mycobacterial infections has been discussed. Further, strategies have been suggested, which include development of constructs coexpressing cytokines or regimens utilizing recombinant proteins for further improving the protective efficacy.     

Comparative studies of intracellular transport of secretory proteins

The physiology of protein intracellular transport and secretion by cell types thought to be free from short-term control has been compared with that of the pancreatic acinar cell, using pulse-chase protocols to follow biosynthetically-labeled secretory products. Data previously obtained (Tartakoff, A.M., and P. Vassalli. J. Exp. Med. 146:1332-1345) has shown that plasma-cell immunoglobulin (Ig) secretion is inhibited by respiratory inhibitors, by partial Na/K equilibration effected by the carboxylic ionophore monensin, and by calcium withdrawal effected by the carboxylic ionophore A 23187 in the presence of ethylene glycol bis (beta-aminoethylether)-N,N,N'',N''-tetraacetic acid (EGTA) and absence of calcium. We report here that both inhibition of respiration and treatment with monensin slow secretion by fibroblasts, and also macrophages and slow intracellular transport (though not discharge per se) by the exocrine pancreatic cells. Attempted calcium withdrawal is inhibitory for fibroblasts but not for macrophages. The elimination of extracellular calcium or addition of 50 mM KCl has no major effect on secretory rate of either fibroblasts or macrophages. Electron microscopic examination of all cell types shows that monensin causes a rapid and impressive dilation of Golgi elements. Combined cell fractionation and autoradiographic studies of the pancreas show that the effect of monensin is exerted at the point of the exit of secretory protein from the Golgi apparatus. Other steps in intracellular transport proceed at normal rates. These observations suggest a common effect of the cytoplasmic Na/K balance at the Golgi level and lead to a model of intracellular transport in which secretory product obligatorily passes through Golgi elements (cisternae?) that are sensitive to monensin. Thus, intracellular transport follows a similar course in both regulated and nonregulated secretory cells up to the level of distal Golgi elements.     

Trapping parasite secretory proteins in baker's yeast

Because the function of signal sequences has been conserved during evolution it has been possible to develop both bioinformatics resources to identify them and techniques to clone genes that encode secretory proteins. The latter entail insertion of heterologous signals upstream of signal peptide deleted reporter genes. We discuss the advantages of using Saccharomyces cerevisiae for signal sequence trap technology. The yeast protein-translocation system appears to be less discriminating than that of higher eukaryotes - for example, a Theileria parva cysteine protease gene containing a recessed, nonclassical signal allows access to the secretory pathway--and yeast technology could have general application in studying elements of parasite protein trafficking.     

Wide distribution of cysteine-rich secretory proteins in snake venoms: isolation and cloning of novel snake venom cysteine-rich secretory proteins

Cysteine-rich secretory proteins (CRISPs) are found in epididymis and granules of mammals, and they are thought to function in sperm maturation and in the immune system. Recently, we isolated and obtained clones for novel snake venom proteins that are classified as CRISP family proteins. To elucidate the distribution of snake venom CRISP family proteins, we evaluated a wide range of venoms for immuno-cross-reactivity. Then we isolated, characterized, and cloned genes for three novel CRISP family proteins (piscivorin, ophanin, and catrin) from the venom of eastern cottonmouth (Agkistrodon piscivorus piscivorus), king cobra (Ophiophagus hannah), and western diamondback rattlesnake (Crotalus atrox). Our results show the wide distribution of snake venom CRISP family proteins among Viperidae and Elapidae from different continents, indicating that CRISP family proteins compose a new group of snake venom proteins.     

RFP tags for labeling secretory pathway proteins

Red fluorescent proteins (RFPs) are useful tools for live cell and multi-color imaging in biological studies. However, when labeling proteins in secretory pathway, many RFPs are prone to form artificial puncta, which may severely impede their further uses. Here we report a fast and easy method to evaluate RFPs fusion properties by attaching RFPs to an environment sensitive membrane protein Orai1. In addition, we revealed that intracellular artificial puncta are actually colocalized with lysosome, thus besides monomeric properties, pKa value of RFPs is also a key factor for forming intracellular artificial puncta. In summary, our current study provides a useful guide for choosing appropriate RFP for labeling secretory membrane proteins. Among RFPs tested, mOrange2 is highly recommended based on excellent monomeric property, appropriate pKa and high brightness.     

Retrieval and reuse of pituitary secretory granule proteins

The pituitary contains professional secretory cells, devoting a large fraction of their energy to the synthesis of hormones that are stored for secretion in response to a complex mixture of inputs. Ba2+, a substitute for Ca2+, and phorbol ester, a mimic for diacylglycerol, have a synergistic effect on exocytosis. By using these secretagogues, we developed a paradigm in which phorbol ester potentiation of Ba2+-evoked exocytosis produces a robust secretory response in multiple pituitary cell types. Because cells subjected to this stimulatory paradigm remain healthy despite their greatly reduced hormone content, we used this paradigm to study the fate of granule membrane proteins. We examined the turnover of peptidylglycine alpha-amidating monooxygenase (PAM), a membrane enzyme involved in the final maturation of many peptides, and VAMP2, a vesicle soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE). The stability of recently synthesized PAM was increased by sustained exocytosis. Biotinylation studies established that the appearance of integral membrane PAM at the plasma membrane was stimulated along with hormone secretion. PAM biotinylated on the cell surface undergoes cleavage to yield soluble peptidylglycine-alpha-hydroxylating monooxygenase that can then be secreted in a regulated fashion. Consistent with a kiss-and-run or cavicapture mode of secretion (Taraska, J. W., Perrais, D., Ohara-Imaizumi, M., Nagamatsu, S., and Almers, W. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 2070-2075), biotinylated prolactin was also retained by the cells and later released in response to secretagogues. Thus, pituitary cells can retrieve and reuse components of the machinery involved in the final stages of exocytosis (the SNAREs) as well as soluble and membrane granule proteins.     

Post-translocational folding of secretory proteins in Gram-positive bacteria

The transport of proteins from their site of synthesis in the cytoplasm to their functional location is an essential characteristic of all living cells. In Gram-positive bacteria the majority of proteins that are translocated across the cytoplasmic membrane are delivered to the membrane-cell wall interface in an essentially unfolded form. They must then be folded into their native configuration in an environment that is dominated by a high density of immobilised negative charge-in essence an ion exchange resin. It is essential to the viability of the cell that these proteins do not block the translocation machinery in the membrane, form illegitimate interactions with the cell wall or, through intermolecular interactions, form insoluble aggregates. Native Gram-positive proteins therefore have intrinsic folding characteristics that facilitate their rapid folding, and this is assisted by a variety of folding factors, including enzymes, peptides and metal ions. Despite these intrinsic and extrinsic factors, secretory proteins do misfold, particularly if the cell is subjected to certain types of stress. Consequently, Gram-positive bacteria such as Bacillus subtilis encode membrane- and cell wall-associated proteases that act as a quality control machine, clearing misfolded or otherwise aberrant proteins from the translocase and the cell wall.     

Localization of epididymal secretory proteins on rat spermatozoa

Spermatozoa from the testis and cauda epididymidis of the rat were surface labelled with radioactive iodide. Detergent extracts of radioiodinated spermatozoa immunoprecipitated with antisera against specific epididymal proteins, followed by polyacrylamide gel electrophoresis, revealed two proteins (D and E of Mr 27 000 and 28 000, respectively) which became associated with spermatozoa during epididymal transit. These proteins were observed by immunofluorescence microscopy to be located over a restricted area of the head surface. Proteins with similar molecular weight were labelled on spermatozoa from the cauda epididymidis, but not from the testis, by reaction with sodium boro[3H]hydride in the presence of galactose oxidase. However, failure to immunoprecipitate with antibodies to Proteins D and E and non-coincident migration on two-dimensional gel electrophoresis established the non-identity of these proteins. Compared with Proteins D and E, two other major epididymal secretory proteins (Proteins B and C of Mr 16 000) associated with spermatozoa to a relatively minor extent during epididymal transit.     

Identification of the subcellular localization of mycobacterial proteins using localization motifs

Mycobacterium, the most common disease-causing genus, infects billions of people and is notoriously difficult to treat. Understanding the subcellular localization of mycobacterial proteins can provide essential clues for protein function and drug discovery. In this article, we present a novel approach that focuses on local sequence information to identify localization motifs that are generated by a merging algorithm and are selected based on a binomially distributed model. These localization motifs are employed as features for identifying the subcellular localization of mycobacterial proteins. Our approach provides more accurate results than previous methods and was tested on an independent dataset recently obtained from an experimental study to provide a first and reasonably accurate prediction of subcellular localization. Our approach can also be used for large-scale prediction of new protein entries in the UniportKB database and of protein sequences obtained experimentally. In addition, our approach identified many local motifs involved with the subcellular localization that also interact with the environment. Thus, our method may have widespread applications both in the study of the functions of mycobacterial proteins and in the search for a potential vaccine target for designing drugs.     

The potential use of heat-shock proteins to vaccinate against mycobacterial infections

Over the last few years, some of our experiments in which mycobacterial heat-shock protein (HSP) antigens were presented to the immune system as if they were viral antigens have had a significant impact on our understanding of protective immunity against tuberculosis. They have also markedly enhanced the prospects for new vaccines. We now know that the mycobacterial HSP65 antigen can confer protection equal to that from live BCG vaccine in mice.     

Alterations in recruitment and activation of Rab proteins during mycobacterial infection

At the phagosome level, Mycobacterium spp. alters activation and recruitment of several "Ras gene from rat brain" proteins, commonly known as Rab. Mycobacterial phagosomes have a greater and sustained expression of Rab5, Rab11, Rab14 and Rab22a, and lowered or no expression of Rab7, Rab9 and Rab6. This correlates with increased fusion of the phagosomes with early and recycling endosomes acquiring some features of early phagosomes, allowing the bacteria to gain access to nutrients and preventing the activation of anti-mycobacterial mechanisms. The expression of constitutively active mutants of Rab from the early stage endosomes prevents the maturation of phagosomes containing latex beads or heat-inactivated mycobacteria. Silencing of these mutants by interference RNA or dominant negative forms induces the maturation of mycobacterial phagosomes. The mechanisms have not been established by which mycobacteria alter the expression of these GTPases and thereby shift the phagolysosomal maturation. The problem can be explained by alterations in the recruitment of proteins that interact with Rab, such as phosphoinositide 3-kinases and early endosomal antigen 1. Identifying the mechanisms used by Mycobacterium spp. to disrupt the cycle of Rab activation will be essential to understand the pathophysiology of mycobacterial infections and usefully to potential drug targets.