Cell Envelope Proteins Research Articles

Comparative Genomic Analysis of East Asian and Non-Asian Helicobacter pylori Strains Identifies Rapidly Evolving Genes

Helicobacter pylori infection is a risk factor for the development of gastric adenocarcinoma, a disease that has a high incidence in East Asia. Genes that are highly divergent in East Asian H. pylori strains compared to non-Asian strains are predicted to encode proteins that differ in functional activity and could represent novel determinants of virulence. To identify such proteins, we undertook a comparative analysis of sixteen H. pylori genomes, selected equally from strains classified as East Asian or non-Asian. As expected, the deduced sequences of two known virulence determinants (CagA and VacA) are highly divergent, with 77% and 87% mean amino acid sequence identities between East Asian and non-Asian groups, respectively. In total, we identified 57 protein sequences that are highly divergent between East Asian and non-Asian strains, but relatively conserved within East Asian strains. The most highly represented functional groups are hypothetical proteins, cell envelope proteins and proteins involved in DNA metabolism. Among the divergent genes with known or predicted functions, population genetic analyses indicate that 86% exhibit evidence of positive selection. McDonald-Kreitman tests further indicate that about one third of these highly divergent genes, including cagA and vacA, are under diversifying selection. We conclude that, similar to cagA and vacA, most of the divergent genes identified in this study evolved under positive selection, and represent candidate factors that may account for the disproportionately high incidence of gastric cancer associated with East Asian H. pylori strains. Moreover, these divergent genes represent robust biomarkers that can be used to differentiate East Asian and non-Asian H. pylori strains.

Nasal Colonisation by Staphylococcus aureus Depends upon Clumping Factor B Binding to the Squamous Epithelial Cell Envelope Protein Loricrin

Staphylococcus aureus asymptomatically colonises the anterior nares, but the host and bacterial factors that facilitate colonisation remain incompletely understood. The S. aureus surface protein ClfB has been shown to mediate adherence to squamous epithelial cells in vitro and to promote nasal colonisation in both mice and humans. Here, we demonstrate that the squamous epithelial cell envelope protein loricrin represents the major target ligand for ClfB during S. aureus nasal colonisation. In vitro adherence assays indicated that bacteria expressing ClfB bound loricrin most likely by the “dock, lock and latch” mechanism. Using surface plasmon resonance we showed that ClfB bound cytokeratin 10 (K10), a structural protein of squamous epithelial cells, and loricrin with similar affinities that were in the low µM range. Loricrin is composed of three separate regions comprising GS-rich omega loops. Each loop was expressed separately and found to bind ClfB, However region 2 bound with highest affinity. To investigate if the specific interaction between ClfB and loricrin was sufficient to facilitate S. aureus nasal colonisation, we compared the ability of ClfB+ S. aureus to colonise the nares of wild-type and loricrin-deficient (Lor−/−) mice. In the absence of loricrin, S. aureus nasal colonisation was significantly impaired. Furthermore a ClfB− mutant colonised wild-type mice less efficiently than the parental ClfB+ strain whereas a similar lower level of colonisation was observed with both the parental strain and the ClfB− mutant in the Lor−/− mice. The ability of ClfB to support nasal colonisation by binding loricrin in vivo was confirmed by the ability of Lactococcus lactis expressing ClfB to be retained in the nares of WT mice but not in the Lor−/− mice. By combining in vitro biochemical analysis with animal model studies we have identified the squamous epithelial cell envelope protein loricrin as the target ligand for ClfB during nasal colonisation by S. aureus.

How do keratinizing disorders and blistering disorders overlap?

Inherited keratinizing disorders are caused by mutations in the genes encoding cornified cell envelope proteins, enzymes and their inhibitors, adhesion molecules, cytoskeletal proteins and others in the epidermis. These molecules are known to regulate differentiation, proliferation and cell adhesions. Intriguingly, some keratinizing disorders show blistering skin lesions, while some inherited blistering disorders show abnormal keratinization. Therefore, hereditary keratinizing and blistering diseases are closely related and show overlapping genetic backgrounds. In this review, we overviewed keratinizing and blistering disorders in terms of overlapping of the two disease groups. Gene mutations in desmosomal components cause striate keratoderma, Naxos disease, epidermolytic palmoplantar keratoderma and plakophilin deficiency, which first show skin fragility and blisters and later hyperkeratosis. Gene mutations in hemidesmosomal components cause various forms of epidermolysis bullosa, some of which show hyperkeratosis on the nails, palms and soles, in addition to blister formation. Diseases with gene mutations in calcium pump proteins are Darier disease and Hailey-Hailey disease, which show clinicopathological overlaps and develop both keratinizing and blistering skin lesions. Finally, gene mutations in epidermal keratins cause epidermolysis bullosa simplex, epidermolytic ichthyosis, superficial epidermolytic ichthyosis, epidermolytic palmoplantar keratoderma and pachyonychia congenita/focal palmoplantar keratoderma, which show thickening of the palms and soles with underlying blister formation. In general, responsible proteins for diseases developing both keratinizing and blistering conditions are adhesion molecules, calcium pump proteins and keratins, but not connexins, cornified cell envelop proteins, enzymes or inhibitors. It is still unknown how particular keratinizing diseases develop blisters and vice versa.

Immune-stimulating potential of cell envelope proteins fromVibrio choleraeassociated to chitosan microparticles: Anin vitrostudy

Cholera is a severe diarrheal disease that remains an important cause of illness and death in many parts of the world. This study has been designed to check the immune-stimulating potential of antigens in their native and associated form as chitosan microparticles in vitro. Chitosan microparticles were prepared by the ionic gelation technique. The cell envelope proteins (CEPs) isolated from Vibrio cholerae were loaded as antigenic material. The prepared microparticles were characterized for their morphology, loading efficiency, particle size, and zeta potential. The average particle size of CEPs-loaded chitosan microparticles was 2.24 µm and the zeta potential of loaded microparticles was less than blank microparticles. The in vitro release studies of CEPs from CEPs-loaded chitosan microparticles exhibited slow and extended release over a period of time. The higher release of cytokine profile, including interferon γ (IFN-γ), tumor necrosis factor α (TNF-α), and interlukin-6 (IL-6), was observed for CEPs-loaded chitosan microparticles in comparison to CEPs as native antigen. The particle size of microparticles was within the range for phagocytosis by macropahges, which affects the immunogenicity. The decrease in zeta potential from blank to loaded microparticles further confirms the loading of antigen. The slow and extended release of CEPs provides continuous stimulus of antigen for a longer period of time. The cytokine profiling has shown the advantage of loaded microparticles over native antigen. The in vitro release studies and cytokine profiling strongly suggested that CEPs-associated chitosan microparticles could be a potential candidate for oral vaccination against Vibrio cholerae.

Crystal structures of triosephosphate isomerase from methicillin resistant Staphylococcus aureus MRSA252 provide structural insights into novel modes of ligand binding and unique conformations of catalytic loop

Staphylococcus aureus is one of the most dreaded pathogens worldwide and emergence of notorious antibiotic resistant strains have further exacerbated the present scenario. The glycolytic enzyme, triosephosphate isomerase (TIM) is one of the cell envelope proteins of the coccus and is involved in biofilm formation. It also plays an instrumental role in adherence and invasion of the bacteria into the host cell. To structurally characterize this important enzyme and analyze it's interaction with different inhibitors, substrate and transition state analogues, the present article describes several crystal structures of SaTIM alone and in complex with different ligands: glycerol-3-phosphate (G3P), glycerol-2-phosphate (G2P), 3-phosphoglyceric acid (3PG) and 2-phosphoglyceric acid (2PG). Unique conformations of the catalytic loop 6 (L6) has been observed in the different complexes. It is found to be in "almost closed" conformation in both subunits of the structure complexed to G3P. However L6 adopts the open conformation in presence of G2P and 2PG. The preference of the conformation of the catalytic loop can be correlated with the position of the phosphate group in the ligand. Novel modes of binding have been observed for G2P and 3PG for the very first time. The triose moiety is oriented away from the catalytic residues and occupies an entirely different position in some subunits. A completely new binding site for phosphate has also been identified in the complex with 2PG which differs substantially from the conventional phosphate binding site of the ligand in the crystal structures of TIM determined so far.

Proteomic Analysis of Neisseria gonorrhoeae Biofilms Shows Shift to Anaerobic Respiration and Changes in Nutrient Transport and Outermembrane Proteins

Neisseria gonorrhoeae, the causative agent of gonorrhea, can form biofilms in vitro and in vivo. In biofilms, the organism is more resistant to antibiotic treatment and can serve as a reservoir for chronic infection. We have used stable isotope labeling by amino acids in cell culture (SILAC) to compare protein expression in biofilm and planktonic organisms. Two parallel populations of N. gonorrhoeae strain 1291, which is an arginine auxotroph, were grown for 48 h in continuous-flow chambers over glass, one supplemented with 13C6-arginine for planktonic organisms and the other with unlabeled arginine for biofilm growth. The biofilm and planktonic cells were harvested and lysed separately, and fractionated into three sequential protein extracts. Corresponding heavy (H) planktonic and light (L) biofilm protein extracts were mixed and separated by 1D SDS-PAGE gels, and samples were extensively analyzed by liquid chromatography-mass spectrometry. Overall, 757 proteins were identified, and 152 unique proteins met a 1.5-fold cutoff threshold for differential expression with p-values <0.05. Comparing biofilm to planktonic organisms, this set included 73 upregulated and 54 downregulated proteins. Nearly a third of the upregulated proteins were involved in energy metabolism, with cell envelope proteins making up the next largest group. Of the downregulated proteins, the largest groups were involved in protein synthesis and energy metabolism. These proteomics results were compared with our previously reported results from transcriptional profiling of gonococcal biofilms using microarrays. Nitrite reductase and cytochrome c peroxidase, key enzymes required for anaerobic growth, were detected as highly upregulated in both the proteomic and transcriptomic datasets. These and other protein expression changes observed in the present study were consistent with a shift to anaerobic respiration in gonococcal biofilms, although changes in membrane proteins not explicitly related to this shift may have other functions.

Interaction of the Profilaggrin N-Terminal Domain with Loricrin in Human Cultured Keratinocytes and Epidermis

The relationship between the two coexpressed differentiation markers, profilaggrin and loricrin, is not clear right now. In this study, we explored the interaction of profilaggrin N-terminal domain (PND) with loricrin in keratinocytes and epidermis. Confocal immunofluorescence microscopic analysis of human epidermis showed that PND colocalized with loricrin. Loricrin nucleofected into HaCaT cells colocalized with PND in the nucleus and cytoplasm. The PND localizes to both the nucleus and cytoplasm of epidermal granular layer cells. Nucleofected PND also colocalized with keratin 10 (K10) in the nucleus and cytoplasm. Immunoelectron microscopic analysis of human epidermis confirmed the findings in nucleofected keratinocytes. Yeast two-hybrid assays showed that the B domain of human and mouse PND interacted with loricrin. The glutathione S-transferase (GST) pull-down analysis using recombinant GST-PND revealed that PND interacted with loricrin and K10. Knockdown of PND in an organotypic skin culture model caused loss of filaggrin expression and a reduction in both the size and number of keratohyalin granules, as well as markedly reduced expression of loricrin. Considering that expression of PND is closely linked to keratinocyte terminal differentiation, we conclude that PND interacts with loricrin and K10 in vivo and that these interactions are likely to be relevant for cornified envelope assembly and subsequent epidermal barrier formation.

Chemical Biology Approaches Reveal Conserved Features of a C‐Terminal Processing PDZ Protease

Several proteases like the high temperature requirement A (HtrA) protein family containing internal or C-terminal PDZ domains play key roles in protein quality control in the cell envelope of Gram-negative bacteria. While several HtrA proteases have been extensively characterized, many features of C-terminal processing proteases such as tail-specific protease (Tsp) are still unknown. To fully understand these cellular control systems, individual domains need to be targeted by specific peptides acting as activators or inhibitors. Here, we describe the identification and design of potent inhibitors and activators of Tsp. Suitable synthetic substrates of Tsp were identified and served as a basis for the generation of boronic acid-based peptide inhibitors. In addition, a proteomic screen of E. coli cell envelope proteins using a synthetic peptide library was performed to identify peptides capable of amplifying Tsp's proteolytic activity. The implications of these findings for the regulation of PDZ proteases and for future mechanistic studies are discussed.

Generation and envelope protein analysis of internalization defective Brucella abortus mutants in professional phagocytes, RAW 264.7

Brucella abortus is a facultative intracellular bacteria that replicates within a macrophage without producing any classical virulence factors. It can become internalized to cells by zipper-like and/or swimming internalization mechanisms. However, the bacterial proteins involved in internalization remain unclear. To define these bacterial proteins, random insertion mutants of B. abortus were generated by the Tn5 transposome complexes. In all, 132 mutants were screened, cellular internalization-defective mutants were selected, and these genomic and envelope proteomic features were identified. The transposon insertion sites were ccmC,ppk and BruAb2_0168 for the mutant C10, C29 and D7, respectively. Mutant C10 showed a deficiency in internalization without any changes in expression of the cell envelope proteins; however, mutant C29 showed a reduced expression of OMP25, and a mutant D7 also showed reduced expression of OMP25, OMP28 and Porin2b. These results suggest OMP25 is not an essential factor, but might be involved in host cellular internalization. We identified the ppk gene and BruAb2_0168 locus which are associated to expression of OMP25, OMP28 and Porin2b as well as pleiotropic effects of ccmC gene.

Acral Peeling Skin Syndrome: A Clinically and Genetically Heterogeneous Disorder

Acral peeling skin syndrome (APSS) is a rare, autosomal, recessive genodermatosis characterized by painless spontaneous exfoliation of the skin of the hands and feet at a subcorneal or intracorneal level. It usually presents at birth or appears later in childhood or early adulthood. Some cases result from mutations in the TGM5 gene that encodes transglutaminase 5, which has an important role in cross-linking cornified cell envelope proteins. We report a new APSS pedigree from Jordan that contains at least 10 affected family members, although sequencing of the TGM5 gene failed to disclose any pathogenic mutation(s). On the basis of probable consanguinity, we performed homozygosity mapping and identified areas of homozygosity on chromosomes 1, 6, 10, 13, and 16, although none of the intervals contained genes of clear relevance to cornification. APSS is a clinically and genetically heterogeneous disorder, and this Jordanian pedigree underscores the likelihood of still further heterogeneity.

Helicobacter pylori in Pediatrics

AbstractThis article reviewed the important publications on Helicobacter pylori research with children between April 2010 and March 2011. The most interesting studies in the last year lend further weight to the evidence for vertical transmission of H. pylori. The discovery of a potential role for jhp0562, the gene which encodes for the cell envelope protein glycosyltransferase, in the progression to peptic ulcer disease is also very interesting as it may provide a novel way to distinguish children at risk of peptic ulcer disease from those who are not, and so determine those who requires treatment to eradicate H. pylori. The rise in non‐H. pylori‐associated ulcers and erosions continues to be reported with no apparent risk factors for these ulcers identified to date. High levels of treatment failure continue to be reported, and there remains an urgent need for more effective treatment regimes for children.

Current methodologies for proteomics of bacterial surface‐exposed and cell envelope proteins

The study of surface-exposed proteins has received increasing attention following the advent of genomic sequencing, which in turn has enabled predictive tools and facilitated the technologies for their analysis by proteomics. The exterior topology of a bacterial pathogen is the interface between the cell and environment and thus is the initial mediator for infection, providing an important reservoir for components that may be used for novel vaccine development as well as the characterization of new drug targets. The study of such biological molecules has however, been under-represented in proteomics studies due to the difficulty involved in their analysis. Cell-envelope proteins in bacteria are typically difficult to characterize due to their low abundance, poor solubility, and the problematic isolation of pure surface fractions with only minimal contamination. Here, we describe different cell envelope preparations for proteomic characterization, focused principally on gel-free technologies. Fractionation techniques popularly used in proteomics are also explained with emphasis on surface and membrane-derived proteins/peptides. Conditional confirmation of localization is also explored with emphasis on different prediction algorithms as well as on analyses of surface peptide fractions by the use of different search programs and their implications for the unambiguous identification of surface-exposed and membrane-embedded proteins. Finally, different quantification techniques are discussed that are important for the validation of identifications and for highlighting novel proteins that may warrant further study by independent techniques.

Quantitative proteomic analysis of the chemolithoautotrophic bacterium Nitrosomonas europaea: Comparison of growing- and energy-starved cells

Obligately aerobic ammonia-oxidizing bacteria (AOB) like Nitrosomonas europaea play a pivotal role in the global nitrogen cycle. Although starvation tolerance is a key environmental adaptation, little is known about this response in AOB. The goal of these studies was to compare the composition of the N. europaea proteome in growing- and energy-starved cells using ¹⁵N labeling and HPLC-ESI-MS/MS. More than 6500 peptides were sequenced with high confidence, and matched to 876 proteins (34% of the protein coding genes). Of these, 126 proteins had two or more peptide forms identified by 10 or more scans, and were used in quantitative analysis and 27 were found to be significantly different in abundance between growing and starved cells. Proteins showing greater abundance in growing cells are geared toward biosynthesis, particularly DNA replication. Energy-starved cells were shifted away from biosynthesis and toward survival functions that included: cell envelope modification, protein protection/degradation, detoxification, and implementation of alternative energy generation mechanisms. Most of these activities have not previously been reported as associated with energy-starvation stress in N. europaea. This study provides insights into the potential effects of fluctuating environmental conditions on the regulation of physiological networks in N. europaea.

Profiling the Outer Membrane Proteome during Growth and Development of the Social Bacterium Myxococcus xanthus by Selective Biotinylation and Analyses of Outer Membrane Vesicles

Social behavior in the bacterium Myxococcus xanthus relies on contact-dependent activities involving cell-cell and cell-substratum interactions. To identify outer membrane proteins that have a role in these activities, we profiled the outer membrane proteome of growing and starving cells using two strategies. First, outer membrane proteins were enriched by biotinylation of intact cells using the reagent NHS (N-hydroxysuccinimide)-PEO(12) (polyethylene oxide)-biotin with subsequent membrane solubilization and affinity chromatography. Second, the proteome of outer membrane vesicles (OMV) was determined. Comparisons of detected proteins show that these methods have different detection profiles and together provide a comprehensive view of the outer membrane proteome. From 362 proteins identified, 274 (76%) were cell envelope proteins including 64 integral outer membrane proteins and 85 lipoproteins. The majority of these proteins were of unknown function. Among integral outer membrane proteins with homologues of known function, TonB-dependent transporters comprise the largest group. Our data suggest novel functions for these transporters. Among lipoproteins with homologues of known function, proteins with hydrolytic functions comprise the largest group. The luminal load of OMV was enriched for proteins with hydrolytic functions. Our data suggest that OMV have functions in predation and possibly in transfer of intercellular signaling molecules between cells.

Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variants

The recalcitrance of lignocellulosic biomass to hydrolysis is the bottleneck in cellulosic ethanol production. Efficient degradation of biomass by the anaerobic bacterium Clostridium thermocellum is carried out by the multicomponent cellulosome complex. The bacterial cell-surface attachment of the cellulosome is mediated by high-affinity protein-protein interactions between the Type II cohesin domain borne by the cell envelope protein and the Type II dockerin domain, together with neighboring X-module present at the C-terminus of the scaffolding protein (Type II coh-Xdoc). Here, the Type II coh-Xdoc interaction is probed using molecular dynamics simulations, free-energy calculations and essential dynamics analyses on both the wild type and various mutants of the C. thermocellum Type II coh-Xdoc in aqueous solution. The simulations identify the hot spots, i.e. the amino acid residues that may lead to a dramatic decrease in binding affinity upon mutation and also probe the effects of mutations on the mode of binding. The results suggest that bulky and hydrophobic residues at the protein interface, which make specific contacts with their counterparts, may play essential roles in retaining a rigid cohesin-dockerin interface. Moreover, dynamical cross-correlation analysis indicates that the X-module has a dramatic effect on the cohesin-dockerin interaction and is required for the dynamical integrity of the interface.

Fluoroquinolone and multidrug resistance phenotypes associated with the overexpression of AcrAB and an orthologue of MarA in Yersinia enterocolitica

Quinolone resistance among clinical isolates is of increasing importance. This phenotype particularly affects the nalidixic acid resistance levels and is also increasing among Yersinia enterocolitica strains. This study investigated the quinolone resistance mechanisms acquired in vitro by a Y. enterocolitica clinical isolate exposed to increasing concentrations of ciprofloxacin in a multi-step selection process. The fluoroquinolone-susceptible clinical isolate, Y.83-wt, the fluoroquinolone-resistant mutant, Y.83-64, and intermediate mutants were analysed by QRDR sequencing and MIC determination. Four different QRDRs (quinolone resistance-determining regions) mutations were characterised in Y.83-64: one in gyrA, one in gyrB, and two in parC. A significant increase in the MICs of ciprofloxacin, norfloxacin, nalidixic acid, and other unrelated antibiotics was detected in Y.83-64. Furthermore, the bacterial growth rate was assessed for strains Y.83-wt and Y.83-64. The analysis reported no significant differences between both strains. Cell envelope protein approach revealed an overexpression of both AcrA and AcrB proteins in Y.83-64. RT-PCR analyses were also carried out as was sequencing of known AcrAB regulators in Yersinia. The RT-PCR analysis showed an increased transcriptional level of a marA orthologue, marA Ye , in Y.83-64. The sequencing results reported no change in the acrR gene or in the promoter sequence of the acrAB operon when comparing Y.83-wt with Y.83-64. One differential mutation was detected within the marA Ye promoter in Y.83-64. Thus, the fluoroquinolone resistance phenotype acquired by Y.83-64 relies on the acquisition of 4 QRDR mutations in addition to the overexpression of AcrAB, which is likely triggered by increased expression levels of marA Ye .

A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis

BackgroundAnaerobic ammonium-oxidizing (anammox) bacteria perform a key step in global nitrogen cycling. These bacteria make use of an organelle to oxidize ammonia anaerobically to nitrogen (N2) and so contribute ~50% of the nitrogen in the atmosphere. It is currently unknown which proteins constitute the organellar proteome and how anammox bacteria are able to specifically target organellar and cell-envelope proteins to their correct final destinations. Experimental approaches are complicated by the absence of pure cultures and genetic accessibility. However, the genome of the anammox bacterium Candidatus "Kuenenia stuttgartiensis" has recently been sequenced. Here, we make use of these genome data to predict the organellar sub-proteome and address the molecular basis of protein sorting in anammox bacteria.ResultsTwo training sets representing organellar (30 proteins) and cell envelope (59 proteins) proteins were constructed based on previous experimental evidence and comparative genomics. Random forest (RF) classifiers trained on these two sets could differentiate between organellar and cell envelope proteins with ~89% accuracy using 400 features consisting of frequencies of two adjacent amino acid combinations. A physicochemically distinct organellar sub-proteome containing 562 proteins was predicted with the best RF classifier. This set included almost all catabolic and respiratory factors encoded in the genome. Apparently, the cytoplasmic membrane performs no catabolic functions. We predict that the Tat-translocation system is located exclusively in the organellar membrane, whereas the Sec-translocation system is located on both the organellar and cytoplasmic membranes. Canonical signal peptides were predicted and validated experimentally, but a specific (N- or C-terminal) signal that could be used for protein targeting to the organelle remained elusive.ConclusionsA physicochemically distinct organellar sub-proteome was predicted from the genome of the anammox bacterium K. stuttgartiensis. This result provides strong in silico support for the existing experimental evidence for the existence of an organelle in this bacterium, and is an important step forward in unravelling a geochemically relevant case of cytoplasmic differentiation in bacteria. The predicted dual location of the Sec-translocation system and the apparent absence of a specific N- or C-terminal signal in the organellar proteins suggests that additional chaperones may be necessary that act on an as-yet unknown property of the targeted proteins.

In this issue

AbstractProhibition that works: Prohibitin 1Prohibitin 1 (Phb1) was cloned in 1991 based on its ability to suppress the regrowth of liver tissue. That task was not trivial – Phb1 turned out to be a buddy of just about anyone of any importance. It is highly conserved, ubiquitous among eukaryotes, and exerts a controlling interest in apoptosis, cell cycle, differentiation, and senescence. It, in turn, is controlled by a variety of post‐translational modifications. Did I say it is a tumor suppressor, too? It is. Sánchez‐Quiles et al. set out to survey the effects of changing levels of Phb1 on a variety of cell functions in cultured human hematoma cells. Using si technology, they found more that than 500 genes were stimulated or repressed in one liver cell line. One partial explanation is the observation that Phb1 is also involved in tissue homeostasis through two interacting networks.magnified imagepp. 1609–1620Myxobacter mixes mean mixture for mealsMost of us learned what we know of microbiology in medical settings, concerned about infectivity, clinical symptoms and drug resistance. Some of us (“molecular biologists”) never got beyond Escherichia coli and Bacillus subtilis. The excuse for working with so few species of bacteria was that it took too long to move all the genetic and biochemical tools into a new species. We can no longer hide behind that excuse. Entire genomes can be sequenced in a matter of weeks (or days). In this study, Chao et al. analyze the proteomic response of Anaeromyxobacter dehalogenans to changes in nutrients including uranium(VI), halogenated phenols, Fe(III) to fumarate as electron acceptors. Applying commonly used proteomic tools (2‐DE/MALDI‐TOF), they found spots for 559 unique proteins. Pathway analysis revealed an unusually wide array of means of living off of amino acid metabolism (like lysine to butyrate fermentation).magnified imagepp. 1685–1693“Brain must be in gear before starting mouth”This group clearly had their brain in gear. Sievers et al. gave Staphylococcus aureus every chance to respond “normally” to the deletion of a critical gene but virtually nothing changed on first glance. It was expected that deletion of lysyl‐phosphatidylglycerol synthase (lys‐PGS) would cause a major change in the cell membrane proteome. Only 1.5–3.5% of cell envelope proteins shifted up or down out of more than 35% of theoretical. The levels of lipid biosynthetic enzymes were unchanged. What was affected were the stress sensing regulatory proteins and their targets. When it comes to specifying new drug targets, lys‐PGS must be approached with care – it's mouth may already be engaged.magnified imagepp. 1694–1698

Cover Picture: Proteomics 8'10

AbstractProhibition that works: Prohibitin 1Prohibitin 1 (Phb1) was cloned in 1991 based on its ability to suppress the regrowth of liver tissue. That task was not trivial – Phb1 turned out to be a buddy of just about anyone of any importance. It is highly conserved, ubiquitous among eukaryotes, and exerts a controlling interest in apoptosis, cell cycle, differentiation, and senescence. It, in turn, is controlled by a variety of post‐translational modifications. Did I say it is a tumor suppressor, too? It is. Sánchez‐Quiles et al. set out to survey the effects of changing levels of Phb1 on a variety of cell functions in cultured human hematoma cells. Using si technology, they found more that than 500 genes were stimulated or repressed in one liver cell line. One partial explanation is the observation that Phb1 is also involved in tissue homeostasis through two interacting networks.Sánchez‐Quiles, V. et al., Proteomics 2010, 10, 1609–1620.Myxobacter mixes mean mixture for mealsMost of us learned what we know of microbiology in medical settings, concerned about infectivity, clinical symptoms and drug resistance. Some of us (“molecular biologists”) never got beyond Escherichia coli and Bacillus subtilis. The excuse for working with so few species of bacteria was that it took too long to move all the genetic and biochemical tools into a new species. We can no longer hide behind that excuse. Entire genomes can be sequenced in a matter of weeks (or days). In this study, Chao et al. analyze the proteomic response of Anaeromyxobacter dehalogenans to changes in nutrients including uranium(VI), halogenated phenols, Fe(III) to fumarate as electron acceptors. Applying commonly used proteomic tools (2‐DE/MALDI‐TOF), they found spots for 559 unique proteins. Pathway analysis revealed an unusually wide array of means of living off of amino acid metabolism (like lysine to butyrate fermentation).Chao, T.‐C. et al., Proteomics 2010, 10, 1685–1693.“Brain must be in gear before starting mouth”This group clearly had their brain in gear. Sievers et al. gave Staphylococcus aureus every chance to respond “normally” to the deletion of a critical gene but virtually nothing changed on first glance. It was expected that deletion of lysyl‐phosphatidylglycerol synthase (lys‐PGS) would cause a major change in the cell membrane proteome. Only 1.5–3.5% of cell envelope proteins shifted up or down out of more than 35% of theoretical. The levels of lipid biosynthetic enzymes were unchanged. What was affected were the stress sensing regulatory proteins and their targets. When it comes to specifying new drug targets, lys‐PGS must be approached with care – it's mouth may already be engaged.Sievers, S. et al. Proteomics 2010, 10, 1694–1698.

In this issue

AbstractProhibition that works: Prohibitin 1Prohibitin 1 (Phb1) was cloned in 1991 based on its ability to suppress the regrowth of liver tissue. That task was not trivial – Phb1 turned out to be a buddy of just about anyone of any importance. It is highly conserved, ubiquitous among eukaryotes, and exerts a controlling interest in apoptosis, cell cycle, differentiation, and senescence. It, in turn, is controlled by a variety of post‐translational modifications. Did I say it is a tumor suppressor, too? It is. Sánchez‐Quiles et al. set out to survey the effects of changing levels of Phb1 on a variety of cell functions in cultured human hematoma cells. Using si technology, they found more that than 500 genes were stimulated or repressed in one liver cell line. One partial explanation is the observation that Phb1 is also involved in tissue homeostasis through two interacting networks.magnified imagepp. 1609–1620Myxobacter mixes mean mixture for mealsMost of us learned what we know of microbiology in medical settings, concerned about infectivity, clinical symptoms and drug resistance. Some of us (“molecular biologists”) never got beyond Escherichia coli and Bacillus subtilis. The excuse for working with so few species of bacteria was that it took too long to move all the genetic and biochemical tools into a new species. We can no longer hide behind that excuse. Entire genomes can be sequenced in a matter of weeks (or days). In this study, Chao et al. analyze the proteomic response of Anaeromyxobacter dehalogenans to changes in nutrients including uranium(VI), halogenated phenols, Fe(III) to fumarate as electron acceptors. Applying commonly used proteomic tools (2‐DE/MALDI‐TOF), they found spots for 559 unique proteins. Pathway analysis revealed an unusually wide array of means of living off of amino acid metabolism (like lysine to butyrate fermentation).magnified imagepp. 1685–1693“Brain must be in gear before starting mouth”This group clearly had their brain in gear. Sievers et al. gave Staphylococcus aureus every chance to respond “normally” to the deletion of a critical gene but virtually nothing changed on first glance. It was expected that deletion of lysyl‐phosphatidylglycerol synthase (lys‐PGS) would cause a major change in the cell membrane proteome. Only 1.5–3.5% of cell envelope proteins shifted up or down out of more than 35% of theoretical. The levels of lipid biosynthetic enzymes were unchanged. What was affected were the stress sensing regulatory proteins and their targets. When it comes to specifying new drug targets, lys‐PGS must be approached with care – it's mouth may already be engaged.magnified imagepp. 1694–1698