Two-dimensional Sodium Dodecyl Sulfate-polyacrylamide Gel Research Articles

Protein profile changes during priming explants to embryogenic response in Coffea canephora: identification of the RPN12 proteasome subunit involved in the protein degradation.

Plant somatic embryogenesis encompasses somatic cells switch into embryogenic cells that can later produce somatic embryos with the ability to produce plantlets. Previously, we defined in vitro culture settings for the somatic embryogenesis process of Coffea canephora that comprise adequate plantlets with auxin plus cytokinin followed by cut-leaf explant cultivation with cytokinin, producing embryos with the ability to regenerate plantlets. Here, we confirmed that cultivating cut-leaf explants with cytokinin is sufficient to promote somatic embryos proliferation and the high yield of somatic embryos in the protocol requires adequate plantlets with auxin plus cytokinin. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels reveal auxin-plus cytokinin-dependent regulated proteins in plantlets with up and down abundance. Chitinase A class III, proteins involved in the metabolism and folding of proteins, photosynthesis, antioxidant activity, and chromatin organization were identified. The RPN12 protein, which is a subunit of the proteasome 26S, has an abundance that is not associated with transcript changes, suggesting post-translational regulation.

Proteomic Analysis of Fresh and Liquid-Stored Boar Spermatozoa.

Simple SummaryMale gametes can be stored for a long period of time for the purpose of preserving genetic material. Cryopreservation and liquid preservation are two main storage procedures commonly used for boar semen. There is evidence in the literature suggesting that cryopreservation changes the profile of proteins that are linked to the motility and function of spermatozoa. It was postulated that they can affect motility, capacitation, oocyte binding ability, and the acrosome reaction of spermatozoa. On the other hand, little is known about changes in protein levels in sperm that occur during liquid storage. Therefore, the objective of this study was to investigate whether liquid storage also causes an alteration in the proteomic profile of stored spermatozoa. A comparative proteomic approach was used to analyze protein samples from fresh spermatozoa and spermatozoa stored for three days at 15–17 °C. Results obtained show that liquid preservation causes quantitative changes in the boar sperm proteome with the over-expression of three out of four proteins in the liquid-stored sperm. Our findings can help elucidate the events involved in liquid preservation. In this study comparative proteomics was used to define changes in the expression of the spermatozoa proteins during liquid storage. Semen from eight boars was analyzed on the day of collection and after liquid preservation at 15–17 °C for three days. Sperm parameters (concentration, motility, morphology, vitality) and percentage of non-capacitated and acrosomal-reacted spermatozoa were determined. Sperm proteins were extracted and separated by two-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and proteomic profiles were computationally compared to highlight differentially expressed protein spots that were, in turn, identified by mass spectrometry. The intensities of four spots were significantly different between fresh and liquid stored sperm. Namely: ATP citrate lyase, chaperonin containing T-complex polypeptide 1 (TCP1) subunit ε and probable phospholipid-transporting ATP-ase were over-expressed in liquid stored sperm, whereas cytosolic non-specific dipeptidase was over-expressed in fresh sperm. These differentially expressed proteins could be used as plausible biomarkers for the evaluation of boar semen quality and spermatozoa survival after liquid storage and could help to address problems associated with sperm preservation.

Counterion Dye Staining of Proteins in One- and Two-Dimensional Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Tryptic Gel Digestion of Stained Protein for Mass Spectrometry.

A fast and matrix-assisted laser desorption/ionization-mass spectrometry compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis is described. It is based on the counterion dye staining method that employs oppositely charged two dyes, zincon and ethyl violet to form an ion-pair complex. The protocol including fixing, staining, and quick washing steps can be completed in 1-1.5h depending upon gel thickness. It has the sensitivity comparable to the colloidal Coomassie Brilliant Blue G stain using phosphoric acid as a component of staining solution (4-8ng). The counterion dye stain does not induce protein modifications that complicate interpretation of peptide mapping data from mass spectrometry. Considering the speed, sensitivity, and compatibility with mass spectrometry, the counterion dye stain may be more practical than any other dye-based protein stains for routine proteomic researches.

Developments on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for identifying dissolved and particulate proteins in seawater after two-dimensional sodium dodecyl sulfate–polyacrylamide gel electrophoresis

Two-dimensional sodium dodecyl sulfate–polyacrylamide gel electrophoresis (2D-SDS–PAGE) was applied to separate protein in dissolved organic matter (DOM) and in particulate organic matter (POM) from seawater. Dissolved proteins were concentrated and purified using tangential flow ultrafiltration (UF) and centrifugal ultrafiltration. Twelve proteins (Sypro Ruby stained 2D-gels) exhibited isoelectric points (pIs) ranging from 3.5 to 6.0, and molecular weights (MWs) within the 10–50kDa range.Marine plankton were concentrated by centrifugation, and proteins were isolated by grounding the biomass under liquid nitrogen before several washing stages [10% trichloroacetic acid (TCA) in acetone followed by 0.1M ammonium acetate in 80/20 methanol/water] and extraction with a phenol–SDS mixture. 2D-SDS–PAGE showed the presence of approximately 140 different protein spots (Sypro Ruby stained 2D-gels), and plankton proteins exhibited MWs ranging from 12 to 150kDa with pIs between 3 and 10.Electrophoretically separated proteins were further enzymatically in-gel digested (trypsin) and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Dissolved proteins in eight of the twelve resolved spots were identified by mass mapping (eleven different proteins were assigned); whereas, seven of the twenty-four resolved plankton protein spots were identified, and four different proteins were successfully assigned.

Proteomic identification of calcium-binding chaperone calreticulin as a potential mediator for the neuroprotective and neuritogenic activities of fruit-derived glycoside amygdalin

Amygdalin is a fruit-derived glycoside with the potential for treating neurodegenerative diseases. This study was designed to identify the neuroprotective and neuritogenic activities of amygdalin. We initially demonstrated that amygdalin enhanced nerve growth factor (NGF)-induced neuritogenesis and attenuated 6-hydroxydopamine (6-OHDA)-induced neurotoxicity in rat dopaminergic PC12 cells. To define protein targets for amygdalin, we selected a total of 11 mostly regulated protein spots from two-dimensional sodium dodecyl sulfate–polyacrylamide gel electrophoresis gels for protein identification by matrix-assisted laser desorption/ionization–time-of-flight–mass spectrometry. We verified the effect of amygdalin on six representative proteins (i.e., calreticulin, Hsp90β, Grp94, 14-3-3η, 14-3-3ζ/δ and Rab GDI-α) for biological relevance to neuronal survival and differentiation. Calcium-binding chaperone calreticulin is of special interest for its activities to promote folding, oligomeric assembly and quality control of proteins that modulate cell survival and differentiation. We transiently knocked down calreticulin expression by specific siRNA and studied its effect on the neuroprotective and neuritogenic activities of amygdalin. We found that amygdalin failed to enhance NGF-induced neuritogenesis in calreticulin-siRNA transfected cells. On the other hand, amygdalin rescued 6-OHDA-induced loss of calreticulin expression. We also found that amygdalin increased the intracellular calcium concentration possibly via inducing calreticulin. Collectively, our results demonstrated the role of calreticulin in mediating the neuroprotective and neuritogenic activities of amygdalin.

Unraveling the Equine Lymphocyte Proteome: Differential Septin 7 Expression Associates with Immune Cells in Equine Recurrent Uveitis

Equine recurrent uveitis is a spontaneous, lymphocyte-driven autoimmune disease. It affects horses worldwide and presents with painful remitting-relapsing inflammatory attacks of inner eye structures eventually leading to blindness. Since lymphocytes are the key players in equine recurrent uveitis, we were interested in potential changes of their protein repertoire which may be involved in disease pathogenesis. To create a reference for differential proteome analysis, we first unraveled the equine lymphocyte proteome by two-dimensional sodium dodecyl sulfate - polyacrylamide gel electrophoresis and subsequently identified 352 protein spots. Next, we compared lymphocytes from ERU cases and healthy horses with a two-dimensional fluorescence difference in gel electrophoresis approach. With this technique, we identified seven differentially expressed proteins between conditions. One of the significantly lower expressed candidates, septin 7, plays a role in regulation of cell shape, motility and migration. Further analyses revealed T cells as the main cell type with decreased septin 7 abundance in equine recurrent uveitis. These findings point to a possible pathogenetic role of septin 7 in this sight-threatening disease.

Early molecular events involved inPinus pinasterAit. somatic embryo development under reduced water availability: transcriptomic and proteomic analyses

Maritime pine somatic embryos (SEs) require a reduction in water availability (high gellan gum concentration in the maturation medium) to reach the cotyledonary stage. This key switch, reported specifically for pine species, is not yet well understood. To facilitate the use of somatic embryogenesis for mass propagation of conifers, we need a better understanding of embryo development. Comparison of both transcriptome (Illumina RNA sequencing) and proteome [two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis with mass spectrometry (MS) identification] of immature SEs, cultured on either high (9G) or low (4G) gellan gum concentration, was performed, together with analysis of water content, fresh and dry mass, endogenous abscisic acid (ABA; gas chromatography-MS), soluble sugars (high-pressure liquid chromatography), starch and confocal laser microscope observations. This multiscale, integrated analysis was used to unravel early molecular and physiological events involved in SE development. Under unfavorable conditions (4G), the glycolytic pathway was enhanced, possibly in relation to cell proliferation that may be antagonistic to SE development. Under favorable conditions (9G), SEs adapted to culture constraint by activating specific protective pathways, and ABA-mediated molecular and physiological responses promoting embryo development. Our results suggest that on 9G, germin-like protein and ubiquitin-protein ligase could be used as predictive markers of SE development, whereas protein phosphatase 2C could be a biomarker for culture adaptive responses. This is the first characterization of early molecular mechanisms involved in the development of pine SEs following an increase in gellan gum concentration in the maturation medium, and it is also the first report on somatic embryogenesis in conifers combining transcriptomic and proteomic datasets.

Differential seminal plasma proteome according to semen retrieval in men with spinal cord injury

To evaluate protein expression profile and to quantify proteins present in seminal plasma from men with spinal cord injury (SCI) and healthy men without SCI. Experimental study. University hospital. Twelve SCI patients divided into two groups, six who underwent electroejaculation (EEJ) and six who underwent penile vibratory stimulation (PVS); and ten control subjects presenting normal sperm motility and concentration. EEJ and PVS. The seminal plasma protein profile was analyzed by two proteomic strategies: data-independent label-free quantitative proteomics (MS(E)) and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (2D SDS-PAGE). A total of 638 different proteins were identified by MS(E) and 18 by 2D SDS-PAGE followed by tandem mass spectrometry. Interactome analysis showed key reproductive biologic processes-insemination, sperm and oocyte fusion, and acrosome reaction-related to all groups, as were triglyceride stimuli. Processes related to actin and muscle function and to iron oxidation, transportation, and homeostasis were found only in the EEJ and PVS groups; response to hydrogen peroxide and increased immune response was found only in the PVS group. This study was able to demonstrate differential protein expression among control, PVS, and EEJ groups; SCI is responsible for alterations in seminal plasma protein profile leading to a deviation from homeostasis; proteins reported in both PVS and EEJ groups correlate with the pathophysiology of SCI-related infertility.

Matrix effects during monitoring of antibody and host cell proteins using attenuated total reflection spectroscopy

Production of recombinant proteins, e.g. antibodies, requires constant real-time monitoring to optimize yield and quality attributes and to respond to changing production conditions, such as host cell protein (HCP) titers. To date, this monitoring of mammalian cell culture-based processes is done using laborious and time consuming enzyme-linked immunosorbent assays (ELISA), two-dimensional sodium dodecylsulphate polyacrylamide gel electrophoresis, and chromatography-based systems. Measurements are usually performed off-line, requiring regular sample withdrawal associated with increased contamination risk. As information is obtained retrospectively, the reaction time to adapt to process changes is too long, leading to lower yield and higher costs. To address the resulting demand for continuous online-monitoring systems, we present a feasibility study using attenuated total reflection spectroscopy (ATR) to monitor mAb and HCP levels of NS0 cell culture in situ, taking matrix effects into account. Fifty-six NS0 cell culture samples were treated with polyelectrolytes for semi-selective protein precipitation. Additionally, part of the samples was subjected to filtration prior to analysis, to change the background matrix and evaluate effects on chemometric quantification models. General models to quantify HCP and mAb in both filtered and unfiltered matrix showed lower prediction accuracy compared to models designed for a specific matrix. HCP quantification in the range of 2,000-55,000 ng mL(-1) using specific models was accurate for most samples, with results within the accepted limit of an ELISA assay. In contrast, mAb prediction was less accurate, predicting mAb in the range of 0.2-1.7 g L(-1) . As some samples deviated substantially from reference values, further investigations elucidating the suitability of ATR for monitoring are required.

Do Prokaryotes Have More Kinetically Stable Proteins Than Eukaryotic Organisms?

Upon folding, some proteins become conformationally trapped, presumably to protect against aggregation or premature degradation. To probe the occurrence of this property, known as kinetic stability, we used a diagonal two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis method to probe biologically diverse organisms. The results show that kinetic stability is prevalent in prokaryotes, especially thermophiles, but uncommon in eukaryotic organisms, thereby suggesting that this property might be crucial for the adaptation and survival of less complex prokaryotic organisms.

Glucanases and Chitinases as Causal Agents in the Protection ofAcaciaExtrafloral Nectar from Infestation by Phytopathogens

Nectars are rich in primary metabolites and attract mutualistic animals, which serve as pollinators or as an indirect defense against herbivores. Their chemical composition makes nectars prone to microbial infestation. As protective strategy, floral nectar of ornamental tobacco (Nicotiana langsdorffii x Nicotiana sanderae) contains "nectarins," proteins producing reactive oxygen species such as hydrogen peroxide. By contrast, pathogenesis-related (PR) proteins were detected in Acacia extrafloral nectar (EFN), which is secreted in the context of defensive ant-plant mutualisms. We investigated whether these PR proteins protect EFN from phytopathogens. Five sympatric species (Acacia cornigera, A. hindsii, A. collinsii, A. farnesiana, and Prosopis juliflora) were compared that differ in their ant-plant mutualism. EFN of myrmecophytes, which are obligate ant-plants that secrete EFN constitutively to nourish specialized ant inhabitants, significantly inhibited the growth of four out of six tested phytopathogenic microorganisms. By contrast, EFN of nonmyrmecophytes, which is secreted only transiently in response to herbivory, did not exhibit a detectable inhibitory activity. Combining two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis with nanoflow liquid chromatography-tandem mass spectrometry analysis confirmed that PR proteins represented over 90% of all proteins in myrmecophyte EFN. The inhibition of microbial growth was exerted by the protein fraction, but not the small metabolites of this EFN, and disappeared when nectar was heated. In-gel assays demonstrated the activity of acidic and basic chitinases in all EFNs, whereas glucanases were detected only in EFN of myrmecophytes. Our results demonstrate that PR proteins causally underlie the protection of Acacia EFN from microorganisms and that acidic and basic glucanases likely represent the most important prerequisite in this defensive function.

Rapid clearance of circulating haptoglobin from plasma during acute pulmonary embolism in rats results in HMOX1 up-regulation in peripheral blood leukocytes.

Acute pulmonary embolism (PE) causes pulmonary hypertension (PH) via several mechanisms including pulmonary vasospasm. We hypothesize that PE with associated PH leads to alterations in plasma protein concentrations indicative of disease severity and prognosis. To identify plasma proteins altered in abundance by PE in rats. Plasma samples were obtained from rats at 2, 6 and 18 h after experimental PE produced with intrajugular injection of polystyrene beads at three different levels of severity (mild, moderate and severe). Total plasma protein was separated using two-dimensional sodium dodecylsulfate-polyacrylamide gel electrophoresis (2D SDS-PAGE) and candidate protein spots altered in expression by PE were identified by mass spectroscopy. Haptoglobin identity and amount was verified by western blot analysis. The PE model produced a dose-dependent increase in right ventricular systolic pressure (RVSP) (mmHg) at 2 h: mild 39+/-1.7, moderate 40+/-1.8 and severe 51+/-1.3 mmHg, coincident with significant increases in free plasma (hemoglobin). Combined 2D SDS-PAGE and Western blot analysis indicated time- and dose-dependant loss of plasma haptoglobin levels in response to acute PE. Haptoglobin (HP) was essentially absent from plasma within 2 h of severe PE. Clearance of HP from plasma was accompanied by increased expression of heme oxygenase-1 (hmox1) in peripheral blood leukocytes and in HMOX1 enzyme activity in the liver. PE that causes pulmonary hypertension is associated with haptoglobin depletion and up-regulation of HMOX1 enzyme.

Diminished Exoproteome of Frankia spp. in Culture and Symbiosis

Frankia species are the most geographically widespread gram-positive plant symbionts, carrying out N(2) fixation in root nodules of trees and woody shrubs called actinorhizal plants. Taking advantage of the sequencing of three Frankia genomes, proteomics techniques were used to investigate the population of extracellular proteins (the exoproteome) from Frankia, some of which potentially mediate host-microbe interactions. Initial two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of culture supernatants indicated that cytoplasmic proteins appeared in supernatants as cells aged, likely because older hyphae lyse in this slow-growing filamentous actinomycete. Using liquid chromatography coupled to tandem mass spectrometry to identify peptides, 38 proteins were identified in the culture supernatant of Frankia sp. strain CcI3, but only three had predicted export signal peptides. In symbiotic cells, 42 signal peptide-containing proteins were detected from strain CcI3 in Casuarina cunninghamiana and Casuarina glauca root nodules, while 73 and 53 putative secreted proteins containing signal peptides were identified from Frankia strains in field-collected root nodules of Alnus incana and Elaeagnus angustifolia, respectively. Solute-binding proteins were the most commonly identified secreted proteins in symbiosis, particularly those predicted to bind branched-chain amino acids and peptides. These direct proteomics results complement a previous bioinformatics study that predicted few secreted hydrolytic enzymes in the Frankia proteome and provide direct evidence that the symbiosis succeeds partly, if not largely, because of a benign relationship.

Induction of copper/zinc‐superoxide dismutase by CCL5/CCR5 activation causes tumour necrosis factor‐α and reactive oxygen species production in macrophages

Using two-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis, we found that copper/zinc superoxide dismutase (Cu/Zn-SOD, SOD-1) was induced in constructed CCR5 stably transfected HEK 293 cells, but not in mock cells, treated with CCL5. CCL5-induced SOD-1 expression was also confirmed in HEK 293-CCR5 cells and CCR5-positive granulocyte-macrophage colony-stimulating factor-induced human macrophages and murine macrophage RAW264.7 cells. CCL5 and CCR5 interaction induced SOD-1 expression mainly via MEK-ERK activation. In addition, we provided evidence that upregulation of SOD-1 by CCL5/CCR5 activation occurred in parallel with the increased release of tumour necrosis factor-alpha and nitric oxide and production of intracellular reactive oxygen species as well as enhanced nuclear factor-kappaB transcriptional activity in CCR5-positive RAW264.7 cells. Conversely, the MEK1/2 inhibitor PD98059 significantly inhibited SOD-1 expression with the decrease of these biological responses. More importantly, inhibition of SOD-1 activity by disulfiram also strongly inhibited the CCL5-induced biological effects. These data suggest that SOD-1 mediates CCR5 activation by CCL5 and that pharmacological modulation of SOD-1 may be beneficial to CCR5-associated diseases.

Identification of novel protein targets regulated by maternal dietary fatty acid composition in neonatal rat liver

Polyunsaturated fatty acids regulate metabolic pathways, which in early development could have important consequences to adaptation to extra-uterine life and programming of metabolic pathways. Female rats were fed one of two diets identical in all nutrients, except that the fat in one diet was high in unsaturated fatty acids (UFA) and the other low UFA, through gestation and lactation. Two-dimensional sodium dodecylsulfate polyacrylamide gel electrophoresis of protein extracts from 3-day old pup liver resolved over 800 proteins. Employing MALDI-TOF MS and peptide mapping we identified 11 proteins that differed more than three-fold between the groups, 10 up regulated and one down regulated in the high UFA group. The up-regulated proteins included fructose-1,6-bisphosphatase 1, glycerol-3-phosphate dehydrogenase, galactokinase 1, 40S ribosomal protein SA, elongation factor 1-gamma, protein disulfide-isomerase A6, catalase, cytokeratin-8 and 60 kDa heat shock protein, and the down-regulated protein was argininosuccinate synthase, none having been previously reported to be regulated by fatty acids in the developing liver. We further determined that fructose-1,6-biphosphatase is acetylated at the N-terminus. We demonstrate that early fatty acid nutrition impacts hepatic metabolic pathways relevant to gluconeogenesis, redox balance and nitric oxide signaling.

Electrospray ionization mass spectrometry as a critical tool for revealing new properties of snake venom phospholipase A2

Results from high-performance liquid chromatography/nano-electrospray ionization tandem mass spectrometry (HPLC/nESI-MS/MS) coupled to two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (2D SDS-PAGE) indicated that the monomer and dimer of phospholipase A(2) (PLA(2)) coexisted in crude Chinese Agkistrodon blomhoffii Ussurensis snake venom (ABUSV). Then, an acidic PLA(2) with the accurate molecular mass of 13979.6 Da was purified from ABUSV (mo-ABUSV-aPLA(2)). MS/MS-derived peptides from ABUSV-aPLA(2) were compared with other homologous snake venom PLA(2)s, which in turn showed that ABUSV-aPLA(2) is a novel snake venom PLA(2). Meanwhile, the ABUSV-aPLA(2) dimer (di-ABUSV-aPLA(2)) was also obtained. MS/MS analysis identified the same peptides from di-ABUSV-aPLA(2) as from mo-ABUSV-aPLA(2), which indicates that di-ABUSV-aPLA(2) is a homodimer. One Ca(2+) ion is contained per ABUSV-aPLA(2). The Ca(2+) ion is critical for both the hydrolytic activity and the structure of ABUSV-aPLA(2). Pro-Q Emerald and Pro-Q Diamond specific glycoprotein and phosphoprotein staining combined with MS/MS analysis indicated that the ABUSV-aPLA(2) is both a glycoprotein and a phosphoprotein, which to our knowledge is the first such report for a snake venom PLA(2) and thus provides new threads for the study of the functions and structures of snake venom PLA(2)s. One phosphorylation site and the size of the glycan chain are determined by using HPLC/nESI-MS/MS and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. The delicate utilization of ESI-MS can exert tremendous impact on protein sciences.

Stimulation of Expression of a Silica-Induced Protein (Sip) in Thermus thermophilus by Supersaturated Silicic Acid

The effects of silicic acid on the growth of Thermus thermophilus TMY, an extreme thermophile isolated from a siliceous deposit formed from geothermal water at a geothermal power plant in Japan, were examined at 75 degrees C. At concentrations higher than the solubility of amorphous silica (400 to 700 ppm SiO(2)), a silica-induced protein (Sip) was isolated from the cell envelope fraction of log-phase TMY cells grown in the presence of supersaturated silicic acid. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed the molecular mass and pI of Sip to be about 35 kDa and 9.5, respectively. Induction of Sip expression occurred within 1 h after the addition of a supersaturating concentration of silicic acid to TM broth. Expression of Sip-like proteins was also observed in other thermophiles, including T. thermophilus HB8 and Thermus aquaticus YT-1. The amino acid sequence of Sip was similar to that of the predicted solute-binding protein of the Fe(3+) ABC transporter in T. thermophilus HB8 (locus tag, TTHA1628; GenBank accession no. NC_006461; GeneID, 3169376). The sip gene (987-bp) product showed 87% identity with the TTHA1628 product and the presumed Fe(3+)-binding protein of T. thermophilus HB27 (locus tag TTC1264; GenBank accession no. NC_005835; GeneID, 2774619). Within the genome, sip is situated as a component of the Fbp-type ABC transporter operon, which contains a palindromic structure immediately downstream of sip. This structure is conserved in other T. thermophilus genomes and may function as a terminator that causes definitive Sip expression in response to silica stress.

Vitamin K Induces Osteoblast Differentiation through Pregnane X Receptor-Mediated Transcriptional Control of the Msx2 Gene

Vitamin K is a fat-soluble vitamin that serves as a coenzyme for vitamin K-dependent carboxylase. Besides its canonical action, vitamin K binds to the steroid and xenobiotic receptor (SXR)/pregnane X receptor (PXR) and modulates gene transcription. To determine if the osteoprotective action of vitamin K is the result of the PXR/SXR pathway, we screened by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis the PXR/SXR target genes in an osteoblastic cell line (MC3T3-E1) treated with a vitamin K2 (menaquinone 4 [MK4]). Osteoblastic differentiation of MC3T3-E1 cells was induced by MK4. Msx2, an osteoblastogenic transcription factor, was identified as an MK4-induced gene. Functional analysis of the Msx2 gene promoter mapped a vitamin K-responsive element (PXR-responsive element [PXRE]) that was directly bound by a PXR/retinoid X receptor alpha heterodimer. In a chromatin immunoprecipitation analysis, PXR was recruited together with a coactivator, p300, to the PXRE in the Msx2 promoter. MK4-bound PXR cooperated with estrogen-bound estrogen receptor alpha to control transcription at the Msx2 promoter. Knockdown of either PXR or Msx2 attenuated the effect of MK4 on osteoblastic differentiation. Thus, the present study suggests that Msx2 is a target gene for PXR activated by vitamin K and suggests that the osteoprotective action of MK4 in the human mediates, at least in part, a genomic pathway of vitamin K signaling.

Analysis of LuxR Regulon Gene Expression during Quorum Sensing inVibrio fischeri

The regulation of the lux operon (luxICDABEG) of Vibrio fischeri has been intensively studied as a model for quorum sensing in proteobacteria. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis previously identified several non-Lux proteins in V. fischeri MJ-100 whose expression was dependent on LuxR and 3-oxo-hexanoyl-l-homoserine lactone (3-oxo-C6-HSL). To determine if the LuxR-dependent regulation of the genes encoding these proteins was due to direct transcriptional control by LuxR and 3-oxo-C6-HSL or instead was due to indirect control via an unidentified regulatory element, promoters of interest were cloned into a lacZ reporter and tested for their LuxR and 3-oxo-C6-HSL dependence in recombinant Escherichia coli. The promoters for qsrP, acfA, and ribB were found to be directly activated via LuxR-3-oxo-C6-HSL. The sites of transcription initiation were established via primer extension analysis. Based on this information and the position of the lux box-binding site near position -40, all three promoters appear to have a class II-type promoter structure. In order to more fully characterize the LuxR regulon in V. fischeri MJ-100, real-time reverse transcription-PCR was used to study the temporal expression of qsrP, acfA, and ribB during the exponential and stationary phases of growth, and electrophoretic mobility shift assays were used to compare the binding affinities of LuxR to the promoters under investigation. Taken together, the results demonstrate that regulation of the production of QsrP, RibB, and AcfA is controlled directly by LuxR at the level of transcription, thereby establishing that there is a LuxR regulon in V. fischeri MJ-100 whose genes are coordinately expressed during mid-exponential growth.

Proteomic and Immunoblot Analyses of Bartonella quintana Total Membrane Proteins Identify Antigens Recognized by Sera from Infected Patients

Bartonella quintana is a fastidious, gram-negative, rod-shaped bacterium that causes prolonged bacteremia in immunocompetent humans and severe infections in immunocompromised individuals. We sought to define the outer membrane subproteome of B. quintana in order to obtain insight into the biology and pathogenesis of this emerging pathogen and to identify the predominant B. quintana antigens targeted by the human immune system during infection. We isolated the total membrane proteins of B. quintana and identified 60 proteins by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and peptide mass fingerprinting. Using the newly constructed proteome map, we then utilized two-dimensional immunoblotting with sera from 21 B. quintana-infected patients to identify 24 consistently recognized, immunoreactive B. quintana antigens that have potential relevance for pathogenesis and diagnosis. Among the outer membrane proteins, the variably expressed outer membrane protein adhesins (VompA and VompB), peptidyl-prolyl cis-trans-isomerase (PpI), and hemin-binding protein E (HbpE) were recognized most frequently by sera from patients, which is consistent with surface expression of these virulence factors during human infection.