PON-P2: Prediction Method for Fast and Reliable Identification of Harmful Variants

More reliable and faster prediction methods are needed to interpret enormous amounts of data generated by sequencing and genome projects. We have developed a new computational tool, PON-P2, for classification of amino acid substitutions in human proteins. The method is a machine learning-based classifier and groups the variants into pathogenic, neutral and unknown classes, on the basis of random forest probability score. PON-P2 is trained using pathogenic and neutral variants obtained from VariBench, a database for benchmark variation datasets. PON-P2 utilizes information about evolutionary conservation of sequences, physical and biochemical properties of amino acids, GO annotations and if available, functional annotations of variation sites. Extensive feature selection was performed to identify 8 informative features among altogether 622 features. PON-P2 consistently showed superior performance in comparison to existing state-of-the-art tools. In 10-fold cross-validation test, its accuracy and MCC are 0.90 and 0.80, respectively, and in the independent test, they are 0.86 and 0.71, respectively. The coverage of PON-P2 is 61.7% in the 10-fold cross-validation and 62.1% in the test dataset. PON-P2 is a powerful tool for screening harmful variants and for ranking and prioritizing experimental characterization. It is very fast making it capable of analyzing large variant datasets. PON-P2 is freely available at http://structure.bmc.lu.se/PON-P2/.     

PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations

Transfer RNAs (tRNAs) are essential for encoding the transcribed genetic information from DNA into proteins. Variations in the human tRNAs are involved in diverse clinical phenotypes. Interestingly, all pathogenic variations in tRNAs are located in mitochondrial tRNAs (mt-tRNAs). Therefore, it is crucial to identify pathogenic variations in mt-tRNAs for disease diagnosis and proper treatment. We collected mt-tRNA variations using a classification based on evidence from several sources and used the data to develop a multifactorial probability-based prediction method, PON-mt-tRNA, for classification of mt-tRNA single nucleotide substitutions. We integrated a machine learning-based predictor and an evidence-based likelihood ratio for pathogenicity using evidence of segregation, biochemistry and histochemistry to predict the posterior probability of pathogenicity of variants. The accuracy and Matthews correlation coefficient (MCC) of PON-mt-tRNA are 1.00 and 0.99, respectively. In the absence of evidence from segregation, biochemistry and histochemistry, PON-mt-tRNA classifies variations based on the machine learning method with an accuracy and MCC of 0.69 and 0.39, respectively. We classified all possible single nucleotide substitutions in all human mt-tRNAs using PON-mt-tRNA. The variations in the loops are more often tolerated compared to the variations in stems. The anticodon loop contains comparatively more predicted pathogenic variations than the other loops. PON-mt-tRNA is available at http://structure.bmc.lu.se/PON-mt-tRNA/.     

Proteome analysis of B-cell maturation

Proteins affected by anti-mIgM stimulation during B-cell maturation were identified using 2-DE-based proteomics. We investigated the proteome profiles of stimulated and nonstimulated Ramos B-cells at eight time points during 5 d and compared the obtained proteomic data to the corresponding data from DNA-microarray studies. Anti-mIgM stimulation of the cells resulted in significant differences (> or =twofold) in the protein abundance close to 100 proteins and differences in post-translational protein modifications. Forty-eight up- or down-regulated proteins were identified by mass spectrometric methods and database searches. The identities of a further nine proteins were revealed by comparing their positions to the known proteins in other lymphocyte 2-DE databases. Several of the proteins are directly related to the functional and morphological characteristics of B-cells, such as cytoskeleton rearrangement and intracellular signalling triggered by the crosslinking of B-cell receptors. In addition to proteins known to be involved in human B-cell maturation, we identified several proteins that were not previously linked to lymphocyte differentiation. The results provide deeper insights into the process of B-cell maturation and may lead to novel therapeutic strategies for immunodeficiencies. An interactive 2-DE reference map is available at http://bioinf.uta.fi/BcellProteome.     

Proteomic Alterations in B Lymphocytes of Sensitized Mice in a Model of Chemical-Induced Asthma

Introduction and Aim

The role of B-lymphocytes in chemical-induced asthma is largely unknown. Recent work demonstrated that transferring B lymphocytes from toluene diisocyanate (TDI)-sensitized mice into naïve mice, B cell KO mice and SCID mice, triggered an asthma-like response in these mice after a subsequent TDI-challenge. We applied two-dimensional difference gel electrophoresis (2D-DIGE) to describe the “sensitized signature” of B lymphocytes comparing TDI-sensitized mice with control mice.

Results

Sixteen proteins were identified that were significantly up- or down-regulated in B lymphocytes of sensitized mice. Particularly differences in the expression of cyclophilin A, cofilin 1 and zinc finger containing CCHC domain protein 11 could be correlated to the function of B lymphocytes as initiators of T lymphocyte independent asthma-like responses.

Conclusion

This study revealed important alterations in the proteome of sensitized B cells in a mouse model of chemical-induced asthma, which will have an important impact on the B cell function.     

Megadalton Complexes in the Chloroplast Stroma of Arabidopsis thaliana Characterized by Size Exclusion Chromatography,Mass Spectrometry,and Hierarchical Clustering

To characterize MDa-sized macromolecular chloroplast stroma protein assemblies and to extend coverage of the chloroplast stroma proteome, we fractionated soluble chloroplast stroma in the non-denatured state by size exclusion chromatography with a size separation range up to ∼5 MDa. To maximize protein complex stability and resolution of megadalton complexes, ionic strength and composition were optimized. Subsequent high accuracy tandem mass spectrometry analysis (LTQ-Orbitrap) identified 1081 proteins across the complete native mass range. Protein complexes and assembly states above 0.8 MDa were resolved using hierarchical clustering, and protein heat maps were generated from normalized protein spectral counts for each of the size exclusion chromatography fractions; this complemented previous analysis of stromal complexes up to 0.8 MDa (Peltier, J. B., Cai, Y., Sun, Q., Zabrouskov, V., Giacomelli, L., Rudella, A., Ytterberg, A. J., Rutschow, H., and van Wijk, K. J. (2006) The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Mol. Cell. Proteomics 5, 114–133). This combined experimental and bioinformatics analyses resolved chloroplast ribosomes in different assembly and functional states (e.g. 30, 50, and 70 S), which enabled the identification of plastid homologues of prokaryotic ribosome assembly factors as well as proteins involved in co-translational modifications, targeting, and folding. The roles of these ribosome-associating proteins will be discussed. Known RNA splice factors (e.g. CAF1/WTF1/RNC1) as well as uncharacterized proteins with RNA-binding domains (pentatricopeptide repeat, RNA recognition motif, and chloroplast ribosome maturation), RNases, and DEAD box helicases were found in various sized complexes. Chloroplast DNA (>3 MDa) was found in association with the complete heteromeric plastid-encoded DNA polymerase complex, and a dozen other DNA-binding proteins, e.g. DNA gyrase, topoisomerase, and various DNA repair enzymes. The heteromeric ≥5-MDa pyruvate dehydrogenase complex and the 0.8–1-MDa acetyl-CoA carboxylase complex associated with uncharacterized biotin carboxyl carrier domain proteins constitute the entry point to fatty acid metabolism in leaves; we suggest that their large size relates to the need for metabolic channeling. Protein annotations and identification data are available through the Plant Proteomics Database, and mass spectrometry data are available through Proteomics Identifications database.Chloroplasts are essential plant organelles of prokaryotic origin that perform a variety of metabolic and signaling functions. Best known for their role in photosynthesis, they also carry out the biosynthesis of many primary and secondary metabolites like lipids, amino acids, vitamins, nucleotides, tetrapyrroles, and hormones (1). Subcellular localization prediction by TargetP (2) combined with a correction for false positive and false negative rates suggested that all non-green plastid types and chloroplasts together contain some 3500 proteins in Arabidopsis thaliana (3). More than 95% of the chloroplast proteins are nucleus-encoded and post-translationally imported into the chloroplast (4–6). Over the last decade, several studies were published that aimed to identify (subfractions of) the Arabidopsis chloroplast proteome (e.g. Refs. 7–10). The precise number of bona fide chloroplast proteins from these proteomics studies is probably somewhere around 1000–1300; comparing this number with the predicted chloroplast proteome indicates that ∼50% of the proteome has still not been observed. Recently, we concluded that when compared with the predicted Arabidopsis chloroplast proteome the chloroplast proteome identified to date is particularly underrepresented (40–70%) for proteins involved in signaling, stress, development, unassigned function, and DNA/RNA metabolism (9). To probe deeper into the chloroplast proteome, enrichment for low abundance proteins prior to MS analysis is required.Many biochemical functions are executed by protein assemblies. Several studies have catalogued the assembly states of chloroplast proteins in plants. Separation of the oligomeric Arabidopsis stromal proteome by two-dimensional native gel electrophoresis (CN¹-PAGE) profiled 240 non-redundant proteins and captured information for 124 complexes (11). However, native gel electrophoresis has a practical size limit, and only protein complexes below ∼1000 kDa can be effectively separated, thereby missing megadalton-sized complexes. Several megadalton-sized complexes in plants have been characterized by targeted purification schemes, including the spinach 30 and 50 S ribosomal particles (12–14), cytosolic ribosomes (15, 16), the tobacco plastid-encoded RNA polymerase (PEP) complex (17), maize mitochondrial pyruvate dehydrogenase complex (PDC) (18), and pea chloroplast acetyl-CoA carboxylase (ACCase) complex (19). Proteome characterization of a membrane-depleted, Triton-insoluble, and high density pellet from pea plastids was highly enriched for the chloroplast PDC as well as proteins involved in plastid gene expression and carbon fixation (20). However, because no subsequent fractionation was performed, specific protein associations could not be resolved.To extend chloroplast proteome coverage and characterize MDa-sized macromolecular assemblies to complement the previous CN-PAGE analysis of complexes up to 0.8 MDa, we fractionated the soluble chloroplast stroma by size exclusion chromatography (SEC) with a particular focus on complexes greater than 0.8 MDa. Proteins were identified by mass spectrometry analysis using an LTQ-Orbitrap, a high accuracy and high sensitivity hybrid instrument (21, 22). SEC migration profiles for identified proteins were generated from matched spectral counts. Hierarchical clustering and protein heat maps of the SEC migration profiles revealed that the identified protein complexes include 30, 50, and 70 S ribosomal particles; PDC; PEP; and ACCase, indicating successful MDa size fractionation. In addition, many “new” proteins were detected, and they were enriched for functions in plastid gene expression, in particular putative ribosomal biogenesis factors. Finally, protein annotations and identification data are available via the Plant Proteomics Database (PPDB) at http://ppdb.tc.cornell.edu/, and mass spectrometry data with their metadata were deposited in the Proteomics Identifications database (PRIDE) (http://www.ebi.ac.uk/pride/) under accession numbers 11459–11568.The concept of using chromatography (or other continuous fractionation techniques) of protein complexes (or other types of cellular protein fractions) with mass spectrometry-based quantification to determine co-localization has been applied using stable isotope labeling (23, 24) or label-free techniques (25, 26). When combined with cluster analysis (this study and Ref. 24), principle component analysis (23), or correlation of normalized elution profiles (this study and Refs. 25 and 26), this strategy is clearly a powerful tool and is widely applicable to other subcellular proteomes.     

2D DIGE analysis of the bursa of Fabricius reveals characteristic proteome profiles for different stages of chicken B‐cell development

Antibody producing B‐cells are an essential component of the immune system. In contrast to human and mice where B‐cells develop in the bone marrow, chicken B‐cells develop in defined stages in the bursa of Fabricius, a gut associated lymphoid tissue. In order to gain a better understanding of critical biological processes like immigration of B‐cell precursors into the bursa anlage, their differentiation and final emigration from the bursa we analyzed the proteome dynamics of this organ during embryonic and posthatch development. Samples were taken from four representative developmental stages (embryonic day (ED) 10, ED18, day 2, and day 28) and compared in an extensive 2D DIGE approach comprising six biological replicates per time point. Cluster analysis and PCA demonstrated high reliability and reproducibility of the obtained data set and revealed distinctive proteome profiles for the selected time points, which precisely reflect the differentiation processes. One hundred fifty three protein spots with significantly different intensities were identified by MS. We detected alterations in the abundance of several proteins assigned to retinoic acid metabolism (e.g. retinal‐binding protein 5) and the actin‐cytoskeleton (e.g. vinculin and gelsolin). By immunohistochemistry, desmin was identified as stromal cell protein associated with the maturation of B‐cell follicles. Strongest protein expression difference (10.8‐fold) was observed for chloride intracellular channel 2. This protein was thus far not associated with B‐cell biology but our data suggest an important function in bursa B‐cell development.     

Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling

We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754).Proteins rarely work as monomers to carry out all the biological processes needed for cells to function. An estimate of the total number of protein-protein interactions within the human proteome, based on currently available data sets, is ∼650,000 (1). This is likely an underestimate, given that many proteins form either transient, or weak interactions within intact cells that may not yet have been detected. This suggests that the majority of human proteins can participate in protein complex formation, at least under some conditions. This includes the many well-studied soluble protein complexes in the cytoplasm, exemplified by the proteasome, ribosomes and cytoskeletal network. It also includes many membrane-associated complexes, for example receptor tyrosine kinase signaling complexes, integrin networks and transmembrane transporters (2). To characterize the many roles of multi-protein complexes in biological regulatory mechanisms, it is important to have convenient methods for the rapid and efficient analysis of their composition and dynamics (3). Ideally, such methods should be applicable to system-wide studies and allow the analysis of endogenous proteins, rather than exclusively use tagged and/or over-expressed baits.The methods available for the proteome-wide analysis of protein interactions have developed swiftly over the last ten years. This field is dominated by affinity-enrichment based approaches, using either tagged constructs, or antibodies specific for endogenous proteins. Another approach is in vivo proximity labeling, based, for example, on the exogenous expression of a protein of interest, fused either to a promiscuous biotin-ligase (BioID) (4), or to a peroxidase enzyme that activates biotin-phenol (APEX) (5). While these data sets have proved very useful, there are some downsides. For example, a large expense in terms of both time and money to generate the thousands of individual “bait” proteins required for global interaction analyses. In addition, each of these affinity enrichments will be performed in only one type of buffer system, which is unlikely to be compatible with the maintenance of all protein-protein interactions. Another dimension to the analytical problem is that many proteins are expressed as different sized isoforms and/or in different post-translationally modified forms, resulting in formation of multiple, related, but functionally distinct complexes, with different combinations of interaction partners (6). Using affinity-enrichment/pull-down methods alone makes it difficult to resolve such mixtures of different forms of related protein complexes, complicating a detailed understanding of biological response mechanisms.An alternative strategy involves protein correlation profiling-MS, i.e. correlating similarities in the fractionation profiles of proteins detected by mass spectrometry, assuming that proteins in a common complex will cofractionate. This approach was previously applied to the analysis of subcellular organelle proteomes (7, 8), and subsequently extended to analyze soluble protein complexes. Thus, recent studies have shown that chromatography-based separation of soluble protein complexes, combined with fraction collection and high-throughput liquid chromatography-tandem mass spectrometry (LC-MS/MS)¹, facilitates analysis of many hundreds of soluble complexes from a single experiment (6, 9–11). A limitation of all of these studies, however, is that the native extraction conditions used to preserve protein-protein interactions isolates predominantly stable, soluble complexes. For example, many proteins that are integral to membranes are not recovered (12). Similarly, soluble protein complexes that have weakly bound protein subunits can dissociate upon cell lysis and the inevitable dilution associated with extraction. Thus, the potential value of this approach for the system-wide analysis of protein complexes is limited without a covalent tether to hold protein-protein interactions intact during extraction and subsequent chromatographic separation (13).Covalent protein crosslinking has been used extensively to stabilize protein complexes, cultured cells and tissues for subsequent analysis, either by microscopy, nucleotide sequencing or mass spectrometry. The agents employed to crosslink proteins to each other include various chemical groups able to react with the side-chains of either amino acids, nucleotides, carbohydrates or lipids (14). These crosslinking agents vary in the efficiency with which they perfuse into unbroken cells/tissues and the speed of their reaction when in proximity to a suitable chemical group. One of the most widely used crosslinkers is formaldehyde, which can reversibly form a covalent crosslink to stabilize both protein-protein and protein-nucleotide interactions (15–21). One of the main benefits of using formaldehyde is that because of its small size, it readily permeates intact cells and tissues. Another benefit of using formaldehyde is the easy reversal of the crosslinks by heating and subsequent compatibility with mass spectrometry-based proteome analysis.Here, we describe a mass spectrometry-based proteomic approach for the efficient global analysis of protein complexes, including membrane proteins, using in vivo protein crosslinking combined with denaturing extraction. Using high-resolution, size-exclusion chromatography (SEC) to separate crosslinked complexes under denaturing conditions and MS analysis of fractionated proteins, we could identify membrane bound and membrane associated complexes not accessible in native extracts. We present a detailed comparison of the sets of protein complexes that can be identified using protein correlation profiling MS analysis in conjunction with both formaldehyde crosslinked and native extracts from U2OS cells. We provide access to the entire proteome-wide data sets of both in vivo crosslinked and native U2OScell protein complexes via a searchable online database (http://www.peptracker.com/epd/).     

Changes to the Natural Killer Cell Repertoire after Therapeutic Hepatitis B DNA Vaccination

Background

Improvements to the outcome of adaptive immune responses could be achieved by inducing specific natural killer (NK) cell subsets which can cooperate with dendritic cells to select efficient T cell responses. We previously reported the induction or reactivation of T cell responses in chronic hepatitis B patients vaccinated with a DNA encoding hepatitis B envelope proteins during a phase I clinical trial.

Methodology/Principal Findings

In this study, we examined changes in the peripheral NK cell populations occurring during this vaccine trial using flow cytometry analysis. Despite a constant number of NK cells in the periphery, a significant increase in the CD56^bright population was observed after each vaccination and during the follow up. Among the 13 different NK cell markers studied by flow cytometry analysis, the expression of CD244 and NKG2D increased significantly in the CD56^bright NK population. The ex vivo CD107a expression by CD56^bright NK cells progressively increased in the vaccinated patients to reach levels that were significantly higher compared to chronically HBV-infected controls. Furthermore, modifications to the percentage of the CD56^bright NK cell population were correlated with HBV-specific T cell responses detected by the ELISPOT assay.

Conclusions/Significance

These changes in the CD56^bright population may suggest a NK helper effect on T cell adaptive responses. Activation of the innate and adaptive arms of the immune system by DNA immunization may be of particular importance to the efficacy of therapeutic interventions in a context of chronic infections.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00988767","term_id":"NCT00988767"}}NCT00988767     

Organization of lymphocyte plasma membrane. Surface protein-membrane matrix interactions in B-cell lines of different stages of differentiation

Composition of surface proteins and their interactions with cytoskeleton or membrane matrix were compared in tumor B-cell lines of different stages of B-lymphocyte maturation. All studied B-cell lines were found to share a similar set of cell surface proteins, which are tightly associated with the cytoskeleton. The increase in amount of detergent-unextractable cell surface proteins with B-cell maturation suggested that differentiation of B lymphocytes was accompanied by development of specific interactions between surface proteins and elements of the cytoskeleton or membrane matrix. Using a recently developed procedure for lymphocyte plasma membrane fractionation we demonstrate changes in distribution of cell surface proteins in membrane matrix-rich and membrane matrix-poor plasma membrane fractions during B-lymphocyte maturation. Thus, cell surface proteins of the mature B-cell line MOPC-315 were predominantly found in the plasma membrane vesicles of a high buoyant density. These vesicles mostly contained plasma membrane proteins tightly associated with elements of the membrane matrix. In immature B cells (line 70Z3) virtually all surface proteins were detected in both low and high buoyant density membrane vesicles. The tendency to increased associations between surface proteins and cytoskeleton/membrane matrix with maturation of B cells could not be explained by increased amounts of filamentous actin, since no correlation was found between the amount of globular or filamentous actin and the degree of surface protein-cytoskeleton (membrane matrix) interactions.     

Trypsin-induced proteome alteration during cell subculture in mammalian cells

Background

It is essential to subculture the cells once cultured cells reach confluence. For this, trypsin is frequently applied to dissociate adhesive cells from the substratum. However, due to the proteolytic activity of trypsin, cell surface proteins are often cleaved, which leads to dysregulation of the cell functions.

Methods

In this study, a triplicate 2D-DIGE strategy has been performed to monitor trypsin-induced proteome alterations. The differentially expressed spots were identified by MALDI-TOF MS and validated by immunoblotting.

Results

36 proteins are found to be differentially expressed in cells treated with trypsin, and proteins that are known to regulate cell metabolism, growth regulation, mitochondrial electron transportation and cell adhesion are down-regulated and proteins that regulate cell apoptosis are up-regulated after trypsin treatment. Further study shows that bcl-2 is down-regulated, p53 and p21 are both up-regulated after trypsinization.

Conclusions

In summary, this is the first report that uses the proteomic approach to thoroughly study trypsin-induced cell physiological changes and provides researchers in carrying out their experimental design.     

Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome

As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions). A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC) of 0.77 with high precision (94%) and high sensitivity (65%). We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA)] is available as an on-line server at http://sparks-lab.org.     

Reconstruction of Metabolic Pathways,Protein Expression,and Homeostasis Machineries across Maize Bundle Sheath and Mesophyll Chloroplasts: Large-Scale Quantitative Proteomics Using the First Maize Genome Assembly

Chloroplasts in differentiated bundle sheath (BS) and mesophyll (M) cells of maize (Zea mays) leaves are specialized to accommodate C₄ photosynthesis. This study provides a reconstruction of how metabolic pathways, protein expression, and homeostasis functions are quantitatively distributed across BS and M chloroplasts. This yielded new insights into cellular specialization. The experimental analysis was based on high-accuracy mass spectrometry, protein quantification by spectral counting, and the first maize genome assembly. A bioinformatics workflow was developed to deal with gene models, protein families, and gene duplications related to the polyploidy of maize; this avoided overidentification of proteins and resulted in more accurate protein quantification. A total of 1,105 proteins were assigned as potential chloroplast proteins, annotated for function, and quantified. Nearly complete coverage of primary carbon, starch, and tetrapyrole metabolism, as well as excellent coverage for fatty acid synthesis, isoprenoid, sulfur, nitrogen, and amino acid metabolism, was obtained. This showed, for example, quantitative and qualitative cell type-specific specialization in starch biosynthesis, arginine synthesis, nitrogen assimilation, and initial steps in sulfur assimilation. An extensive overview of BS and M chloroplast protein expression and homeostasis machineries (more than 200 proteins) demonstrated qualitative and quantitative differences between M and BS chloroplasts and BS-enhanced levels of the specialized chaperones ClpB3 and HSP90 that suggest active remodeling of the BS proteome. The reconstructed pathways are presented as detailed flow diagrams including annotation, relative protein abundance, and cell-specific expression pattern. Protein annotation and identification data, and projection of matched peptides on the protein models, are available online through the Plant Proteome Database.Plants can be classified as C₃ or C₄ species based on the primary product of carbon fixation in photosynthesis. The primary product of carbon fixation is a four-carbon compound (oxaloacetate [OAA]) in C₄ plants but a three-carbon compound (3-phosphoglycerate [3PGA]) in C₃ plants. In leaves of C₄ grasses such as maize (Zea mays), photosynthetic activities are partitioned between two anatomically and biochemically distinct bundle sheath (BS) and mesophyll (M) cells. A single ring of BS cells surrounds the vascular bundle, followed by a concentric ring of specialized M cells, creating the classical Kranz anatomy. Active carbon transport (in the form of C₄ organic acids) from M cell to BS cells and specific expression of Rubisco in the BS cells allows Rubisco, the carboxylating enzyme in the Calvin cycle, to operate in a high CO₂ concentration. The high CO₂ concentration suppresses the oxygenation reaction by Rubisco (and the subsequent energy-wasteful photorespiratory pathway), resulting in increased photosynthetic yield and more efficient use of water and nitrogen. The history of C₄ research has been described (Nelson and Langdale, 1992; Sage and Monson, 1999; Edwards et al., 2001). At present, there is renewed interest in C₄ photosynthesis, stimulated in part by the potential use of C₄ plants as a source of biofuels (Carpita and McCann, 2008) and the genetic engineering of C₄ rice (Oryza sativa; Sheehy et al., 2007; Hibberd et al., 2008; Taniguchi et al., 2008). The use of new genomics and/or proteomics tools has resulted in new insights into cellular differentiation in C₄ plants (Majeran and Van Wijk, 2009).Proteins are responsible for most cellular functions, and knowing their abundance, cell-type specific expression patterns, and subcellular localization is essential to understand C₄ differentiation. Previously, we published a quantitative analysis of purified M and BS chloroplast (soluble) stromal proteomes in which BS-M protein accumulation ratios for 125 accessions were determined; this covered a limited range of plastid functions, although it enabled the integration of information from previous studies (Majeran et al., 2005). A subsequent complementary quantitative proteomics study, using nano-liquid chromatography (LC)-LTQ-Orbitrap mass spectrometry (MS) and label-free spectral counting complemented with other techniques, identified proteins in BS and M thylakoid and envelope membranes of maize chloroplasts and determined cell type-specific differences in (1) the protein assembly state and composition of the four photosynthetic complexes and of a new type of NADPH dehydrogenase (NDH) complex; (2) the auxiliary functions of the thylakoid proteome; and (3) protein and metabolite transport functions of M and BS chloroplast envelopes (Majeran et al., 2008). Comparative MS analysis of chloroplast envelope membranes from leaves of pea (Pisum sativum), a C₃ species, and from M chloroplasts of maize showed an enrichment of several known and putative translocators in the maize M envelopes (Brautigam et al., 2008). The conclusions of these proteome analyses are summarized by Majeran and van Wijk, 2009.Whereas these proteomics studies provide significant progress in understanding the organization of C₄ metabolism in maize, three aspects have not been adequately addressed: (1) the stromal proteomes of BS and M chloroplasts likely each contain more than 1,500 proteins, but the BS-M ratios for only approximately 125 proteins were quantified, resulting in very limited coverage of several important secondary metabolic pathways such as sulfur, fatty acid, amino acid, and nucleotide metabolism; (2) information about relative concentrations of stromal proteins in BS and M chloroplasts is lacking but is needed as a basis for quantitative modeling and metabolic engineering of C₄ photosynthesis and other metabolic pathways; the growing “toolbox” of proteomics and MS now allows for such quantitative analyses (Bantscheff et al., 2007; Kumar and Mann, 2009); (3) the soluble (Majeran et al., 2005) and membrane (Majeran et al., 2008) proteome data sets were analyzed by different techniques and mass spectrometers, mostly due to the improvement of commercial mass spectrometers in that time frame. Therefore, it is difficult to understand the quantitative relationships between these data sets. This study addresses these three aspects.So far, maize proteome analyses used essentially ZmGI maize assemblies (for the Z. mays Gene Index) based on ESTs, combined with a limited amount of additional DNA sequence information. The ZmGI was originally generated by The Institute for Genome Research and subsequently supported by the computational Biology and Functional Genomics Laboratory (http://compbio.dfci.harvard.edu/index.html). This ZmGI database did not have annotated gene models (for proteome analysis, the DNA sequences were searched in all six reading frames), and low expressed genes were likely underrepresented. In our most recent BS-M chloroplast analyses (Majeran et al., 2008) as well as a maize envelope analysis (Brautigam et al., 2008), the MS data were searched against ZmGI version 16.0 or 17.0. Since that time, the maize genome has been sequenced (using a bacterial artificial chromosome approach), a physical map was created (the maize accessioned golden path AGP version 1), and its first assembly with gene coordinates and predicted proteins was very recently released (June 2009; http://ftp.maizesequence.org/release-4a.53/sequences/) and published (Schnable et al., 2009). This release contains 32,540 genes with 53,764 gene models; most of the gene models are evidence based. The new maize genome assembly is expected to improve maize proteome analysis with more accurate protein identification and quantitative assessment of protein expression patterns. This also allows for the determination of N-terminal localization signals, which was rarely possible from EST assemblies, as N termini were often lacking.This study presents a quantitative protein expression atlas of differentiated maize leaf M and BS chloroplasts using high-resolution and mass-accuracy MS (using a LTQ-Orbitrap) and the new maize genome assembly. Three biological replicates of stromal proteomes of isolated BS and M chloroplasts were analyzed. Quantification was carried out based on the “spectral counting” method (Zybailov et al., 2005, 2008; Bantscheff et al., 2007; Choi et al., 2008) using a sophisticated bioinformatics “workflow” in particular to deal with gene duplications and extended gene families observed in polyploids such as maize. These new stromal data sets were combined with a reanalysis of our recent BS and M membrane proteome data sets (Majeran et al., 2008) against genome 4a53. Compared with previous maize leaf proteome analyses, this study provides an integrated overview of both primary and especially secondary metabolism, as well as chloroplast gene expression and protein biogenesis, in far greater depth. The reconstructed pathways are presented as figures that include quantitative protein information; pathways include primary carbon metabolism, starch metabolism, nucleotide metabolism, fatty acid and lipid biosynthesis, chlorophyll, heme, and carotenoid synthesis, and nitrogen assimilation. We briefly comment on the use of the new maize genome assembly for proteome analysis. All matched peptides are projected on the predicted protein models via the Plant Proteomics Database (PPDB; http://ppdb.tc.cornell.edu/). Interactive functional annotation, chloroplast localization assignments, as well as details of protein identification are also available via PPDB.     

Ontogeny and distribution of the murine B cell Fc gamma RII.

The distribution and expression of the IgG FcRII (Fc gamma RII) on normal murine B cells was examined. Using multicolor flow cytometry, spleens from neonatal mice of increasing age and adult bone marrow were analyzed for expression of the Fc gamma RII. In addition, B cells from peripheral lymphoid organs, as well as panel of B cell tumors, were tested. The results demonstrate that the Fc gamma RII is expressed on all pre-B cells and immature B cells in the neonatal spleen and adult bone marrow, on all mature B cells in peripheral lymphoid organs, and on switched B cells in Peyer's patches. Furthermore, the Fc gamma RII was found to be present on B cell tumors representative of all stages of B cell maturation and differentiation. Taken together, the results indicate that Fc gamma RII is expressed during the entire lifetime of the B cell. In addition, examination of spleen cells from neonatal mice revealed a large number of pre-B cells, phenotypically defined as B220+, IgM-. These pre-B cells were present at birth, peaked in number between 2 and 3 wk of age, and became a minor population by day 30. Further phenotypic analysis of these cells demonstrated the expression of the BLA-1 and BP-1 Ag, and the lack of T cell and NK cell markers, thus confirming their assignment to the B cell lineage. Finally, the Fc gamma RII present on these pre-B cells was shown to be functional, by virtue of its ability to bind aggregated IgG.     

Effect of Broccoli Sprouts and Live Attenuated Influenza Virus on Peripheral Blood Natural Killer Cells: A Randomized,Double-Blind Study

Enhancing antiviral host defense responses through nutritional supplementation would be an attractive strategy in the fight against influenza. Using inoculation with live attenuated influenza virus (LAIV) as an infection model, we have recently shown that ingestion of sulforaphane-containing broccoli sprout homogenates (BSH) reduces markers of viral load in the nose. To investigate the systemic effects of short-term BSH supplementation in the context of LAIV-inoculation, we examined peripheral blood immune cell populations in non-smoking subjects from this study, with a particular focus on NK cells. We carried out a randomized, double-blinded, placebo-controlled study measuring the effects of BSH (N = 13) or placebo (alfalfa sprout homogenate, ASH; N = 16) on peripheral blood mononuclear cell responses to a standard nasal vaccine dose of LAIV in healthy volunteers. Blood was drawn prior to (day-1) and post (day2, day21) LAIV inoculation and analyzed for neutrophils, monocytes, macrophages, T cells, NKT cells, and NK cells. In addition, NK cells were enriched, stimulated, and assessed for surface markers, intracellular markers, and cytotoxic potential by flow cytometry. Overall, LAIV significantly reduced NKT (day2 and day21) and T cell (day2) populations. LAIV decreased NK cell CD56 and CD158b expression, while significantly increasing CD16 expression and cytotoxic potential (on day2). BSH supplementation further increased LAIV-induced granzyme B production (day2) in NK cells compared to ASH and in the BSH group granzyme B levels appeared to be negatively associated with influenza RNA levels in nasal lavage fluid cells. We conclude that nasal influenza infection may induce complex changes in peripheral blood NK cell activation, and that BSH increases virus-induced peripheral blood NK cell granzyme B production, an effect that may be important for enhanced antiviral defense responses.Trial Registration: ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01269723","term_id":"NCT01269723"}}NCT01269723