Proteome Analysis of the Surface of Trichomonas vaginalis Reveals Novel Proteins and Strain-dependent Differential Expression

The identification of surface proteins on the plasma membrane of pathogens is of fundamental importance in understanding host-pathogen interactions. Surface proteins of the extracellular parasite Trichomonas are implicated in the initial adherence to mucosal tissue and are likely to play a critical role in the long term survival of this pathogen in the urogenital tract. In this study, we used cell surface biotinylation and multidimensional protein identification technology to identify the surface proteome of six strains of Trichomonas vaginalis with differing adherence capacities to vaginal epithelial cells. A combined total of 411 proteins were identified, and of these, 11 were found to be more abundant in adherent strains relative to less adherent parasites. The mRNA levels of five differentially expressed proteins selected for quantitative RT-PCR analysis mirrored their observed protein levels, confirming their up-regulation in highly adherent strains. As proof of principle and to investigate a possible role in pathogenesis for differentially expressed proteins, gain of function experiments were performed using two novel proteins that were among the most highly expressed surface proteins in adherent strains. Overexpression of either of these proteins, TVAG_244130 or TVAG_166850, in a relatively non-adherent strain increased attachment of transfected parasites to vaginal epithelial cells ∼2.2-fold. These data support a role in adhesion for these abundant surface proteins. Our analyses demonstrate that comprehensive profiling of the cell surface proteome of different parasite strains is an effective approach to identify potential new adhesion factors as well as other surface molecules that may participate in establishing and maintaining infection by this extracellular pathogen.The flagellated protozoan parasite Trichomonas vaginalis is the etiologic agent of trichomoniasis, the most common non-viral sexually transmitted infection worldwide with an estimated 174 million new cases annually (1). Although asymptomatic infection by T. vaginalis is common, multiple symptoms and pathologies can arise in both men and women, including vaginitis, urethritis, prostatitis, low birth weight infants and preterm delivery, premature rupture of membranes, and infertility (2–5). T. vaginalis has also emerged as an important cofactor in amplifying human immunodeficiency virus spread (6) as individuals infected with T. vaginalis have a significantly increased incidence of human immunodeficiency virus transmission (7, 8). T. vaginalis infection likewise increases the risk of cervical and aggressive prostate cancers (9–11).Despite the serious consequences that can arise from trichomoniasis, the underlying biochemical processes that lead to T. vaginalis pathogenesis are not well defined. Because T. vaginalis is an obligate extracellular pathogen, adherence to epithelial cells is critical for parasite survival within the human host (12). Several in vitro studies indicate that adhesion of the parasite to target mucosal epithelial cells is essential for the maintenance of infection and for cytopathogenicity (13, 14). T. vaginalis adherence to host cells is mediated, in part, by a lipophosphoglycan (LPG)¹ that coats the surface of the parasite, and altering the sugar content of this LPG reduces both adherence and cytotoxicity (15). Moreover, the mammalian protein galectin-1 binds to T. vaginalis in a carbohydrate-dependent manner via a direct interaction with parasite LPG (16). Knockdown of galectin-1 in mammalian cells, however, reduces parasite binding only by ∼17% (16). Although galectin-1-mediated interactions between T. vaginalis LPG and host cell glycoconjugates may be central in establishing infection, it is clear that parasite adhesion factors in addition to LPG are likely to be involved in host-parasite interaction. Surface proteins are likely to play important roles in the initial adherence to mucosal tissue as well as the long term survival of the pathogen on mucosal surfaces.The outcome of infection with T. vaginalis is highly variable. Possible explanations for this phenomenon include host immunity, host nutritional status, and the vaginal microbiota. Additionally, genetic differences between T. vaginalis isolates leading to differences in adherence and cytotoxicity capacities are likely to result in differences in disease progression. Recently, geographically diverse T. vaginalis strains that are significantly more cytotoxic to host cells than laboratory-adapted strains have become available (17, 18), paving the way toward comparative studies aimed at identifying proteins that correlate with virulent phenotypes.Despite the importance of T. vaginalis surface proteins as a critical interface for pathogen-host interactions, there has been no systematic investigation of the surface proteins of this parasite. The T. vaginalis genome is large and encodes a massive proteome with a considerable and diverse repertoire of candidate surface proteins (19). For example, sequence analysis programs that predict transmembrane protein topology identified over 5100 T. vaginalis proteins with one or more transmembrane domains (20). Furthermore, over 300 annotated proteins with predicted transmembrane domains also contain protein motifs common to surface proteins from other pathogens known to contribute to mucosal colonization and other pathogenic processes (20). The vast number and diversity of possible surface proteins necessitates a multitiered approach using complementary genomics and proteomics analyses to identify candidates for focused functional studies.Biotinylation of proteins at the cell surface with an impermeable reagent followed by specific purification of these proteins using streptavidin has successfully been used for the enrichment and identification of surface proteins (21–24). The high avidity binding of biotin to streptavidin greatly enhances membrane protein purification, a challenging feat because of the low abundance of membrane proteins in total cellular extracts. Here, we used this approach to profile the surface plasma membrane proteome of T. vaginalis and to identify proteins that are differentially expressed in adherent relative to less adherent strains of the parasite. To the best of our knowledge, this is the first study to systematically identify and characterize proteins at the surface of Trichomonas parasites. Defining the parasite cell surface proteome is a critical step toward understanding the relative abundance of surface proteins in strains with varying virulence properties. This information will be critical for defining the role surface proteins play in mediating contact between the parasite and host cells as well as the resulting intracellular and extracellular signals that contribute to establishing and maintaining infection. Additionally, conserved surface molecules unique to T. vaginalis that might serve as specific vaccine candidates can be revealed using this approach. The prevalence of trichomoniasis among women of reproductive age (25) and its correlation with AIDS transmission and cervical and prostate cancers (6, 8–11) provide strong arguments for the need to develop vaccines against this human pathogen.     

The Mouse C2C12 Myoblast Cell Surface N-Linked Glycoproteome: IDENTIFICATION, GLYCOSITE OCCUPANCY, AND MEMBRANE ORIENTATION*

Endogenous regeneration and repair mechanisms are responsible for replacing dead and damaged cells to maintain or enhance tissue and organ function, and one of the best examples of endogenous repair mechanisms involves skeletal muscle. Although the molecular mechanisms that regulate the differentiation of satellite cells and myoblasts toward myofibers are not fully understood, cell surface proteins that sense and respond to their environment play an important role. The cell surface capturing technology was used here to uncover the cell surface N-linked glycoprotein subproteome of myoblasts and to identify potential markers of myoblast differentiation. 128 bona fide cell surface-exposed N-linked glycoproteins, including 117 transmembrane, four glycosylphosphatidylinositol-anchored, five extracellular matrix, and two membrane-associated proteins were identified from mouse C2C12 myoblasts. The data set revealed 36 cluster of differentiation-annotated proteins and confirmed the occupancy for 235 N-linked glycosylation sites. The identification of the N-glycosylation sites on the extracellular domain of the proteins allowed for the determination of the orientation of the identified proteins within the plasma membrane. One glycoprotein transmembrane orientation was found to be inconsistent with Swiss-Prot annotations, whereas ambiguous annotations for 14 other proteins were resolved. Several of the identified N-linked glycoproteins, including aquaporin-1 and β-sarcoglycan, were found in validation experiments to change in overall abundance as the myoblasts differentiate toward myotubes. Therefore, the strategy and data presented shed new light on the complexity of the myoblast cell surface subproteome and reveal new targets for the clinically important characterization of cell intermediates during myoblast differentiation into myotubes.Endogenous regeneration and repair mechanisms are responsible for replacing dead and damaged cells to maintain or enhance tissue and organ function. One of the best examples of endogenous repair mechanisms involves skeletal muscle, which has innate regenerative capacity (for reviews, see Refs. 1–4). Skeletal muscle repair begins with satellite cells, a heterogeneous population of mitotically quiescent cells located in the basal lamina that surrounds adult skeletal myofibers (5, 6), that, when activated, rapidly proliferate (7). The progeny of activated satellite cells, known as myogenic precursor cells or myoblasts, undergo several rounds of division prior to withdrawal from the cell cycle. This is followed by fusion to form terminally differentiated multinucleated myotubes and skeletal myofibers (7, 8). These cells effectively repair or replace damaged cells or contribute to an increase in skeletal muscle mass.The molecular mechanisms that regulate differentiation of satellite cells and myoblasts toward myofibers are not fully understood, although it is known that the cell surface proteome plays an important biological role in skeletal muscle differentiation. Examples include how cell surface proteins modulate myoblast elongation, orientation, and fusion (for a review, see Ref. 8). The organization and fusion of myoblasts is mediated, in part, by cadherins (for reviews, see Refs. 9 and 10), which enhance skeletal muscle differentiation and are implicated in myoblast fusion (11). Neogenin, another cell surface protein, is also a likely regulator of myotube formation via the netrin ligand signal transduction pathway (12, 13), and the family of sphingosine 1-phosphate receptors (Edg receptors) are known key signal transduction molecules involved in regulating myogenic differentiation (14–17). Given the important role of these proteins, identifying and characterizing the cell surface proteins present on myoblasts in a more comprehensive approach could provide insights into the molecular mechanisms involved in skeletal muscle development and repair. The identification of naturally occurring cell surface proteins (i.e. markers) could also foster the enrichment and/or characterization of cell intermediates during differentiation that could be useful therapeutically.Although it is possible to use techniques such as flow cytometry, antibody arrays, and microscopy to probe for known proteins on the cell surface in discrete populations, these methods rely on a priori knowledge of the proteins present on the cell surface and the availability/specificity of an antibody. Proteomics approaches coupled with mass spectrometry offer an alternative approach that is antibody-independent and allows for the de novo discovery of proteins on the surface. One approach, which was used in the current study, exploits the fact that a majority of the cell surface proteins are glycosylated (18). The method uses hydrazide chemistry (19) to immobilize and enrich for glycoproteins/glycopeptides, and previous studies using this chemistry have successfully identified soluble glycoproteins (20–24) as well as cell surface glycoproteins (25–28). A recently optimized hydrazide chemistry strategy by Wollscheid et al. (29) termed cell surface capturing (CSC)¹ technology, reports the ability to identify cell surface (plasma membrane) proteins specifically with little (<15%) contamination from non-cell surface proteins. The specificity stems from the fact that the oligosaccharide structure is labeled using membrane-impermeable reagents while the cells are intact rather than after cell lysis. Consequently, only extracellular oligosaccharides are labeled and subsequently captured. Utilizing information regarding the glycosylation site then allows for a rapid elimination of nonspecifically captured proteins (i.e. non-cell surface proteins) during the data analysis process, a feature that makes this approach unique to methods where no label or tag is used. Additionally, the CSC technology provides information about glycosylation site occupancy (i.e. whether a potential N-linked glycosylation site is actually glycosylated), which is important for determining the protein orientation within the membrane and, therefore, antigen selection and antibody design.To uncover information about the cell surface of myoblasts and to identify potential markers of myoblast differentiation, we used the CSC technology on the mouse myoblast C2C12 cell line model system (30, 31). This adherent cell line derived from satellite cells has routinely been used as a model for skeletal muscle development (e.g. Refs. 1, 32, and 33), skeletal muscle differentiation (e.g. Refs. 34–36), and studying muscular dystrophy (e.g. Refs. 37–39). Additionally, these cells have been used in cell-based therapies (e.g. Refs. 40–42). Using the CSC technology, 128 cell surface N-linked glycoproteins were identified, including several that were found to change in overall abundance as the myoblasts differentiate toward myotubes. The current data also confirmed the occupancy of 235 N-linked glycosites of which 226 were previously unconfirmed. The new information provided by the current study is expected to facilitate the development of useful tools for studying the differentiation of myoblasts toward myotubes.     

Mtv-1 Superantigen Trafficks Independently of Major Histocompatibility Complex Class II Directly to the B-Cell Surface by the Exocytic Pathway

Presentation of the Mtv-1 superantigen (vSag1) to specific V_β-bearing T cells requires association with major histocompatibility complex class II molecules. The intracellular route by which vSag1 trafficks to the cell surface and the site of vSag1-class II complex assembly in antigen-presenting B lymphocytes have not been determined. Here, we show that vSag1 trafficks independently of class II to the plasma membrane by the exocytic secretory pathway. At the surface of B cells, vSag1 associates primarily with mature peptide-bound class II αβ dimers, which are stable in sodium dodecyl sulfate. vSag1 is unstable on the cell surface in the absence of class II, and reagents that alter the surface expression of vSag1 and the conformation of class II molecules affect vSag1 stimulation of superantigen reactive T cells.

T lymphocytes respond to peptide antigens presented by either major histocompatibility complex (MHC) class I or class II molecules. Many viruses have evolved sophisticated strategies that interfere with antigen presentation by infected cells in order to escape recognition by T lymphocytes. Most strategies studied rely on disrupting MHC class I presentation, either by affecting components of the processing machinery that generate and transport viral peptides into the endoplasmic reticulum (ER) or by retarding transport or targeting class I molecules into the degradation pathway (for a review, see reference 73).In contrast, mouse mammary tumor virus (MMTV) utilizes T-cell stimulation to promote its life cycle. MMTVs encode within their 3′ long terminal repeat a viral superantigen (vSag), and coexpression of the Sag glycoprotein with MHC class II molecules on the surface of virally infected B cells induces V_β-specific T-cell stimulation, generating an immune response which is critical for amplification of MMTV and ensures vertical transmission of virus to the next generation (13, 29, 30). In the absence of B cells, MHC class II, or Sag-reactive T cells, the infection is short-lived (5, 6, 24, 28). The assembly and functional expression of vSag-class II complexes are therefore essential to the viral life cycle. When inherited as germ line elements, Mtv proviruses expressing vSags during ontogeny trigger V_β-specific clonal elimination of immature T cells and profoundly shape the T-cell repertoire (for a review, see reference 1).vSags are type II integral membrane glycoproteins (14, 36). They possess up to six potential N-linked glycosylation sites, and carbohydrate addition is essential for vSag stability and activity (45). Their protein sequence is highly conserved among all MMTV strains except at the C-terminal 29 to 32 residues, which vary and confer T-cell V_β specificity (77). Biochemical analyses of vSag7 (minor lymphocyte stimulating locus 1, Mls-1^a) molecular forms after transfection into a murine B-cell line have identified a predominant 45-kDa endo-β-N-acetylglucosaminidase H (endo H)-sensitive ER-resident glycoprotein, as well as multiple highly glycosylated forms (74). It is thought that an 18-kDa C-terminal fragment binds MHC class II products (75). It has also been suggested that vSags associate weakly with class II in the ER and that proteolytic processing is required for the efficient assembly of vSag-class II complexes for presentation to T cells (46, 49, 75). As yet, the intracellular route that vSags take to the cell surface, the compartment in which they bind class II, and whether they associate with peptide-loaded class II dimers have been enigmatic.Newly synthesized MHC class II αβ heterodimers assemble with invariant chain (Ii), a type II integral membrane protein, to form an oligomeric complex in the ER (37). Ii prevents class II heterodimers from binding peptides in the ER and Golgi complex (55), and signals in its cytoplasmic tail sort the complex into the endocytic pathway (4, 42). In this acidic, protease-rich compartment, Ii is degraded and class II binds antigenic peptides. After the formation of peptide-class II dimers, the complexes are exported to the plasma membrane (8, 48). In the absence of Ii, class II αβ heterodimers exhibit defective post-ER transport, and their conversion into functionally mature, sodium dodecyl sulfate (SDS)-stable compact dimers by peptide antigens is affected (7, 16, 22, 70).A specialized endosomal compartment where class II peptide loading occurs, termed the MHC class II-enriched compartment (MIIC or CIIV), has been found recently in antigen-presenting cells (2, 50, 53, 58, 68, 71). Whether nascent Ii-class II complexes traffic directly to the MIIC from the trans-Golgi network (TGN) or transit first to early endosomes, either directly or via the cell surface, before entering late endocytic vesicles and MIIC is still under debate (26, 56, 57). Transport by all these routes most probably occurs to ensure the capture and loading of antigenic peptides throughout the endocytic pathway (12). MIIC vesicles are positive for lysosome-associated membrane proteins (LAMPs) and cathepsin D and are enriched for HLA-DM or H-2M (18, 32, 59), proteins that facilitate the catalytic exchange of class II-associated invariant peptide chain (CLIP) for antigenic peptides (19, 61, 62). The ultrastructural colocalization of DM with intracellular peptide-class II complexes suggests that the MIIC is a main site where class II dimers bind exogenous and endogenous peptide antigens (47, 58).Determining the route by which vSag protein(s) trafficks to the cell surface and the cellular location where vSag1 processing and assembly with class II molecules occurs is central to understanding the mechanism whereby vSags activate T cells to maintain the viral life cycle. It has been unclear whether vSags traffic independently by the constitutive exocytic pathway or with class II and Ii to the MIIC before reaching the cell surface. Reagents that alter class II expression have been shown to affect vSag presentation (43, 46). Furthermore, mice lacking Ii show reduced intrathymic V_β-specific T-cell deletion (70), suggesting that Ii may play a role, either by ensuring proper maturation of class II dimers or by targeting vSag-class II complexes to the MIIC, in promoting efficient vSag-induced immune responses.To investigate these issues, we used immunochemical detection of vSag1 protein in combination with subcellular fractionation and surface reexpression assays. We show that class II is required for stable vSag1 surface expression. vSag1 trafficks directly to the cell surface independently of class II, and reagents that alter the conversion of newly synthesized class II into peptide-loaded SDS-stable dimers affect functional vSag1 surface expression.     

Defining the Structural Basis of Human Plasminogen Binding by Streptococcal Surface Enolase

The flesh-eating bacterium group A Streptococcus (GAS) binds and activates human plasminogen, promoting invasive disease. Streptococcal surface enolase (SEN), a glycolytic pathway enzyme, is an identified plasminogen receptor of GAS. Here we used mass spectrometry (MS) to confirm that GAS SEN is octameric, thereby validating in silico modeling based on the crystal structure of Streptococcus pneumoniae α-enolase. Site-directed mutagenesis of surface-located lysine residues (SEN^{K252 + 255A}, SEN^K304A, SEN^K334A, SEN^K344E, SEN^K435L, and SEN^Δ434–435) was used to examine their roles in maintaining structural integrity, enzymatic function, and plasminogen binding. Structural integrity of the GAS SEN octamer was retained for all mutants except SEN^K344E, as determined by circular dichroism spectroscopy and MS. However, ion mobility MS revealed distinct differences in the stability of several mutant octamers in comparison with wild type. Enzymatic analysis indicated that SEN^K344E had lost α-enolase activity, which was also reduced in SEN^K334A and SEN^Δ434–435. Surface plasmon resonance demonstrated that the capacity to bind human plasminogen was abolished in SEN^{K252 + 255A}, SEN^K435L, and SEN^Δ434–435. The lysine residues at positions 252, 255, 434, and 435 therefore play a concerted role in plasminogen acquisition. This study demonstrates the ability of combining in silico structural modeling with ion mobility-MS validation for undertaking functional studies on complex protein structures.Streptococcus pyogenes (group A Streptococcus, GAS)⁸ is a common bacterial pathogen, causing over 700 million human disease episodes each year (1). These range from serious life-threatening invasive diseases including necrotizing fasciitis and streptococcal toxic shock-like syndrome to non-invasive infections like pharyngitis and pyoderma. Invasive disease, in combination with postinfection immune sequelae including rheumatic heart disease and acute poststreptococcal glomerulonephritis, account for over half a million deaths each year (1). Although a resurgence of GAS invasive infections has occurred in western countries since the mid-1980s, disease burden is much greater in developing countries and indigenous populations of developed nations, where GAS infections are endemic (2–4).GAS is able to bind human plasminogen and activate the captured zymogen to the serine protease plasmin (5–17). The capacity of GAS to do this plays a critical role in virulence and invasive disease initiation (3, 17–19). The plasminogen activation system in humans is an important and highly regulated process that is responsible for breakdown of extracellular matrix components, dissolution of blood clots, and cell migration (20, 21). Plasminogen is a 92-kDa zymogen that circulates in human plasma at a concentration of 2 μm (22). It consists of a binding region of five homologous triple loop kringle domains and an N-terminal serine protease domain that flank the Arg⁵⁶¹–Val⁵⁶² site (23), where it is cleaved by tissue plasminogen activator and urokinase plasminogen activator to yield the active protease plasmin (20, 23). GAS also has the ability to activate human plasminogen by secreting the virulence determinant streptokinase. Streptokinase forms stable complexes with plasminogen or plasmin, both of which exhibit plasmin activity (20, 24). Activation of plasminogen by the plasmin(ogen)-streptokinase complex circumvents regulation by the host plasminogen activation inhibitors, α₂-antiplasmin and α₂-macroglobulin (11, 20). GAS can bind the plasmin(ogen)-streptokinase complex and/or plasmin(ogen) directly via plasmin(ogen) receptors at the bacterial cell surface (6). These receptors include the plasminogen-binding group A streptococcal M-like protein (PAM) (25), the PAM-related protein (19), glyceraldehyde-3-phosphate dehydrogenase (GAPDH; also known as streptococcal plasmin receptor, Plr, or streptococcal surface dehydrogenase) (9, 26), and streptococcal surface enolase (SEN or α-enolase) (27). Interactions with these GAS receptors occurs via lysine-binding sites within the kringle domains of plasminogen (6).In addition to its ability to bind human plasminogen, SEN is primarily the glycolytic enzyme that converts 2-phosphoglycerate to phosphoenolpyruvate (27–29). SEN is abundantly expressed in the cytosol of most bacterial species but has also been identified as a surface-located protein in GAS and other bacteria including pneumococci, despite lacking classical cell surface protein motifs such as a signal sequence, membrane-spanning domain, or cell-wall anchor motif (27, 28, 30, 31). The interaction between SEN and plasminogen is reported to be facilitated by the two C-terminal lysine residues at positions 434 and 435 (27, 32). In contrast, an internal binding motif containing lysines at positions 252 and 255 in the closely related α-enolase of Streptococcus pneumoniae has been shown to play a pivotal role in the acquisition of plasminogen in this bacterial species (33). The octameric pneumococcal α-enolase structure consists of a tetramer of dimers. Hence, potential binding sites could be buried in the interface between subunits. In fact, the crystal structure of S. pneumoniae α-enolase revealed that the two C-terminal lysine residues are significantly less exposed than the internal plasminogen-binding motif (34).In this study, we constructed an in silico model of GAS SEN, based on the pneumococcal octameric α-enolase crystal structure, and validated this model using ion mobility (IM) mass spectrometry (MS). Site-directed mutagenesis followed by structural and functional analyses revealed that Lys³⁴⁴ plays a crucial role in structural integrity and enzymatic function. Furthermore, we demonstrate that the plasminogen-binding motif residues Lys²⁵² and Lys²⁵⁵ and the C-terminal Lys⁴³⁴ and Lys⁴³⁵ residues are located adjacently in the GAS SEN structure and play a concerted role in the binding of human plasminogen.     

Recombinant Surface Proteomics as a Tool to Analyze Humoral Immune Responses in Bovines Infected by Mycoplasma mycoides Subsp. mycoides Small Colony Type

A systematic approach to characterize the surface proteome of Mycoplasma mycoides subspecies mycoides small colony type (M. mycoides SC), the causative agent of contagious bovine pleuropneumonia (CBPP) in cattle, is presented. Humoral immune responses in 242 CBPP-affected cattle and controls were monitored against one-third of the surface proteins of M. mycoides SC in a high throughput magnetic bead-based assay. Initially, 64 surface proteins were selected from the genome sequence of M. mycoides SC and expressed as recombinant proteins in Escherichia coli. Binding of antibodies to each individual protein could then be analyzed simultaneously in minute sample volumes with the Luminex suspension array technology. The assay was optimized on Namibian CBPP-positive sera and Swedish negative controls to allow detection and 20-fold mean signal separation between CBPP-positive and -negative sera. Signals were proven to be protein-specific by inhibition experiments, and results agreed with Western blot experiments. The potential of the assay to monitor IgG, IgM, and IgA responses over time was shown in a proof-of-concept study with 116 sera from eight animals in a CBPP vaccine study. In conclusion, a toolbox with recombinant proteins and a flexible suspension array assay that allows multiplex analysis of humoral immune responses to M. mycoides SC has been created.Mycoplasma mycoides subsp. mycoides small colony type (M. mycoides SC)¹ is the causative agent of contagious bovine pleuropneumonia (CBPP), a severe respiratory disease in cattle. It is a disease requiring official declaration to the World Organization for Animal Health (OIE) and that causes vast problems in Africa with severe socioeconomic consequences (1, 2). In 2006, 15 African countries reported 186 outbreaks of CBPP to the OIE. CBPP was eradicated from Europe in the beginning of the 20th century (3) but has reemerged in every decade since (4). Eradication was largely facilitated by slaughtering infected herds, which is still considered as the most efficient means of disease control and was successfully performed in Botswana in 1995 (5). However, this campaign was directly correlated to increased malnutrition in children (6) and is also considered to be too expensive for other African countries (2, 7). The use of chemotherapy in CBPP control is a debated subject, has long been discouraged, and is even illegal in some countries (1), mainly because of the risk of creating silent carriers of the disease (8). However, new antibiotics have shown positive effects (9), but extensive vaccinations are still considered the preferred option for prevention and control of CBPP in Africa (2, 10, 11). The vaccines currently in use are based on live attenuated M. mycoides SC strains and have several disadvantages such as short term immunity (12), poor protection as indicated in recent trials (4, 13), and even pathogenicity (13, 14).The two currently available tests for serological diagnosis of CBPP recommended by the OIE, the complement fixation test (15) and a competitive ELISA (16), are based on whole cell M. mycoides SC. For subcellular components of the organism, the genome sequence of M. mycoides SC strain PG1 (17) offers an emerging possibility to improve both diagnostic and therapeutic approaches with selected antigens. However, as for the 10 other Mycoplasma genomes sequenced, the genome sequences per se did not reveal any primary virulence factors common in other bacteria, such as adhesins or toxins (18). The few known molecular mechanisms of pathogenicity were recently reviewed (18) and include five lipoproteins studied in detail: LppA (19, 20), LppB (21), LppC (22) LppQ (23), and Vmm (24). Of these, LppQ has been used to develop an indirect ELISA (25), and Vmm, a variable surface protein, has recently been studied along with five novel putative variable surface proteins as recombinant proteins expressed in Escherichia coli (26). That study demonstrated the feasibility of producing recombinant surface proteins from M. mycoides SC in E. coli and screening for antibodies in sera from CBPP-affected bovines by Western and dot blotting.To explore further the immunogenicity of the M. mycoides SC surface proteome, a platform for multiplexed analysis of proteins using minute serum samples such as bead-based array systems (27) is desirable. One method is available from Luminex Corp. and uses spectrally distinguishable beads (28) to form an array in suspension. The array is analyzed in a flow cytometer-like instrument and can perform up to 100 simultaneous assays in a single reaction well. This platform has recently been used to determine binding specificities to antigens produced in a similar fashion (29) and to profile antibodies in serum toward six antigens of Mycobacterium tuberculosis (30).The aim of this study was to develop a rapid and highly multiplex method for affinity analysis of antibody levels in serum samples from CBPP-affected bovines against recombinant M. mycoides SC surface proteins. To facilitate this, a large set of surface proteins were cloned, expressed in E. coli, and purified. Furthermore, the bead-based assay conditions had to be optimized and verified for detection of immunoglobulin levels in bovine sera. This methodology would enable monitoring and protein-specific characterization of humoral immune responses during CBPP infections. As a secondary aim, the study was expanded to include specific IgG, IgA, and IgM responses in sera from a vaccine study with time series sampling from each animal over 8 months, covering prevaccination and 4 months postinfection.     

Splitting the BLOSUM Score into Numbers of Biological Significance

Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum). These relate respectively to the sequence convergence (the stochastic similarity of the two protein sequences), to the background frequency divergence (typicality of the amino acid probability distribution in each sequence), and to the target frequency divergence (compliance of the amino acid variations between the two sequences to the protein model implicit in the BLOCKS database). This treatment sharpens the protein sequence comparison, providing a rationale for the biological significance of the obtained score, and helps to identify weakly related sequences. Moreover, the BLOSpectrum can guide the choice of the most appropriate scoring matrix, tailoring it to the evolutionary divergence associated with the two sequences, or indicate if a compositionally adjusted matrix could perform better.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Chimeric Plant Virus Particles Administered Nasally or Orally Induce Systemic and Mucosal Immune Responses in Mice

The humoral immune responses to the D2 peptide of fibronectin-binding protein B (FnBP) of Staphylococcus aureus, expressed on the plant virus cowpea mosaic virus (CPMV), were evaluated after mucosal delivery to mice. Intranasal immunization of these chimeric virus particles (CVPs), either alone or in the presence of ISCOM matrix, primed CPMV-specific T cells and generated high titers of CPMV- and FnBP-specific immunoglobulin G (IgG) in sera. Furthermore, CPMV- and FnBP-specific IgA and IgG could also be detected in the bronchial, intestinal, and vaginal lavage fluids, highlighting the ability of CVPs to generate antibody at distant mucosal sites. IgG2a and IgG2b were the dominant IgG subclasses in sera to both CPMV and FnBP, demonstrating a bias in the response toward the T helper 1 type. The sera completely inhibited the binding of human fibronectin to the S. aureus FnBP. Oral immunization of the CVPs also generated CPMV- and FnBP-specific serum IgG; however, these titers were significantly lower and more variable than those generated by the intranasal route, and FnBP-specific intestinal IgA was undetectable. Neither the ISCOM matrix nor cholera toxin enhanced these responses. These studies demonstrate for the first time that recombinant plant viruses have potential as mucosal vaccines without the requirement for adjuvant and that the nasal route is most effective for the delivery of these nonreplicating particles.Replicating vaccines such as live-attenuated bacterial (13) and virus (36, 40, 45) vaccines, as well as naked DNA vaccines (31), induce stronger and longer-lasting immune responses than conventional killed-subunit vaccines and also elicit protective cell-mediated immunity, often without the need for adjuvant. There are however, safety concerns over the use of these vaccines (24, 49), where persistence or reversion to virulence of the live vaccine strains and integration of the naked DNA vaccine into the host chromosome are of major concern. Recent technological advances, such as the use of more-effective adjuvants for both mucosal and systemic delivery (12, 16), liposome and ISCOM encapsulation of proteins and peptides (3, 19, 27), multiple antigenic peptides (35), and virus-like particles (VLPs) (1), have led to the development of more-effective subunit vaccines. To circumvent the safety concerns of replicating vaccines and to avoid the need for peptide synthesis and chemical coupling to a carrier such as keyhole limpet hemocyanin, we have been examining the utility of the plant virus cowpea mosaic virus (CPMV) as a carrier of peptides for immune recognition. CPMV is composed of 2 subunits, the small (S) and large (L) coat proteins, of which there are 60 copies of each per virus particle (46). Foreign peptides up to 37 amino acids in length can be expressed on either the L or S proteins; hence, 60 to 120 copies of a peptide can be displayed on a single virus particle (4b, 34). A peptide from the human immunodeficiency virus (HIV) gp41 glycoprotein is highly immunogenic when displayed on CPMV, eliciting high titers of HIV neutralizing antibodies (28, 29). Furthermore, a peptide derived from the VP2 protein of canine parvovirus (CPV) expressed on CPMV is immunogenic when administered to mink and subsequently protected the mink from a lethal challenge with the CPV-related mink enteritis virus (10).Most infectious viral and bacterial diseases involve colonization or invasion through mucosal surfaces by the pathogen, and hence it is important to develop vaccines that induce strong protective mucosal immune responses as a first line of defense. Where the organism, such as Vibrio cholerae and enterotoxigenic Escherichia coli, is restricted to the mucosa, strong mucosal immunity is often sufficient. However, when the organism disseminates from the mucosa into the bloodstream, a strong systemic response is also required to engender sterile immunity. Hence, the ideal mucosal vaccine should generate local immune responses at mucosal surfaces but also elicit generalized vaccine-specific immunity in the systemic lymphoid organs. The potential of CPMV-based vaccines for mucosal vaccination has not previously been determined.Oral immunization with particulate antigens, especially when presented as viable organisms, which can colonize the mucosa better than killed organisms, is effective at inducing local and generalized secretory and systemic immune responses (5, 43). However, the acidic pH and the presence of degradative enzymes in the gastrointestinal tract mean that when nonreplicating antigens are used, high concentrations are often required to elicit high levels of immunity (6). Another way to elicit mucosal immunity but circumvent the problems of oral immunization is to vaccinate via the intranasal route (2). Intranasal immunization requires up to 10-fold less immunogen for effective immunization and avoids the problems of low pH. Live vaccines (15, 37), virus-like particles (4, 25, 32), and synthetic peptides (17, 33, 44) in the absence of adjuvant have been shown to stimulate strong immunity when administered by this route. Furthermore, stimulation of the nasal mucosa, like stimulation of the intestinal mucosa, has been shown to be effective at generating protective immunity at distant mucosal sites (reviewed in reference 2).To assess the potential of CVPs as mucosal vaccines, mice were immunized intranasally or orally with CPMV expressing a peptide derived from the fibronectin-binding protein B (FnBP) D2 motif of Staphylococcus aureus (14, 42). The three fibronectin-binding domains, termed D1, D2, and D3, of FnBP have been shown to be immunogenic in mice and rats (7, 41). The CVPs were shown to be more immunogenic when administered (without adjuvant) via the intranasal route than when administered by the oral route, generating high titers of D2-specific antibody in serum and mucosa, and the serum antibody inhibited fibronectin binding to FnBP.     

Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 Reveals a Tight Link between Tyrosine Phosphorylation and Virulence

Encapsulated Klebsiella pneumoniae is the predominant causative agent of pyogenic liver abscess, an emerging infectious disease that often complicates metastatic meningitis or endophthalmitis. The capsular polysaccharide on K. pneumoniae surface was determined as the key to virulence. Although the regulation of capsular polysaccharide biosynthesis is largely unclear, it was found that protein-tyrosine kinases and phosphatases are involved. Therefore, the identification and characterization of such kinases, phosphatases, and their substrates would advance our knowledge of the underlying mechanism in capsule formation and could contribute to the development of new therapeutic strategies. Here, we analyzed the phosphoproteome of K. pneumoniae NTUH-K2044 with a shotgun approach and identified 117 unique phosphopeptides along with 93 in vivo phosphorylated sites corresponding to 81 proteins. Interestingly, three of the identified tyrosine phosphorylated proteins, namely protein-tyrosine kinase (Wzc), phosphomannomutase (ManB), and undecaprenyl-phosphate glycosyltransferase (WcaJ), were found to be distributed in the cps locus and thus were speculated to be involved in the converging signal transduction of capsule biosynthesis. Consequently, we decided to focus on the lesser studied ManB and WcaJ for mutation analysis. The capsular polysaccharides of WcaJ mutant (WcaJY5F) were dramatically reduced quantitatively, and the LD₅₀ increased by 200-fold in a mouse peritonitis model compared with the wild-type strain. However, the capsular polysaccharides of ManB mutant (ManBY26F) showed no difference in quantity, and the LD₅₀ increased by merely 6-fold in mice test. Our study provided a clear trend that WcaJ tyrosine phosphorylation can regulate the biosynthesis of capsular polysaccharides and result in the pathogenicity of K. pneumoniae NTUH-K2044.Protein phosphorylation is one of the most biologically relevant and ubiquitous post-translational modifications in both eukaryotic and prokaryotic organisms. It is best known that protein phosphorylation is a reversible enzyme-catalyzed process that is controlled by various kinases and phosphatases. The aberrant functions often result in irregular protein phosphorylation and ultimately lead to serious disease states such as malignant transformation, immune disorders, and pathogenic infections in mammals (1, 2). Recently, accumulating evidences suggest that Ser/Thr/Tyr phosphorylations also contribute to regulate a diverse range of cellular responses and physiological processes in prokaryotes (1). Among them, tyrosine phosphorylation in encapsulated bacteria has been discovered to play key roles in capsular polysaccharide (CPS1; K antigen) biosynthesis, which leads to virulence (3, 4). This thick layer of exopolysaccharide on many pathogenic bacteria can act as a physical boundary to evade phagocytosis and complement-mediated killing and further inhibit complement activation of the host (1, 5, 6).In 1996, Acinetobacter johnsonii protein-tyrosine kinase (Ptk) was first discovered and categorized under the bacterial protein-tyrosine kinase (BY-kinase) family (1, 7, 8). Shortly after, its function in bacterial exopolysaccharide production and transport was characterized (1, 7, 8). From then on, many more bacterial tyrosine kinases such as Wzc of Escherichia coli (1, 9) and EpsB of Pseudomonas solanacearum (10, 11) were found to possess this conserved property; deletion of such tyrosine kinases will result in the loss of exopolysaccharide production (12). Therefore, several experiments were conducted to investigate the role of the downstream substrates of the tyrosine kinases in different strains of bacteria, and some targeted proteins were found to participate in the exopolysaccharide anabolism (13, 14). These findings demonstrated a direct relationship between bacterial tyrosine phosphorylation and exopolysaccharide biosynthesis that was directly reflected in the strain virulence.In the past, the functional roles of the critical components involved in protein phosphorylation were defined by basic biochemical and genetic approaches (1). However, there exists a salient gap between the growing number of identified protein-tyrosine kinases/phosphatases and the relative paucity of protein substrates characterized to date. Genomic sequence analyses and advanced high resolution/high accuracy MS systems with vastly improved phosphopeptide enrichment strategies are among the two key enabling technologies that allow a high efficiency identification of the scarcely detectable site-specific phosphorylations in bacterial systems (15). Mann et al. (16) were the first to initiate a systematic study of the phosphoproteome of B. subtilis in 2007 followed by similar site-specific phosphoproteomics analyses of E. coli (17), Lactococcus lactis (18), and Halobacterium salinarum (19). These pioneering works have since set the foundation in bacterial phosphoproteomics but have not been specifically carried out to address a particular biological issue of causal relevance to virulence or pathogenesis.Klebsiella pneumoniae is a Gram-negative, non-motile, facultative anaerobic, and rod-shaped bacterium. It is commonly found in water and soil (20) as well as on plants (21) and mucosal surfaces of mammals, such as human, horse, and swine (22, 23). It was demonstrated that CPS on the surface of K. pneumoniae is the prime factor of virulence and toxicity in causing pyogenic liver abscess (PLA), a common intra-abdominal infection with a high 10–30% mortality rate worldwide (24–29). There are also variations in virulence in regard to different capsular serotypes; K1 and K2 were found to be especially pathogenic in causing PLA in a mouse model (30) compared with other serotypes, which show little or no effect (31–34). The K. pneumoniae NTUH-K2044 (K2044) strain, encapsulated with K1 antigen (35), was isolated from clinical K. pneumoniae liver abscess patients. It has become an important emerging pathogen (36) because it usually complicates metastatic septic endophthalmitis and irreversible central nervous system infections independent of host underlying diseases (30, 34). The transmission rate is high (37), and it often rapidly leads to outbreaks of community-acquired infections, such as bacteremia, nosocomial pneumonia, and sepsis, common in immunocompromised individuals (38).In this study, we wanted to prove that the biosynthesis of CPS is mediated through tyrosine phosphorylation of a subset of proteins. An MS-based systematic phosphoproteomics analysis was conducted on K2044 to identify tyrosine phosphorylated proteins that are also associated with CPS biosynthesis. We further validated the relationship between tyrosine phosphorylation on those proteins and virulence of K2044 by site-directed mutagenesis, CPS quantification, serum killing, and mouse lethality assay.