Molecular signatures for the phylum Synergistetes and some of its subclades

Species belonging to the phylum Synergistetes are poorly characterized. Though the known species display Gram-negative characteristics and the ability to ferment amino acids, no single characteristic is known which can define this group. For eight Synergistetes species, complete genome sequences or draft genomes have become available. We have used these genomes to construct detailed phylogenetic trees for the Synergistetes species and carried out comprehensive analysis to identify molecular markers consisting of conserved signature indels (CSIs) in protein sequences that are specific for either all Synergistetes or some of their sub-groups. We report here identification of 32 CSIs in widely distributed proteins such as RpoB, RpoC, UvrD, GyrA, PolA, PolC, MraW, NadD, PyrE, RpsA, RpsH, FtsA, RadA, etc., including a large >300 aa insert within the RpoC protein, that are present in various Synergistetes species, but except for isolated bacteria, these CSIs are not found in the protein homologues from any other organisms. These CSIs provide novel molecular markers that distinguish the species of the phylum Synergistetes from all other bacteria. The large numbers of other CSIs discovered in this work provide valuable information that supports and consolidates evolutionary relationships amongst the sequenced Synergistetes species. Of these CSIs, seven are specifically present in Jonquetella, Pyramidobacter and Dethiosulfovibrio species indicating a cladal relationship among them, which is also strongly supported by phylogenetic trees. A further 15 CSIs that are only present in Jonquetella and Pyramidobacter indicate a close association between these two species. Additionally, a previously described phylogenetic relationship between the Aminomonas and Thermanaerovibrio species was also supported by 9 CSIs. The strong relationships indicated by the indel analysis provide incentives for the grouping of species from these clades into higher taxonomic groups such as families or orders. The identified molecular markers, due to their specificity for Synergistetes and presence in highly conserved regions of important proteins suggest novel targets for evolutionary, genetic and biochemical studies on these bacteria as well as for the identification of additional species belonging to this phylum in different environments.     

Reactivation of Fetal Splicing Programs in Diabetic Hearts Is Mediated by Protein Kinase C Signaling

Diabetic cardiomyopathy is one of the complications of diabetes that eventually leads to heart failure and death. Aberrant activation of PKC signaling contributes to diabetic cardiomyopathy by mechanisms that are poorly understood. Previous reports indicate that PKC is implicated in alternative splicing regulation. Therefore, we wanted to test whether PKC activation in diabetic hearts induces alternative splicing abnormalities. Here, using RNA sequencing we identified a set of 22 alternative splicing events that undergo a developmental switch in splicing, and we confirmed that splicing reverts to an embryonic pattern in adult diabetic hearts. This network of genes has important functions in RNA metabolism and in developmental processes such as differentiation. Importantly, PKC isozymes α/β control alternative splicing of these genes via phosphorylation and up-regulation of the RNA-binding proteins CELF1 and Rbfox2. Using a mutant of CELF1, we show that phosphorylation of CELF1 by PKC is necessary for regulation of splicing events altered in diabetes. In summary, our studies indicate that activation of PKCα/β in diabetic hearts contributes to the genome-wide splicing changes through phosphorylation and up-regulation of CELF1/Rbfox2 proteins. These findings provide a basis for PKC-mediated cardiac pathogenesis under diabetic conditions.     

Plasmodium falciparum PhIL1-associated complex plays an essential role in merozoite reorientation and invasion of host erythrocytes

The human malaria parasite, Plasmodium falciparum possesses unique gliding machinery referred to as the glideosome that powers its entry into the insect and vertebrate hosts. Several parasite proteins including Photosensitized INA-labelled protein 1 (PhIL1) have been shown to associate with glideosome machinery. Here we describe a novel PhIL1 associated protein complex that co-exists with the glideosome motor complex in the inner membrane complex of the merozoite. Using an experimental genetics approach, we characterized the role(s) of three proteins associated with PhIL1: a glideosome associated protein- PfGAPM2, an IMC structural protein- PfALV5, and an uncharacterized protein—referred here as PfPhIP (PhIL1 Interacting Protein). Parasites lacking PfPhIP or PfGAPM2 were unable to invade host RBCs. Additionally, the downregulation of PfPhIP resulted in significant defects in merozoite segmentation. Furthermore, the PfPhIP and PfGAPM2 depleted parasites showed abrogation of reorientation/gliding. However, initial attachment with host RBCs was not affected in these parasites. Together, the data presented here show that proteins of the PhIL1-associated complex play an important role in the orientation of P. falciparum merozoites following initial attachment, which is crucial for the formation of a tight junction and hence invasion of host erythrocytes.     

Cdc42 and the Phosphatidylinositol 3-Kinase-Akt Pathway Are Essential for PspC-mediated Internalization of Pneumococci by Respiratory Epithelial Cells

The pneumococcal surface protein C (PspC) is a major adhesin of Streptococcus pneumoniae, the cause of lobar pneumonia and invasive diseases. PspC interacts in a human-specific manner with the ectodomain of the human polymeric immunoglobulin receptor (pIgR) produced by respiratory epithelial cells. By adopting the retrograde machinery of human pIgR, this protein-protein interaction promotes colonization and transcytosis across the epithelial layer. Here, we explored the role of Rho family guanosine triphosphatases (GTPases), phosphatidylinositol 3-kinase (PI3K) and protein kinase B (Akt) for ingestion of pneumococci via the human pIgR. Inhibition experiments suggested that the host-cell actin microfilaments and microtubules are essential for this pneumococcal uptake mechanism. By using specific GTPase-modifying toxins, inhibitors, and GTPase expression constructs we demonstrate that Cdc42, but not Rac1 and RhoA are involved in PspC-mediated invasion of pneumococci into host cells. Accordingly, Cdc42 is time-dependently activated during ingestion of pneumococci. In addition, PI3K and Akt are essential for ingestion of pneumococci by respiratory epithelial cells via the PspC-pIgR interaction. The subunit p85α of PI3K and Akt was activated during the infection process. Moreover, Akt activation upon pneumococcal invasion depends on PI3K. In conclusion, our results illustrate for the first time key signaling molecules of host cells that are required for PspC-pIgR-mediated invasion of pneumococci into epithelial cells. This unique and specific bacterial entry process is dependent on the cooperation and activation of Rho family GTPase Cdc42, PI3K, and Akt.Streptococcus pneumoniae (pneumococci) is (are) the etiologic agent of community-acquired pneumonia and life-threatening invasive diseases such as septicemia and bacterial meningitis (1). Pneumococci use several strategies to colonize the respiratory tract, which is considered to be the initial and essential step prior to their transmigration into the lungs and bloodstream. Adherence of pneumococci to host cells is facilitated by serum or matrix proteins such as Factor H, thrombospondin-1, and vitronectin (2–4). More importantly, pneumococci produce adhesins, which interact directly with cellular receptors and, consequently, these interactions promote bacterial adherence to and invasion into host cells (5). The pneumococcal surface protein C (PspC),³ also referred to as CbpA or SpsA, is a multifunctional choline-binding protein and a major adhesin of pneumococci residing on mucosal respiratory surfaces. PspC interacts directly and in a human-specific manner with the ectodomain of the polymeric immunoglobulin receptor (pIgR), which is also known as the secretory component (SC) (6). The PspC-hpIgR interaction has been characterized in detail on the molecular level and also on the structural level with regard to the PspC protein. A hexameric peptide within the N-terminal repeat domains (termed R1 or R2) of PspC recognizes human-specific amino acids in ectodomains D3 and D4 of pIgR (6–9). After binding to pIgR, pneumococci are ingested and transcytosed across epithelial cells by adopting the pIgR retrograde transcytosis machinery (7, 10). Additionally, the N terminus of PspC interacts in a human-specific manner with the innate immune regulator Factor H, and this interaction mediates immune evasion and adherence to host cells (2, 11–13).The pIgR, which is broadly expressed by epithelial cells of the respiratory tract, mediates the transport of polymeric IgA (dIgA) or pIgM across the mucosal epithelial barriers from the basolateral to apical surface (14). Although unloaded pIgR undergoes constitutive transcytosis, binding of dIgA stimulates the receptor transcytosis in in vitro and in vivo situations (15, 16). The model of pIgR-dIgA transcytosis from the basolateral to the apical cell surface is based largely on studies using Madin-Darby canine kidney (MDCK) cells expressing exogenous rabbit or rat pIgR (15–17). The studies provided important insights into receptor sorting, intracellular compartments involved in transcytosis, and regulation of the endocytic pathways (14). After endocytosis in clathrin-coated vesicles at the basolateral surface, pIgR is delivered in an actin- and microtubule-dependent manner to the common recycling endosomes. At the apical surface unloaded receptor can be recycled and transported in retrograde. The dIgA-stimulated pIgR transcytosis is regulated by Rho family GTPases, phosphatidylinositol-3-kinase (PI3K), and requires the production of secondary messengers, including inositol 1,4,5-triphosphate and free intracellular calcium (17–23). In addition, the activation of these signaling molecules depends on the Src family protein tyrosine kinase p62^yes and may stimulate a network of downstream pathways (24). Although it has become clear that pneumococci can adopt the pIgR-transcytosis machinery for invasion, the induced signal transduction cascades have not yet been explored. The goal of this study was, therefore, to assess the induced intracellular signaling pathways during PspC-hpIgR-mediated pneumococcal invasion into host cells. We asked whether this process depends on the dynamics of the actin cytoskeleton as suggested by earlier observations by electron microscopy (5) and which member(s) of the Rho family of small GTPases are the key players in this uptake mechanism. In addition, we have analyzed the role of the PI3K and of protein kinase B (Akt; also known as PKB). Akt is phosphorylated during activation, and phosphorylation at Ser-473 depends on PI3K activity (25, 26). By using GTPase-modifying toxins, pharmacological inhibitors, GTPase constructs, and GTPase activation assays we demonstrate for the first time that pneumococcal invasion via the PspC-hpIgR interaction requires the small GTPase member Cdc42, PI3K, and Akt activity.     

A novel role for phagocytosis-like uptake in herpes simplex virus entry

It is becoming increasingly clear that herpesviruses can exploit the endocytic pathway to infect cells, yet several important features of this process remain poorly defined. Using herpes simplex virus-1 (HSV-1) as a model, we demonstrate that endocytosis of the virions mimic many features of phagocytosis. During entry, HSV-1 virions associated with plasma membrane protrusions followed by a phagocytosis-like uptake involving rearrangement of actin cytoskeleton and trafficking of the virions in large phagosome-like vesicles. RhoA GTPase was activated during this process and the mode of entry was cell type-specific. Clathrin-coated vesicles had no detectable role in virion trafficking as Eps15 dominant-negative mutants failed to affect HSV-1 uptake. Binding and fusion of the virion envelope with the phagosomal membrane is likely facilitated by clustering of nectin-1 (or HVEM) in phagosomes, which was observed in infected cells. Collectively, our data suggests a novel mode of uptake by which the virus can infect both professional and nonprofessional phagocytes.     

Complement Regulator Factor H Mediates a Two-step Uptake of Streptococcus pneumoniae by Human Cells

Streptococcus pneumoniae, a human pathogen, recruits complement regulator factor H to its bacterial cell surface. The bacterial PspC protein binds Factor H via short consensus repeats (SCR) 8–11 and SCR19–20. In this study, we define how bacterially bound Factor H promotes pneumococcal adherence to and uptake by epithelial cells or human polymorphonuclear leukocytes (PMNs) via a two-step process. First, pneumococcal adherence to epithelial cells was significantly reduced by heparin and dermatan sulfate. However, none of the glycosaminoglycans affected binding of Factor H to pneumococci. Adherence of pneumococci to human epithelial cells was inhibited by monoclonal antibodies recognizing SCR19–20 of Factor H suggesting that the C-terminal glycosaminoglycan-binding region of Factor H mediates the contact between pneumococci and human cells. Blocking of the integrin CR3 receptor, i.e. CD11b and CD18, of PMNs or CR3-expressing epithelial cells reduced significantly the interaction of pneumococci with both cell types. Similarly, an additional CR3 ligand, Pra1, derived from Candida albicans, blocked the interaction of pneumococci with PMNs. Strikingly, Pra1 inhibited also pneumococcal uptake by lung epithelial cells but not adherence. In addition, invasion of Factor H-coated pneumococci required the dynamics of host-cell actin microfilaments and was affected by inhibitors of protein-tyrosine kinases and phosphatidylinositol 3-kinase. In conclusion, pneumococcal entry into host cells via Factor H is based on a two-step mechanism. The first and initial contact of Factor H-coated pneumococci is mediated by glycosaminoglycans expressed on the surface of human cells, and the second step, pneumococcal uptake, is integrin-mediated and depends on host signaling molecules such as phosphatidylinositol 3-kinase.     

Regional variations in the nonlinearity and anisotropy of bovine aortic elastin

Arterial walls have a regular and lamellar organization of elastin present as concentric fenestrated networks in the media. In contrast, elastin networks are longitudinally oriented in layers adjacent to the media. In a previous model exploring the biomechanics of arterial elastin, we had proposed a microstructurally motivated strain energy function modeled using orthotropic material symmetry. Using mechanical experiments, we showed that the neo-Hookean term had a dominant contribution to the overall form of the strain energy function. In contrast, invariants corresponding to the two fiber families had smaller contributions. To extend these investigations, we use biaxial force-controlled experiments to quantify regional variations in the anisotropy and nonlinearity of elastin isolated from bovine aortic tissues proximal and distal to the heart. Results from this study show that tissue nonlinearity significantly increases distal to the heart as compared to proximally located regions ( $p<0.05$ ). Distally located samples also have a trend for increased anisotropy ( $p=0.07$ ), with the circumferential direction stiffer than the longitudinal, as compared to an isotropic and relatively linear response for proximally located elastin samples. These results are consistent with the underlying tissue histology from proximally located samples that had higher optical density ( $p<0.05$ ), fiber thickness ( $p<0.05$ ), and trend for lower tortuosity ( $p<0.07$ ) in elastin fibers as compared to the thinner and highly undulating elastin fibers isolated from distally located samples. Our studies suggest that it is important to consider elastin fiber orientations in investigations that use microstructure-based models to describe the contributions of elastin and collagen to arterial mechanics.     

Mass spectrometry assay for studying kinetic properties of dipeptidases: characterization of human and yeast dipeptidases

Chemical modifications of substrate peptides are often necessary to monitor the hydrolysis of small bioactive peptides. We developed an electrospray ionization mass spectrometry (ESI–MS) assay for studying substrate distributions in reaction mixtures and determined steady-state kinetic parameters, the Michaelis–Menten constant (K_m), and catalytic turnover rate (V_max/[E]_t) for three metallodipeptidases: two carnosinases (CN1 and CN2) from human and Dug1p from yeast. The turnover rate (V_max/[E]_t) of CN1 and CN2 determined at pH 8.0 (112.3 and 19.5 s⁻¹, respectively) suggested that CN1 is approximately 6-fold more efficient. The turnover rate of Dug1p for Cys-Gly dipeptide at pH 8.0 was found to be slightly lower (73.8 s⁻¹). In addition, we determined kinetic parameters of CN2 at pH 9.2 and found that the turnover rate was increased by 4-fold with no significant change in the K_m. Kinetic parameters obtained by the ESI–MS method are consistent with results of a reverse-phase high-performance liquid chromatography (RP–HPLC)-based assay. Furthermore, we used tandem MS (MS/MS) analyses to characterize carnosine and measured its levels in CHO cell lines in a time-dependent manner. The ESI–MS method developed here obviates the need for substrate modification and provides a less laborious, accurate, and rapid assay for studying kinetic properties of dipeptidases in vitro as well as in vivo.