Differences in the aromatic domain of homologous streptococcal fibronectin-binding proteins trigger different cell invasion mechanisms and survival rates

Group A streptococci (GAS, Streptococcus pyogenes) and Group G streptococci (GGS, Streptococcus dysgalactiae ssp. equisimilis) adhere to and invade host cells by binding to fibronectin. The fibronectin-binding protein SfbI from GAS acts as an invasin by using a caveolae-mediated mechanism. In the present study we have identified a fibronectin-binding protein, GfbA, from GGS, which functions as an adhesin and invasin. Although there is a high degree of similarity in the C-terminal sequence of SfbI and GfbA, the invasion mechanisms are different. Unlike caveolae-mediated invasion by SfbI-expressing GAS, the GfbA-expressing GGS isolate trigger cytoskeleton rearrangements. Heterologous expression of GfbA on the surface of a commensal Streptococcus gordonii and purified recombinant protein also triggered actin rearrangements. Expression of a truncated GfbA (lacking the aromatic domain) and chimeric GfbA/SfbI protein (replacing the aromatic domain of SfbI with the GfbA aromatic domain) on S. gordonii or recombinant proteins alone showed that the aromatic domain of GfbA is responsible for different invasion mechanisms. This is the first evidence for a biological function of the aromatic domain of fibronectin-binding proteins. Furthermore, we show that streptococci invading via cytoskeleton rearrangements and intracellular trafficking along the classical endocytic pathway are less persistence than streptococci entering via caveolae.     

Lactobacillus fermentum BCS87 expresses mucus‐ and mucin‐binding proteins on the cell surface

Aims: To identify and characterize adhesion‐associated proteins in the potential probiotic Lactobacillus fermentum BCS87. Methods and Results: Protein suspensions obtained from the treatment of Lact. fermentum BCS87 with 1 mol 1^?1 LiCl were analysed by Western blotting using HRP‐labelled porcine mucus and mucin. Two adhesion‐associated proteins with relative molecular weight of 29 and 32 kDa were identified. The N‐terminal and internal peptides of the 32 kDa protein (32‐Mmubp) were sequenced, and the corresponding gene (32‐mmub) was found by inverse polymerase chain reaction. The complete nucleotide sequence of 32‐mmub revealed an open reading frame of 903 bp encoding a primary protein of 300 amino acids and a mature protein of 272 residues. A basic local alignment search showed 47–99% identity to solute‐binding components of ATP binding cassette transporter proteins in Lactobacillus, Streptococcus and Clostridium. An OpuAC‐conserved domain was identified and phylogenetic relationship analysis confirmed that 32‐Mmubp belongs to the OpuAC family. Conclusions: Adhesion of Lact. fermentum BCS87 appeared to be mediated by two surface‐associated proteins. 32‐Mmubp is a component of ABC transporter system that also functions as an adhesin. Significance and Impact of the Study: Characterization of 32‐Mmubp and 32‐mmub will contribute to understanding the host–bacteria interactions of Lact. fermentum with the intestinal tract of pigs.     

Yeast freeze-thaw survival rates as a function of different stages in the cell cycle

In the present study we demonstrate that the ?80 °C freeze-thaw survival rate in the yeast, Saccharomyces cerevisiae, is dependent upon specific stages in the cell cycle. Samples removed from synchronous cultures at appropriate intervals during the first three consecutive synchronous cell cycles were subjected to a ?80 °C freeze-thaw protocol employing 10% glycerol as a cryoprotectant. Distinct cyclic changes in the percentage of viable cells in response to our freeze-thaw protocol were observed during each of the three consecutive synchronous cell generations examined. Maximum rates of survival occurred at the initiation of each new cell cycle and minimum rates of survival occurred approximately 30 min prior to each new cell cycle. These maximum and minimum rates of survival were shown to be correlated in time with maximum and minimum ratios of cellular phospholipid to membrane during each individual cell cycle.     

Quantifying the mechanisms of domain gain in animal proteins

Background  

Protein domains are protein regions that are shared among different proteins and are frequently functionally and structurally independent from the rest of the protein. Novel domain combinations have a major role in evolutionary innovation. However, the relative contributions of the different molecular mechanisms that underlie domain gains in animals are still unknown. By using animal gene phylogenies we were able to identify a set of high confidence domain gain events and by looking at their coding DNA investigate the causative mechanisms.     

Differences in osteoblast miRNA induced by cell binding domain of collagen and silicate-based synthetic bone

Summary PerioGlas (PG) is an silicate-based (i.e. anorganic) material used for grafting periodontal osseous defects since the ninety whereas P-15 is an analog of the cell binding domain of collagen (i.e. organic material) that is successfully used in clinical trial to promote bone formation. However, how PG (i.e anorganic material) and P-15 (i.e. collagen) differentially alter osteoblast activity to promote bone formation is unknown. We therefore attempted to get more insight by using microRNA microarray techniques to investigate the translation process in osteoblasts differentially exposed to PG and P-15. We identified 3 up-regulated miRNA (i.e. mir-30b, mir-26a, mir-92) and 8 down-regulated miRNA (i.e. mir-337, mir-377, mir-25, mir-200b, mir-129, mir-373, mir-133b, mir-489). The data reported are, to our knowledge, the first study on translation regulation in osteoblatsts differentially exposed to cell binding domain of collagen and to silicate-based material. Both enhance the translation of several miRNA belonging to osteogenetic genes, but P-15 acts preferentially on homeobox genes.     

Identification of homologous binding proteins in porcine and bovine gametes

The purpose of this study was to determine if sperm and oocyte proteins that mediate plasma membrane interaction during mammalian fertilization are conserved among porcine and bovine gametes. We examined homologous and heterologous sperm and zona-free oocyte interactions to determine the extent of cross-reactivity between the gametes of these two ungulate species. First, the numbers of ejaculated porcine and bovine sperm bound to the oocyte plasma membrane of intact porcine and bovine oocytes were determined in vitro. There was no significant difference between the number of porcine or bovine sperm that bound to porcine or bovine oocytes (P > 0.25). Second, individual porcine and bovine sperm plasma membrane proteins were identified by binding of homologous or heterologous oocyte plasma membrane to whole sperm plasma membrane on Western ligand blots. The relative amount of labeled oocyte plasma membrane bound to individual sperm plasma membrane proteins was analyzed by laser densitometry. Eight porcine sperm plasma membrane proteins and seven bovine sperm plasma membrane proteins were bound by both porcine and bovine oocyte plasma membrane. A significantly greater relative amount of porcine oocyte plasma membrane than bovine oocyte plasma membrane was bound to the 14- and 10-kD porcine sperm plasma membrane proteins (P < 0.001 and P < 0.01, respectively). A 27-kD bovine sperm plasma membrane protein bound proportionally more bovine oocyte plasma membrane probe than porcine oocyte plasma membrane probe (P < 0.04). These results are consistent with conservation of similar receptor ligand interactions at the gamete plasma membrane among porcine and bovine gametes.     

Expression of different group A streptococcal M proteins in an isogenic background demonstrates diversity in adherence to and invasion of eukaryotic cells

The M protein of group A streptococcus (GAS) is considered to be a major virulence factor because it renders GAS resistant to phagocytosis and allows bacterial growth in human blood. There are more than 80 known serotypes of M proteins, and protective opsonic antibodies produced during disease in humans are serotype specific. M proteins also mediate bacterial adherence to epithelial cells of skin and pharynx. GAS strains vary in the genomic organization of the mga regulon, which contains the genes encoding M and M-like proteins and other virulence factors. This diversity of organization makes it difficult to assess virulence of M proteins of different serotypes, unless they can be expressed in an isogenic background. Here, we express M proteins of different serotypes in the M protein- and protein F1-deficient GAS strain, SAM2, which also lacks M-like proteins. Genes encoding M proteins of different serotypes (emmXs) have been integrated into the SAM2 chromosome in frame with the emm6.1 promoter and its mga regulon, resulting in similar levels of emmX expression. Although SAM2 exhibits a very low level of adherence to and invasion of HEp-2 and HaCaT cells, a SAM2-derived strain expressing M6 protein adheres to and invades both cell types. In contrast, the isogenic strain expressing M18 protein adheres to both cell types, but invades with a very low efficiency. A strain expressing M3 protein adheres to both types of cells, but its invasion of HEp-2 cells is serum dependent. A GAS strain expressing M6 protein does not compete with the isogenic strain expressing M18 protein for adherence to or invasion of HaCaT cells. We conclude that M proteins of different serotypes recognize different repertoires of receptors on the surfaces of eukaryotic cells.     

A charge‐sensitive loop in the FKBP38 catalytic domain modulates Bcl‐2 binding

The Bcl‐2 inhibitor FKBP38 is regulated by the Ca²⁺‐sensor calmodulin (CaM). Here we show a hitherto unknown low‐affinity cation‐binding site in the FKBP domain of FKBP38, which may afford an additional level of regulation based on electrostatic interactions. Fluorescence titration experiments indicate that in particular the physiologically relevant Ca²⁺ ion binds to this site. NMR‐based chemical shift perturbation data locate this cation‐interaction site within the β5–α1 loop (Leu90–Ile96) of the FKBP domain, which contains the acidic Asp92 and Asp94 side‐chains. Binding constants were subsequently determined for K⁺, Mg²⁺, Ca²⁺, and La³⁺, indicating that the net charge and the radius of the ion influences the binding interaction. X‐ray diffraction data furthermore show that the conformation of the β5–α1 loop is influenced by the presence of a positively charged guanidinium group belonging to a neighboring FKBP38 molecule in the crystal lattice. The position of the cation‐binding site has been further elucidated based on pseudocontact shift data obtained by NMR via titration with Tb³⁺. Elimination of the Ca²⁺‐binding capacity by substitution of the respective aspartate residues in a D92N/D94N double‐substituted variant reduces the Bcl‐2 affinity of the FKBP38^35–153/CaM complex to the same degree as the presence of Ca²⁺ in the wild‐type protein. Hence, this charge‐sensitive site in the FKBP domain participates in the regulation of FKBP38 function by enabling electrostatic interactions with ligand proteins and/or salt ions such as Ca²⁺. Copyright © 2010 John Wiley & Sons, Ltd.     

Guild‐specific shifts in visitation rates of frugivores with habitat loss and plant invasion

Habitat loss and plant invasions are two major drivers of global change in subtropical and tropical ecosystems. Both lead to a loss of biodiversity and alter species interactions, which may imperil vital ecosystem processes such as seed dispersal by frugivores. Reponses of frugivores to disturbance are often linked to their specialization on certain habitats or resources. Yet, it is poorly understood how habitat loss and plant invasion structure interactions between plants and different habitat or feeding guilds. Here we investigated whether visitation rates of frugivores change guild‐specifically with increasing habitat loss and invasion level in a heterogeneous subtropical landscape. In 756 h of observations, we recorded 1446 plant–frugivore interactions among 18 plant species and 42 avian frugivore species. Visitation rates of forest specialists decreased with increasing habitat loss, but not with changes in invasion level. In contrast forest generalists and forest visitors were unaffected by either driver. Similarly, obligate frugivores that overall showed a generalized fruit choice were unaffected by habitat loss and changes in invasion level. Contrary, visitation rates of specialized partial and opportunistic frugivores decreased with higher invasion level. Importantly, the negative effect of plant invasion on partial frugivores was more pronounced as habitat loss in the same study site increased, indicating a synergistic effect of the two drivers. The implications of our study are twofold: first, frugivores respond guild‐specifically to habitat loss and plant invasion. Thereby forest dependency is mainly related to habitat loss, and degree of frugivory mainly related to plant invasion. Forest generalists and obligate frugivores in turn may play a key‐role for forest regeneration in disturbed forest landscapes. Second, particularly frugivores with a specialized fruit choice may be threatened by synergistic effects between habitat loss and plant invasion.     

Fast folding of a prototypic polypeptide: the immunoglobulin binding domain of streptococcal protein G.

The folding of the small (56 residues) highly stable B1 immunoglobulin binding domain (GB1) of streptococcal protein G has been investigated by quenched-flow deuterium-hydrogen exchange. This system represents a paradigm for the study of protein folding because it exhibits no complicating features superimposed upon the intrinsic properties of the polypeptide chain. Collapse to a semicompact state exhibiting partial order, reflected in protection factors for ND-NH exchange up to 10-fold higher than that expected for a random coil, occurs within the dead time (< or = 1 ms) of the quenched flow apparatus. This is followed by the formation of the fully native state, as monitored by the fractional proton occupancy of 26 backbone amide groups spread throughout the protein, in a single rapid concerted step with a half-life of 5.2 ms at 5 degrees C.     

Actin binding proteins that change extent and rate of actin monomer-polymer distribution by different mechanisms

Actin binding proteins control actin assembly and disassembly by altering the critical concentration and by changing the kinetics of polymerization. All of these control mechanisms in some way or the other make use of the energy of hydrolysis of actin-bound ATP. Capping of barbed filament ends increases the critical concentration as long as ATP hydrolysis maintains a difference in the actin monomer binding constants of the two ends. A further increase in the critical concentration on adding a second cap, tropomodulin, to the other, pointed filament end also requires ATP hydrolysis as described by the model presented here. Changes in the critical concentration are amplified into much larger changes of the monomer pool by actin sequestering proteins, provided their actin binding equilibrium constants fall within a relatively narrow range around the values for the two critical concentrations of actin. Cofilin greatly speeds up treadmilling, which requires ATP hydroysis, by increasing the rate constant of depolymerization. Profilin increases the rate of elongation at the barbed filament end, coupled to a lowering of the critical concentration, only if ATP hydrolysis makes profilin binding to the barbed end independent of its binding constant for actin monomers.     

Differences in the mechanisms of proapoptotic BH3 proteins binding to Bcl-XL and Bcl-2 quantified in live MCF-7 cells

Overexpression of antiapoptotic proteins including Bcl-XL and/or Bcl-2 contributes to tumor initiation, progression, and resistance to therapy by direct interactions with proapoptotic BH3 proteins. Release of BH3 proteins from antiapoptotic proteins kills some cancer cells and sensitizes others to chemotherapy. Binding of Bcl-XL and Bcl-2 to the BH3 proteins Bad, Bid, and the three major isoforms of Bim was measured for fluorescent protein fusions in live cells using fluorescence lifetime imaging microscopy and fluorescence resonance energy transfer. In cells the binding of the proteins at mitochondria is similar to the results from in vitro measurements. However, mutations in the BH3 region of Bim known to inhibit binding to Bcl-XL and Bcl-2 in vitro had much less effect in MCF-7 cells. Moreover, the BH3 mimetic ABT-737 inhibited Bad and Bid but not Bim binding to Bcl-XL and Bcl-2. Thus, the selectivity of ABT-737 also differs markedly from predictions made from in vitro measurements.     

Large‐scale analysis of secondary structure changes in proteins suggests a role for disorder‐to‐order transitions in nucleotide binding proteins

Conformational changes in proteins often involve secondary structure transitions. Such transitions can be divided into two types: disorder‐to‐order changes, in which a disordered segment acquires an ordered secondary structure (e.g., disorder to α‐helix, disorder to β‐strand), and order‐to‐order changes, where a segment switches from one ordered secondary structure to another (e.g., α‐helix to β‐strand, α‐helix to turn). In this study, we explore the distribution of these transitions in the proteome. Using a comprehensive, yet highly conservative method, we compared solved three‐dimensional structures of identical protein sequences, looking for differences in the secondary structures with which they were assigned. Protein chains in which such secondary structure transitions were detected, were classified into two sets according to the type of transition that is involved (disorder‐to‐order or order‐to‐order), allowing us to characterize each set by examining enrichment of gene ontology terms. The results reveal that the disorder‐to‐order set is significantly enriched with nucleotide binding proteins, whereas the order‐to‐order set is more diverse. Remarkably, further examination reveals that >22% of the purine nucleotide binding proteins include segments which undergo disorder‐to‐order transitions, suggesting that such transitions play an important role in this process. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Molecular mechanisms of imidazole and benzene ring binding in proteins

Aromatic bonds of amino acid radicals play an important role in arrangement of protein primary structure. Previously, the existence of a number of preferable conformations of aromatic dimers was shown theoretically and experimentally, the best known of which are parallel-displaced and perpendicular T conformations. To reveal principles that define preference of various conformations for His-His and Phe-His dimers, non-empirical quantum-chemical calculations of diimidazole and benzene-imidazole were carried out. Calculations were performed using the 6-31G** basis with account for electronic correlations in frames of MP2 and MP4 methods of perturbation theory. Comparative analysis of energetic and geometric parameters of the systems points to the preference of stacking contact or classical hydrogen bond in diimidazole. On the contrary, T conformation is maximally advantageous for benzene-imidazole.     

Differences in binding specificity for the homologous gamma- and beta-chain "holes" on fibrinogen: exclusive binding of Ala-His-Arg-Pro-amide by the beta-chain hole

The beta-chain amino-terminal sequences of all known mammalian fibrins begin with the sequence Gly-His-Arg-Pro- (GHRP-), but the homologous sequence in chicken fibrin begins with the sequence Ala-His-Arg-Pro- (AHRP-). Nonetheless, chicken fibrinogen binds the synthetic peptide GHRPam, and a previously reported crystal structure has revealed that the binding is in exact conformance with that observed for the human GHRPam-fragment D complex. We now report that human fibrinogen, which is known not to bind APRP, binds the synthetic peptide AHRPam. Moreover, a crystal structure of AHRPam complexed with fragment D from human fibrinogen shows that AHRPam binds exclusively to the beta-chain hole and, unlike GHRPam, not at all to the homologous gamma-chain hole. The difference can be attributed to the methyl group of the alanine residue clashing with a critical carboxyl group in the gammaC hole but being accommodated in the roomier betaC hole where the equivalent carboxyl is situated more flexibly.     

Stereoselective oxidation of aromatic sulfides and sulfoxides in the binding domain of bovine serum albumin

The oxidation of aromatic sulfides with achiral oxidizing agents, e.g., sodium metaperiodate (NaIO₄) and hydrogen peroxide (H₂O₂) in the binding domain of bovine serum albumin (BSA), furnished a strong asymmetric bias (max 81%) of the product sulfoxides in fairly high chemical yields. The kinetic resolution of racemic aromatic sulfoxides was also carried out in the chiral binding domain, and the remaining unchanged sulfoxides showed optical purities ranging over 1–33% at ca. 50% completion of oxidation. The combination of the two stereoselective oxidations above mentioned produced several optically active sulfoxides of >90% optical purity in ca. 50% chemical yield. The present method constitutes a successful biomimetic approach to achieving stereoselectivities as high as obtained by sulfur-oxidizing microorganisms.