Anne Marie Di Guilmi

Oligomerization of type III secretion proteins PopB and PopD precedes pore formation in Pseudomonas

Pseudomonas aeruginosa is the agent of opportunistic infections in immunocompromised individuals and chronic respiratory illnesses in cystic fibrosis patients. Pseudomonas aeruginosa utilizes a type III secretion system for injection of toxins into the host cell cytoplasm through a channel on the target membrane (the ‘translocon’). Here, we have functionally and structurally characterized PopB and PopD, membrane proteins implicated in the formation of the P.aeruginosa translocon. PopB and PopD form soluble complexes with their common chaperone, PcrH, either as stable heterodimers or as metastable heterooligomers. Only oligomeric forms are able to bind to and disrupt cholesterol‐rich membranes, which occurs within a pH range of 5–7 in the case of PopB/PcrH, and only at acidic pH for PcrH‐free PopD. Electron microscopy reveals that upon membrane association PopB and PopD form 80 Å wide rings which encircle 40 Å wide cavities. Thus, formation of metastable oligomers precedes membrane association and ring generation in the formation of the Pseudomonas translocon, a mechanism which may be similar for other pathogens that employ type III secretion systems.

Structural Basis of Host Cell Recognition by the Pilus Adhesin from Streptococcus pneumoniae

Pili are fibrous virulence factors associated directly to the bacterial surface that play critical roles in adhesion and recognition of host cell receptors. The human pathogen Streptococcus pneumoniae carries a single pilus-related adhesin (RrgA) that is key for infection establishment and provides protection from bacterial challenge in animal infection models, but details of these roles remain unclear. Here we report the high-resolution crystal structure of RrgA, a 893-residue elongated macromolecule whose fold contains four domains presenting both eukaryotic and prokaryotic origins. RrgA harbors an integrin I collagen-recognition domain decorated with two inserted arms that fold into a positively charged cradle, as well as three stalk-forming domains. We show by site-specific mutagenesis, mass spectrometry, and thermal shift assays that intradomain isopeptide bonds play key roles in stabilizing RrgAs stalk. The high sequence similarity between RrgA and its homologs in other Gram-positive microorganisms suggests common strategies for ECM recognition and immune evasion.

AdcAII, a new pneumococcal Zn-binding protein homologous with ABC transporters: biochemical and structural analysis.

Regulation of metal homeostasis is vital for pathogenic bacteria facing drastic metal concentration changes in various locations within the host during invasion. Metal-binding receptors (MBRs), one of the extracellular components of ATP-binding cassette transporters, have been shown to be essential in this process. Streptococcus pneumoniae expresses two characterized MBRs: PsaA and AdcA, two extracellular lipoproteins encoded by the psaABCD and adcRCBA operons, respectively. The Mn- and Zn-uptake functions of PsaA and AdcA, respectively, have been well established. Here we describe AdcAII as a third putative S. pneumoniae MBR. The analysis of a phylogenetic tree built from the sequence alignment of 68 proteins reveals a subgroup of members displaying an unusual genetic operon organisation. The adcAII gene belongs to a 6670-nucleotide-long transcript spanning the spr0903 to spr0907 loci encoding for the CcdA, thioredoxine, YfnA, AdcAII and PhtD proteins. Two adjacent repeats of imperfect AdcR-binding consensus sequence were identified upstream of the adcAII gene, suggesting a transcriptional co-regulation of adcAII and phtD genes. Biophysical and structural studies of recombinant AdcAII were performed to identify the metal specificity of the protein. Using electrospray mass spectrometry in native conditions, we found that Zn was bound to recombinant AdcAII. Screening of the effect of 10 cationic ions on the thermal stability of AdcAII revealed that Zn had the most pronounced stabilizing effect. The crystal structure of AdcAII has been solved to 2.4 A resolution. One Zn ion is bound to each AdcAII molecule in a symmetrical active site composed of three His and one Glu. The structure almost perfectly superimposed on the known MBR structures. The presence of a flexible 15-residue-long loop close to the metal-binding site is specific to those specialized in Zn transport. Taken together, these functional and structural data provide new perspectives related to the physiological role of AdcAII in pneumococcus Zn homeostasis.

The Interaction of Streptococcus pneumoniae with Plasmin Mediates Transmigration across Endothelial and Epithelial Monolayers by Intercellular Junction Cleavage

ABSTRACT The precise mechanisms by which Streptococcus pneumoniae overcomes epithelial and endothelial barriers to access underlying human tissues remain to be determined. The plasminogen system is highly important for the tissue barrier degradation which allows cell migration. Plasminogen is known to interact with pneumococci via enolase, glyceraldehyde-3-phosphate dehydrogenase, and choline-binding protein E. These observations prompted us to evaluate the role of this proteolytic system in the pneumococcal invasion process. We observed that coating of S. pneumoniae R6 strain with plasminogen or inactivated plasmin increased adherence to pulmonary epithelial A549 and vascular endothelial EaHy cells in vitro. This indicates that plasminogen-mediated adherence is independent of the protease activity and involves plasminogen binding to receptors on eukaryotic cell surfaces. Conversely, decreased adherence of bacterial cells coated with active plasmin was observed, indicating that the protease activity limits bacterial attachment on the cell surface. We were then interested in investigating the role of the proteolytic plasmin activity in the traversal of tissue barriers. We observed that adherence of plasmin-coated D39 (encapsulated) or R6 (unencapsulated) pneumococci induced sporadic disruptions of EaHy and A549 monolayer cell junctions. This was not observed when plasmin was inhibited by aprotinin. Endothelial junction disorganization may proceed by proteolysis of the cell junction components. This is supported by our observation of the in vitro cleavage by plasmin bound to pneumococci of recombinant vascular endothelial cadherin, the main component of endothelial adherens junctions. Finally, junction damage induced by plasmin may be related to tissue barrier traversal, as we measured an increase of S. pneumoniae transmigration across epithelial A549 and endothelial EaHy layers when active plasmin was present on the bacterial surface. Our results highlight a novel function for the plasminogen recruitment at the bacterial surface in facilitating adherence of pneumococci to endothelial and epithelial cells, while active plasmin degrades intercellular junctions. This process promotes migration of pneumococci through cell barriers by a pericellular route, a prerequisite for dissemination of S. pneumoniae in the host organism.

Sortase-Mediated Pilus Fiber Biogenesis in Streptococcus Pneumoniae.

Streptococcus pneumoniae is a piliated pathogen whose ability to circumvent vaccination and antibiotic treatment strategies is a cause of mortality worldwide. Pili play important roles in pneumococcal infection, but little is known about their biogenesis mechanism or the relationship between components of the pilus-forming machinery, which includes the fiber pilin (RrgB), two minor pilins (RrgA, RrgC), and three sortases (SrtC-1, SrtC-2, SrtC-3). Here we show that SrtC-1 is the main pilus-polymerizing transpeptidase, and electron microscopy analyses of RrgB fibers reconstituted in vitro reveal that they structurally mimic the pneumococcal pilus backbone. Crystal structures of both SrtC-1 and SrtC-3 reveal active sites whose access is controlled by flexible lids, unlike in non-pilus sortases, and suggest that substrate specificity is dictated by surface recognition coupled to lid opening. The distinct structural features of pilus-forming sortases suggest a common pilus biogenesis mechanism that could be exploited for the development of broad-spectrum antibacterials.

Mutations in the Active Site of Penicillin-binding Protein PBP2x from Streptococcus pneumoniae ROLE IN THE SPECIFICITY FOR β-LACTAM ANTIBIOTICS

Penicillin-binding protein 2x (PBP2x) isolated from clinical β-lactam-resistant strains of Streptococcus pneumoniae (R-PBP2x) have a reduced affinity for β-lactam antibiotics. Their transpeptidase domain carries numerous substitutions compared with homologous sequences from β-lactam-sensitive streptococci (S-PBP2x). Comparison of R-PBP2x sequences suggested that the mutation Gln552 → Glu is important for resistance development. Mutants selected in the laboratory with cephalosporins frequently contain a mutation Thr550 → Ala. The high resolution structure of a complex between S-PBP2x* and cefuroxime revealed that Gln552 and Thr550, which belong to strand β3, are in direct contact with the cephalosporin. We have studied the effect of alterations at positions 552 and 550 in soluble S-PBP2x (S-PBP2x*) expressed in Escherichia coli. Mutation Q552E lowered the acylation efficiency for both penicillin G and cefotaxime when compared with S-PBP2x*. We propose that the introduction of a negative charge in strand β3 conflicts with the negative charge of the β-lactam. Mutation T550A lowered the acylation efficiency of the protein for cefotaxime but not for penicillin G. Thein vitro data presented here are in agreement with the distinct resistance profiles mediated by these mutations in vivo and underline their role as powerful resistance determinants.

Streptococcus pneumoniae Choline-Binding Protein E Interaction with Plasminogen/Plasmin Stimulates Migration across the Extracellular Matrix

ABSTRACT The virulence mechanisms leading Streptococcus pneumoniae to convert from nasopharyngeal colonization to a tissue-invasive phenotype are still largely unknown. Proliferation of infection requires penetration of the extracellular matrix, which occurs by recruitment of host proteases to the bacterial cell surface. We present evidence supporting the role of choline-binding protein E (CBPE) (a member of the surface-exposed choline-binding protein family) as an important receptor for human plasminogen, the precursor of plasmin. The results of ligand overlay blot analyses, solid-phase binding assays, and surface plasmon resonance experiments support the idea of an interaction between CBPE and plasminogen. We have shown that the phosphorylcholine esterase (Pce) domain of CBPE interacts with the plasminogen kringle domains. Analysis of the crystal structure of the Pce domain, followed by site-directed mutagenesis, allowed the identification of the plasminogen-binding region composed in part by lysine residues, some of which map in a linear fashion on the surface of the Pce domain. The biological relevance of the CBPE-plasminogen interaction is supported by the fact that, compared to the wild-type strain, a mutant of pneumococcus with the cbpE gene deleted (i) displays a reduced level of plasminogen binding and plasmin activation and (ii) shows reduced ability to cross the extracellular matrix in an in vitro model. These results support the idea of a physiological role for the CBPE-plasminogen interaction in pneumococcal dissemination into human tissue.

Structure-Based Phylogeny of the Metallo-β-Lactamases

ABSTRACT The metallo-β-lactamases fall into two groups: Ambler class B subgroups B1 and B2 and Ambler class B subgroup B3. The two groups are so distantly related that there is no detectable sequence homology between members of the two different groups, but homology is clearly detectable at the protein structure level. The multiple structure alignment program MAPS has been used to align the structures of eight metallo-β-lactamases and five structurally homologous proteins from the metallo-β-lactamase superfamily, and that alignment has been used to construct a phylogenetic tree of the metallo-β-lactamases. The presence of genes from Eubacteria, Archaebacteria, and Eukaryota on that tree is consistent with a very ancient origin of the metallo-β-lactamase family.

Crystal Structure of a Peptidoglycan Synthesis Regulatory Factor (PBP3) from Streptococcus pneumoniae

Penicillin-binding proteins (PBPs) are membrane-associated enzymes which perform critical functions in the bacterial cell division process. The single d-Ala,d-Ala (d,d)-carboxypeptidase in Streptococcus pneumoniae, PBP3, has been shown to play a key role in control of availability of the peptidoglycal substrate during cell growth. Here, we have biochemically characterized and solved the crystal structure of a soluble form of PBP3 to 2.8 Å resolution. PBP3 folds into an NH2-terminal, d,d-carboxypeptidase-like domain, and a COOH-terminal, elongated β-rich region. The carboxypeptidase domain harbors the classic signature of the penicilloyl serine transferase superfamily, in that it contains a central, five-stranded antiparallel β-sheet surrounded by α-helices. As in other carboxypeptidases, which are present in species whose peptidoglycan stem peptide has a lysine residue at the third position, PBP3 has a 14-residue insertion at the level of its omega loop, a feature that distinguishes it from carboxypeptidases from bacteria whose peptidoglycan harbors a diaminopimelate moiety at this position. PBP3 performs substrate acylation in a highly efficient manner (kcat/Km = 50,500 m–1·s–1), an event that may be linked to role in control of pneumococcal peptidoglycan reticulation. A model that places PBP3 poised vertically on the bacterial membrane suggests that its COOH-terminal region could act as a pedestal, placing the active site in proximity to the peptidoglycan and allowing the protein to “skid” on the surface of the membrane, trimming pentapeptides during the cell growth and division processes.

Sortase Activity is Controlled by a Flexible Lid in the Pilus Biogenesis Mechanism of Gram-Positive Pathogens.

Pili are surface-linked virulence factors that play key roles in infection establishment in a variety of pathogenic species. In Gram-positive pathogens, pilus formation requires the action of sortases, dedicated transpeptidases that covalently associate pilus building blocks. In Streptococcus pneumoniae, a major human pathogen, all genes required for pilus formation are harbored in a single pathogenicity islet which encodes three structural proteins (RrgA, RrgB, RrgC) and three sortases (SrtC-1, SrtC-2, SrtC-3). RrgB forms the backbone of the streptococcal pilus, to which minor pilins RrgA and RrgC are covalently associated. SrtC-1 is the main sortase involved in polymerization of the RrgB fiber and displays a lid which encapsulates the active site, a feature present in all pilus-related sortases. In this work, we show that catalysis by SrtC-1 proceeds through a catalytic triad constituted of His, Arg, and Cys and that lid instability affects protein fold and catalysis. In addition, we show by thermal shift analysis that lid flexibility can be stabilized by the addition of substrate-like peptides, a feature shared by other periplasmic transpeptidases. We also report the characterization of a trapped acyl-enzyme intermediate formed between SrtC-1 and RrgB. The presence of lid-encapsulated sortases in the pilus biogenesis systems in many Gram-positive pathogens points to a common mechanism of substrate recognition and catalysis that should be taken into consideration in the development of sortase inhibitors.