On the role of penicillin-binding protein SpoVD in endospore cortex assembly

Bacteria of the genera Bacillus and Clostridium can form endospores as a strategy to survive unfavourable environmental conditions. Endospore formation involves synthesis of cortex, a thick layer of modified peptidoglycan that surrounds the spore. This layer is required for heat resistance of the spore and mutant spores lacking the cortex layer can be identified by a simple heat shock assay. B. subtilis SpoVD is a class B, high molecular weight, penicillin-binding protein (PBP) essential for spore cortex peptidoglycan synthesis. The exact role of the protein in cortex assembly is nknown but it most likely catalyses the formation of cross-links between glycan strands in nascent peptidoglycan. SpoVD deficient strains produce heat sensitive spores without cortex layer. Two conserved cysteine residues (Cys332 and Cys351) in the transpeptidase domain of SpoVD seem important for activity of the enzyme. They can form an intramolecular disulfide bond and this is catalysed by the membrane-bound thiol-disulfide oxidoreductase BdbD. The disulfide bond in SpoVD is located close to the transpeptidase active site and blocks the function of the protein. The bond is broken by the action of StoA, a sporulation-specific membrane-bound thiol-disulfide oxidoreductase. Based on these findings a thiol-based redox switch regulation of SpoVD activity was proposed in 2010. The aim of this PhD project was to elucidate the function of SpoVD in cortex synthesis and to find out the physiological role of the proposed switch and the two cysteine residues in SpoVD. In depth investigation of the process of cortex assembly contribute to our understanding of peptidoglycan synthesis in general. This is of considerable medicinal interest since, e.g., bacterial cell wall synthesis is an effective target for many antibiotics in clinical use, such as penicillins and cephalosporins and eventual new drugs. I demonstrate, by the use of a constructed SpoVD active site mutant strain, that synthesis of cortex explicitly depends on the transpeptidase activity of the protein. I show that the C-terminal PASTA domain of SpoVD is not important for the function of the protein in cortex synthesis. My results from in vitro experiments with several isolated protein variants strengthen the view that SpoVD is a specific target for StoA. My findings, supported by data available in the literature, indicate that the two cysteine residues in SpoVD affect the dynamics of the transpeptidase domain. Finally, I propose a revised model for the function of BdbD and StoA in modulation of the redox state of SpoVD, where BdbD and StoA are suggested to act (mainly) during the folding of newly synthesised SpoVD

A Genomic Signature and the Identification of New Sporulation Genes

Bacterial endospores are the most resistant cell type known to humans, as they are able to withstand extremes of temperature, pressure, chemical injury, and time. They are also of interest because the endospore is the infective particle in a variety of human and livestock diseases. Endosporulation is characterized by the morphogenesis of an endospore within a mother cell. Based on the genes known to be involved in endosporulation in the model organism Bacillus subtilis, a conserved core of about 100 genes was derived, representing the minimal machinery for endosporulation. The core was used to define a genomic signature of about 50 genes that are able to distinguish endospore-forming organisms, based on complete genome sequences, and we show this 50-gene signature is robust against phylogenetic proximity and other artifacts. This signature includes previously uncharacterized genes that we can now show are important for sporulation in B. subtilis and/or are under developmental control, thus further validating this genomic signature. We also predict that a series of polyextremophylic organisms, as well as several gut bacteria, are able to form endospores, and we identified 3 new loci essential for sporulation in B. subtilis: ytaF, ylmC, and ylzA. In all, the results support the view that endosporulation likely evolved once, at the base of the Firmicutes phylum, and is unrelated to other bacterial cell differentiation programs and that this involved the evolution of new genes and functions, as well as the cooption of ancestral, housekeeping functions.FCT grant: (PEst-OE/EQB/LA0004/2011), FCT Ph.D. fellowship: (SFRH/BPD/36328/2007), FCT postdoc fellowship: (SFRH/BPD/65605/2009), Instituto Gulbenkian de Ciência research fellowship

Studies on polar cell wall growth and antibiotic susceptibility of Corynebacterium glutamicum

Corynebacterium glutamicum is a Gram positive soil bacterium with high industrial importance in ton scale production of amino acids. Apart from that, it becomes more and more important for medical studies, where it serves as model organism due to its close relation to bacteria causing several pathogens such as tuberculosis, diphtheria and leprosy. C. glutamicum, like Mycobacterium tuberculosis, has a distinct cell wall which is composed of a peptidoglycan layer (murein) with covalently bound polysaccharide layers that are capped with mycolic acids. In addition, both organisms have a polar cell wall synthesis machinery which is spatially regulated by DivIVA (Wag31 in M. tuberculosis). The present study shows that DivIVA regulates cell wall synthesis upon direct interaction with the lipid II flippase RodA. RodA determines morphology and growth in C. glutamicum and is localized to the poles and septa. The absence of rodA results in growth defects and cell shape alterations as well as altered lipid II proliferation of the poles (polar cell growth is sustained). DivIVA is furthermore involved in chromosome segregation upon direct interaction with the partitioning ParB protein, which binds to parS sites on the chromosome, thus tethering the replicated nucleoids to the cell poles. Interactions of DivIVA with ParB and RodA were identified in a synthetic in vivo protein-protein interaction assay where fluorescently labeled proteins of interest are expressed in E. coli cells and interaction is analyzed microscopically. A decisive improvement of this assay is the application of FRET, which is more sensitive and allows quantification of interaction. In order to test whether ParB and RodA compete for the same interaction site in DivIVA, we mapped interaction sites of both proteins. It turned out that ParB binds to a middle region of DivIVA, whereas RodA binds to the N-terminal domain of DivIVA where one lysine residue is essential for interaction. To fight bacterial infections, that cause thousands of casualties each year, it is mandatory to understand mechanisms in cellular processes, such as cell division and growth, to find new targets for antibiotic intervention. Unfortunately, bacteria are able to develop resistances against many antibiotics. The mycolic acid or arabinan layer and synthesis machinery are good candidates for new antibiotics. Amongst others, two of them have emerged as useful drugs against M. tuberculosis, ethambutol (EMB) and BTZ043. In this study, we investigated the modes of action and antibiotic susceptibility of C. glutamicum after EMB and BTZ043 treatment. We found that both antibiotics, which target the arabinan synthesis pathway, affect exclusively polar elongation growth, as demonstrated in different staining assays. Interestingly, only 10% of the cells were killed and cells in stationary phase were not affected by EMB or BTZ043. Moreover, we used a chromosomal DivIVA-mCherry fusion and found that DivIVA protein level is drastically increased. The cells show asymmetric recovery after treatment, in which one daughter cell acquires the excess DivIVA whereas the other daughter cell exhibits normal cell growth.Corynebacterium glutamicum ist ein Gram-positives Bodenbakterium mit großer industrieller Bedeutung für die Herstellung von Aminosäuren im Tonnenmaßstab. Des Weiteren bekommt es zunehmende Bedeutung für die medizinische Forschung, wo es aufgrund seiner engen Verwandtschaft zu den pathogenen Erregern von Tuberkulose, Diphtherie und Lepra als idealer Modellorganismus dient. Besonders die Zellwand von C. glutamicum hat große Ähnlichkeit zu der vieler pathogener Vertreter wie Mykobakterium tuberculosis. Sie besteht aus einer Peptidoglycan-Schicht (Murein), an der über weitere Polysaccharid-Schichten die charakteristischen Mycolsäuren gebunden sind. Darüber hinaus besitzen beide Organismen eine polare Zellwandsynthese, die von DivIVA (Wag31 in M. tuberculosis) räumlich reguliert wird. Die Rolle von DivIVA am Zellwachstum wurde vor Jahren erstmals beschrieben, jedoch war seine exakte Funktion bis zuletzt unbekannt. In dieser Studie wird erstmals die Funktion von DivIVA am polaren Zellwachstum durch Interaktion mit der Lipid II-Flippase RodA gezeigt. RodA beeinflusst die Morphologie und das Wachstum von C. glutamicum und wird von DivIVA an die Zellpole lokalisiert. Deletion von rodA resultiert in reduziertem Wachstum und veränderter Morphologie, sowie einer alternativen Lipid II Versorgung der Zellpole, da das polare Zellwachstum erhalten bleibt. DivIVA ist darüber hinaus an der Chromosomensegregation beteiligt, wo es direkt mit ParB interagiert, das über parS-Seiten an die replizierten Chromosomen bindet um sie an die Zellpole zu fixieren. Die Interaktionen zwischen DivIVA und ParB bzw. RodA wurden mit Hilfe eines synthetischen in vivo Assays identifiziert, worin die zu untersuchenden Gene an Fluorophore gekoppelt und in E. coli Zellen exprimiert werden. Somit lässt sich eine Co-Lokalisation nach individueller und Co-Expression der Fusionsproteine mikroskopisch analysieren. Eine entscheidende Verbesserung dieses Assays ist die Verwendung von FRET, das sensitiver ist und eine Quantifizierung der Interaktion ermöglicht. Um herauszufinden, ob ParB und RodA um die gleiche Bindungsstelle an DivIVA konkurrieren, wurden die Interaktionsdomänen beider Proteine ermittelt. Während ParB an eine mittlere Region in DivIVA bindet, bindet RodA an die N-terminale Domäne von DivIVA, in der ein Lysin-Rest für die Bindung essenziell ist. Für den Kampf gegen bakterielle Infektionskrankheiten, die jährlich tausende Todesfälle verursachen, ist es dringend notwendig zelluläre Mechanismen, beispielsweise der Zellteilung und des Wachstums, zu entschlüsseln um Targets für neue Antibiotika zu finden. Insbesondere die kontinuierliche Entstehung neue Resistenzen macht diese Aufgabe wichtiger denn je. Die Mykolsäureschicht und ihre Synthese sind vielversprechende Targets, da bisher nur wenige Antibiotika, wie Ethambutol (EMB) oder BTZ043, dagegen existieren. Wir haben die Wirkungsweise und antibiotische Suszeptibilität von C. glutamicum nach EMB und BTZ043 Behandlung untersucht. Beide Antibiotika, die in die Arabinogalactan-Synthese eingreifen, beeinflussen ausschließlich das polare Zellwachstum, wie in mehrerer Färbeassays gezeigt. Lediglich 10% der Zellen wurden getötet. Zellen, die sich in der stationären Phase befanden, wurde nicht beeinflusst. Darüber hinaus zeigte die Verwendung eines Stammes mit chromosomaler DivIVA-mCherry Fusion, dass das DivIVA Protein Level stark erhöht ist. Erholungsexperimente nach Antibiotikazugabe zeigten, dass die Zellen asymmetrisch reagieren, wobei eine Tochterzelle das überschüssige DivIVA übernimmt, während die andere Zelle normales Wachstum erfährt

Analysis of Spore Shape Determination in Streptomyces

Streptomycetes are Gram-positive, soil-dwelling bacteria that possess a complex life cycle with the alternation of vegetative mycelium, aerial mycelium, and spores. Streptomyces. coelicolor spore maturation is a complex process that involves spore shape metamorphosis from cylindrical pre-spores into ellipsoid spores, but the details of this process have remained enigmatic. Previously, our lab identified a novel gene ssdA that might play a role in spore shape determination using a transposon-based insertion mutagenesis in S. coelicolor. In this study, I isolated a S. coelicolor ssdA-null mutant that showed increased colony hydrophobicity and misshapen spores in sizes and shapes, confirming the phenotype of the ssdA insertion mutant. In order to further investigate the function of ssdA, I switched the model species to S. venezuelae due to its advantages. Here, I demonstrate that a S. venezuelae ssdA mutant showed delayed morphological differentiation on both solid and liquid media, arising in part from germination and growth defects of the mutant. The ssdA mutant also generated heterogeneously-sized spores, possibly due to sporulation and cell-cell separation defects. Deletion of ssdA also resulted in spore sensitivity to heat, osmotic stress, and cell-wall targeting antibiotics. The spore sacculus was isolated and a preliminary HPLC-MS result demonstrated the accumulation of peptidoglycan muropeptides in the ssdA mutant. SsdA-EGFP localizes in vegetative hyphae, sporulation septa, and the periphery of spores, consistent with its roles in cell wall development. A bacterial two-hybrid assay shows that the central cytoplasmic region of SsdA interacts with a dynamin-like, sporulation-specific protein DynB, explaining the septal localization of SsdA-EGFP. Of interest, ssdA also affects Streptomyces’s exploration, a novel growth mode. whiD is a regulatory gene in Streptomyces that potentially controls ssdA expression. Here I show that the S. venezuelae whiD mutant has a white colony and produces heterogeneously sized spores, indicating a sporulation defect. Also the whiD mutant is drastically sensitive to heat and slightly sensitive to salt, different from the sensitivity profile for the ssdA mutant. Further elucidation the regulatory mechanism of WhiD will provide more insights into the sporulation and spore maturation in this filamentous bacterium

Structural and Functional Investigation of Bacterial Membrane Biosynthesis

Integral membrane enzymes contribute a unique repertoire to the cell, as they are capable of synthesizing products from substrates of different chemical character at the membrane-water interface. Membrane-embedded enzymes are often responsible for the synthesis of important components of the cellular membrane and contribute to the structural integrity of the cell, maintenance of cellular homeostasis and signal transduction. One of the main focuses of Dr. Filippo Mancia’s laboratory is understanding how enzymes complete these functions by investigating, at an atomic level, the determinants of substrate binding and catalysis within the membrane and at the membrane surface. Here I will present my investigation of two such integral membrane enzyme systems, which are responsible for the synthesis and processing of membrane-embedded molecules in bacteria. Phosphatidylinositol-phosphate Synthase (PIPS) Phosphaitylinositol (PI) is an essential lipid component in mycobacteria, demonstrated by loss of viability when PI is reduced to 50% of wild-type levels. Phosphatidylinositol (PI) is required for the biosynthesis of key components of the cell wall, such as the glycolipids phosphatidylinositol-mannosides, lipomannan and lipoarabinomannan. For these molecules, PI serves as a common lipid anchor to the membrane. In Mycobacterium tuberculosis, the disease causing pathogen of tuberculosis, these glycolipids function as important virulence factors and modulators of the host immune response. Therefore, the enzyme responsible for PI synthesis in this organism is a potential target for the development of anti-tuberculosis drugs. The defining step in phosphatidylinositol biosynthesis is catalyzed by a member of the CDP-alcohol phosphotransferase enzyme family. The enzyme uses CDP-diacylglycerol as the donor substrate, and either inositol in eukaryotes or inositol-phosphate in prokaryotes as the acceptor alcohol of the synthesis reaction. In prokaryotes, phosphatidylinositol-phosphate synthase (PIPS; a member of the CDP-alcohol phosphotransferase family) catalyzes this reaction to yield phosphatidylinositol-phosphate, which is then dephosphorylated to PI by an uncharacterized enzyme. Structures of PIPS from Renibacterium salmoninarum (RsPIPS), with and without bound CDP-diacylglycerol, have revealed the location of the acceptor site as well as molecular determinants of substrate specificity and catalysis of the enzyme. However, RsPIPS has low activity relative to PIPS from Mycobacterium tuberculosis (MtPIPS) and the two share only 40% protein sequence identity. Therefore, these initial structures have limited potential for meaningful homology modeling and drug design. Presented here are the structures of PIPS from Mycobacterium kansasii (MkPIPS), which is 86% identical to MtPIPS, in an apo state to 3.1 Å resolution, in a nucleotide-bound state to 3.5 Å resolution, and in a novel ligand-bound state to 2.6 Å resolution. This work provides a structural and functional framework to understand the mechanism of phosphatidylinositol-phosphate biosynthesis in the context of mycobacterial pathogens. RodA-PBP2 Complex The cell wall of most gram-negative and gram-positive bacteria (excluding atypical bacteria such as members of Mycoplasmataceae) is composed of peptidoglycan, a mesh of repeating carbohydrates (N-acetylmuramic acid, MurNAc, and N-acetylglucosamine, GlcNAc) cross-linked by small peptides. Peptidoglycan is essential for growth, division and viability of the organism. Any disruption of the biosynthesis of peptidoglycan, whether by genetic mutation, inhibition with antibiotics or degradation by lysozyme, results in bacterial cell lysis. Peptidoglycan helps maintain cell shape and serves as an anchor for accessory proteins and other cell wall components. As essential components of the cell wall, enzymes contributing to the peptidoglycan biosynthetic pathway can be exploited as antibiotic targets. After a hydrophilic peptidoglycan precursor (UDP-MurNAc-pentapeptide) is synthesized in the cytosol, it is attached to the lipid carrier undecaprenyl phosphate (UndP). The lipid-linked precursor (undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide or Lipid I) is modified further to undecaprenyl-pyrophosphoryl-MurNAc-(pentapeptide)-GlcNAc (Lipid II) by addition of a GlcNAc moiety. Lipid II is then flipped across the membrane to the periplasm where its sugars are polymerized to form the glycan strands of the peptidoglycan mesh. SEDS proteins, essential for maintaining bacterial processes that determine shape, elongation, cell division and sporulation, are integral membrane enzyme that have been implicated in this process as either Lipid II flippases, glycosyltransferases responsible for sugar polymerization, or both. SEDS proteins are also known to form a functional complex with type b penicillin-binding proteins (PBPs), which are known as transpeptidase enzymes, responsible for the crosslinking of peptides in the formation of the peptidoglycan mesh. Though structures of both RodA (a SEDS protein involved in bacterial growth and elongation) and type b PBPs are available, the interaction between the two proteins and their joint enzymatic activity is poorly characterized. Here, I present the preliminary structural characterization of a RodA-PBP2 protein complex by single-particle cryo-electron microscopy (cryo-EM). We hope this ongoing work will contribute to the understanding of these enzymes and to the development of antibiotics to combat antibiotic resistance

High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae.

Genome-wide screens have discovered a large set of essential genes in the opportunistic human pathogen <i>Streptococcus pneumoniae</i> However, the functions of many essential genes are still unknown, hampering vaccine development and drug discovery. Based on results from transposon sequencing (Tn-seq), we refined the list of essential genes in <i>S. pneumoniae</i> serotype 2 strain D39. Next, we created a knockdown library targeting 348 potentially essential genes by CRISPR interference (CRISPRi) and show a growth phenotype for 254 of them (73%). Using high-content microscopy screening, we searched for essential genes of unknown function with clear phenotypes in cell morphology upon CRISPRi-based depletion. We show that SPD_1416 and SPD_1417 (renamed to MurT and GatD, respectively) are essential for peptidoglycan synthesis, and that SPD_1198 and SPD_1197 (renamed to TarP and TarQ, respectively) are responsible for the polymerization of teichoic acid (TA) precursors. This knowledge enabled us to reconstruct the unique pneumococcal TA biosynthetic pathway. CRISPRi was also employed to unravel the role of the essential Clp-proteolytic system in regulation of competence development, and we show that ClpX is the essential ATPase responsible for ClpP-dependent repression of competence. The CRISPRi library provides a valuable tool for characterization of pneumococcal genes and pathways and revealed several promising antibiotic targets