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5. AmiA and AliA peptide ligands, found in Klebsiella pneumoniae, are imported into pneumococci and alter the transcriptome

Author

Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectious Diseases, Lux, Janine, Sánchez García, Lucía, Chaparro Fernández, Patricia, Laloli, Laura, Licheri, Manon F., Gallay, Clement, Hermans, Peter W.M., Croucher, Nicholas J., Veening, Jan Willem, Dijkman, Ronald, Straume, Daniel, Hathaway, Lucy J., Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectious Diseases, Lux, Janine, Sánchez García, Lucía, Chaparro Fernández, Patricia, Laloli, Laura, Licheri, Manon F., Gallay, Clement, Hermans, Peter W.M., Croucher, Nicholas J., Veening, Jan Willem, Dijkman, Ronald, Straume, Daniel, and Hathaway, Lucy J.

Published
2024

9. Competence remodels the pneumococcal cell wall exposing key surface virulence factors that mediate increased host adherence

Author

Minhas, Vikrant, primary, Domenech, Arnau, additional, Synefiaridou, Dimitra, additional, Straume, Daniel, additional, Brendel, Max, additional, Cebrero, Gonzalo, additional, Liu, Xue, additional, Costa, Charlotte, additional, Baldry, Mara, additional, Sirard, Jean-Claude, additional, Perez, Camilo, additional, Gisch, Nicolas, additional, Hammerschmidt, Sven, additional, Håvarstein, Leiv Sigve, additional, and Veening, Jan-Willem, additional

Published
2023
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10. Competence remodels the pneumococcal cell wall providing resistance to fratricide and surface exposing key virulence factors

Author

Minhas, Vikrant, primary, Domenech, Arnau, additional, Synefiaridou, Dimitra, additional, Straume, Daniel, additional, Brendel, Max, additional, Cebrero, Gonzalo, additional, Liu, Xue, additional, Costa, Charlotte, additional, Baldry, Mara, additional, Sirard, Jean-Claude, additional, Perez, Camilo, additional, Gisch, Nicolas, additional, Hammerschmidt, Sven, additional, Håvarstein, Leiv Sigve, additional, and Veening, Jan-Willem, additional

Published
2022
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17. Structural Characterization of the Essential Cell Division Protein FtsE and Its Interaction with FtsX in Streptococcus pneumoniae

Author

Ministerio de Ciencia, Innovación y Universidades (España), Research Council of Norway, Alcorlo, Martín, Straume, Daniel, Lutkenhaus, Joe, Håvarstein, Leiv Sigve, Hermoso, Juan A., Ministerio de Ciencia, Innovación y Universidades (España), Research Council of Norway, Alcorlo, Martín, Straume, Daniel, Lutkenhaus, Joe, Håvarstein, Leiv Sigve, and Hermoso, Juan A.

Abstract

FtsEX is a membrane complex widely conserved across diverse bacterial genera and involved in critical processes such as recruitment of division proteins and in spatial and temporal regulation of muralytic activity during cell division or sporulation. FtsEX is a member of the ABC transporter superfamily. The component FtsX is an integral membrane protein, whereas FtsE is an ATPase and is required for the transmission of a conformational signal from the cytosol through the membrane to regulate the activity of cell wall hydrolases in the periplasm. Both proteins are essential in the major human respiratory pathogenic bacterium Streptococcus pneumoniae, and FtsX interacts with the modular peptidoglycan hydrolase PcsB at the septum. Here, we report high-resolution structures of pneumococcal FtsE bound to different nucleotides. Structural analysis revealed that FtsE contains all the conserved structural motifs associated with ATPase activity and afforded interpretation of the in vivo dimeric arrangement in both the ADP and ATP states. Interestingly, three specific FtsE regions with high structural plasticity were identified that shape the cavity in which the cytosolic region of FtsX would be inserted. The residues corresponding to the FtsX coupling helix, responsible for contacting FtsE, were identified and validated by in vivo mutagenesis studies showing that this interaction is essential for cell growth and proper morphology.

Published
2020

18. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae

Author

Morlot, Cécile, Straume, Daniel, Peters, Katharina, Hegnar, Olav A., Simon, Nolwenn, Villard, Anne-Marie, Contreras-Martel, Carlos, Leisico, Francisco, Breukink, Eefjan, Gravier-Pelletier, Christine, Le Corre, Laurent, Vollmer, Waldemar, Pietrancosta, Nicolas, Håvarstein, Leiv Sigve, Zapun, André, Sub Membrane Biochemistry & Biophysics, Membrane Biochemistry and Biophysics, Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Department of Chemical Biology and Organic Chemistry, Utrecht University [Utrecht], Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Centre for Bacterial Cell Biology, Newcastle University [Newcastle], Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Systèmes glutamatergiques normaux et pathologiques = Normal and Pathologic Glutamatergic Neurons (NPS), Neuroscience Paris Seine (NPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Analyse, Interactions Moléculaires et Cellulaires (LBM-E2), Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Chimie Moléculaire de Paris Centre (FR 2769), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universidade Nova de Lisboa (NOVA), Bijvoet Centre for Biomolecular Research [Utrecht, The Netherlands], Laboratoire d'Ingénierie des Macromolécules (LIM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), IMMI INSERM AstraZeneca, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Staphylococcus aureus, MurT ligase, amidation, Glutamine, Science, GatD glutaminase, Glutamic Acid, Peptidoglycan, peptidoglycan, ammonia, Article, Bacterial Proteins, Glutaminase, Protein Domains, Cell Wall, Catalytic Domain, enzyme kinetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Sulfhydryl Compounds, lcsh:Science, ComputingMilieux_MISCELLANEOUS, carboxy terminal sequence, nonhuman, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], pH, zinc, article, ligase, glutaminase, Mycobacterium tuberculosis, Staphylococcal Infections, Lipids, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, operon, Anti-Bacterial Agents, unclassified drug, enzyme activity, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Streptococcus pneumoniae, glutamine, enzyme active site, lcsh:Q, Oxidoreductases
Abstract

The universality of peptidoglycan in bacteria underlies the broad spectrum of many successful antibiotics. However, in our times of widespread resistance, the diversity of peptidoglycan modifications offers a variety of new antibacterials targets. In some Gram-positive species such as Streptococcus pneumoniae, Staphylococcus aureus, or Mycobacterium tuberculosis, the second residue of the peptidoglycan precursor, D-glutamate, is amidated into iso-D-glutamine by the essential amidotransferase MurT/GatD complex. Here, we present the structure of this complex at 3.0 Å resolution. MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD. The mechanism of amidation by MurT is likely similar to the condensation catalyzed by Mur ligases. GatD is a glutaminase providing ammonia that is likely channeled to the MurT active site through a cavity network. The structure and assay presented here constitute a knowledge base for future drug development studies., The amidotransferase MurT/GatD complex catalyzes peptidoglycan precursor amidation in some Gram-positive bacteria. Here the authors present the crystal structure of the Streptococcus pneumoniae MurT/GatD complex and provide mechanistic insights, which are of interest for drug development.

Published
2018

27. Structure of the Large Extracellular Loop of FtsX and Its Interaction with the Essential Peptidoglycan Hydrolase PcsB in Streptococcus pneumoniae

Author

Rued, Britta E., primary, Alcorlo, Martín, additional, Edmonds, Katherine A., additional, Martínez-Caballero, Siseth, additional, Straume, Daniel, additional, Fu, Yue, additional, Bruce, Kevin E., additional, Wu, Hongwei, additional, Håvarstein, Leiv S., additional, Hermoso, Juan A., additional, Winkler, Malcolm E., additional, and Giedroc, David P., additional

Published
2019
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28. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae

Author

Sub Membrane Biochemistry & Biophysics, Membrane Biochemistry and Biophysics, Morlot, Cécile, Straume, Daniel, Peters, Katharina, Hegnar, Olav A., Simon, Nolwenn, Villard, Anne-Marie, Contreras-Martel, Carlos, Leisico, Francisco, Breukink, Eefjan, Gravier-Pelletier, Christine, Le Corre, Laurent, Vollmer, Waldemar, Pietrancosta, Nicolas, Håvarstein, Leiv Sigve, Zapun, André, Sub Membrane Biochemistry & Biophysics, Membrane Biochemistry and Biophysics, Morlot, Cécile, Straume, Daniel, Peters, Katharina, Hegnar, Olav A., Simon, Nolwenn, Villard, Anne-Marie, Contreras-Martel, Carlos, Leisico, Francisco, Breukink, Eefjan, Gravier-Pelletier, Christine, Le Corre, Laurent, Vollmer, Waldemar, Pietrancosta, Nicolas, Håvarstein, Leiv Sigve, and Zapun, André

Published
2018

31. Structure of the large extracellular loop of FtsX and its interaction with the essential peptidoglycan hydrolase PcsB inStreptococcus pneumoniae

Author

Rued, Britta E., primary, Alcorlo, Martín, additional, Edmonds, Katherine A., additional, Martínez-Caballero, Siseth, additional, Straume, Daniel, additional, Fu, Yue, additional, Bruce, Kevin E., additional, Wu, Hongwei, additional, Håvarstein, Leiv Sigve, additional, Hermoso, Juan A., additional, Winkler, Malcolm E., additional, and Giedroc, David P., additional

Published
2018
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40. Structural basis of PcsB-mediated cell separation in Streptococcus pneumoniae

Author

Bartual, Sergio G., Straume, Daniel, Stamsås, Gro Anita, Muñoz, Inés G., Alfonso, Carlos, Martínez-Ripoll, Martín, Håvarstein, Leiv Sigve, Hermoso, Juan A., Bartual, Sergio G., Straume, Daniel, Stamsås, Gro Anita, Muñoz, Inés G., Alfonso, Carlos, Martínez-Ripoll, Martín, Håvarstein, Leiv Sigve, and Hermoso, Juan A.

Abstract

Separation of daughter cells during bacterial cell division requires splitting of the septal cross wall by peptidoglycan hydrolases. In Streptococcus pneumoniae, PcsB is predicted to perform this operation. Recent evidence shows that PcsB is recruited to the septum by the transmembrane FtsEX complex, and that this complex is required for cell division. However, PcsB lacks detectable catalytic activity in vitro, and while it has been proposed that FtsEX activates PcsB, evidence for this is lacking. Here we demonstrate that PcsB has muralytic activity, and report the crystal structure of full-length PcsB. The protein adopts a dimeric structure in which the V-shaped coiled–coil (CC) domain of each monomer acts as a pair of molecular tweezers locking the catalytic domain of each dimeric partner in an inactive configuration. This suggests that the release of the catalytic domains likely requires an ATP-driven conformational change in the FtsEX complex, conveyed towards the catalytic domains through coordinated movements of the CC domain.

Published
2014

41. Identification of pneumococcal proteins that are functionally linked to penicillin-binding protein 2b (PBP2b).

Author

Straume, Daniel, Stamsås, Gro Anita, Berg, Kari Helene, Salehian, Zhian, and Håvarstein, Leiv Sigve

Subjects
*PENICILLIN-binding proteins, *PEPTIDOGLYCANS, *STREPTOCOCCUS pneumoniae, *CROSSLINKING (Polymerization), *DNA
Abstract

The oval shape of pneumococci results from a combination of septal and lateral peptidoglycan synthesis. The septal cross-wall is synthesized by the divisome, while the elongasome drives cell elongation by inserting new peptidoglycan into the lateral cell wall. Each of these molecular machines contains penicillin-binding proteins (PBPs), which catalyze the final stages of peptidoglycan synthesis, plus a number of accessory proteins. Much effort has been made to identify these accessory proteins and determine their function. In the present paper we have used a novel approach to identify members of the pneumococcal elongasome that are functionally closely linked to PBP2b. We discovered that cells depleted in PBP2b, a key component of the elongasome, display several distinct phenotypic traits. We searched for proteins that, when depleted or deleted, display the same phenotypic changes. Four proteins, RodA, MreD, DivIVA and Spr0777, were identified by this approach. Together with PBP2b these proteins are essential for the normal function of the elongasome. Furthermore, our findings suggest that DivIVA, which was previously assigned as a divisomal protein, is required to correctly localize the elongasome at the negatively curved membrane region between the septal and lateral cell wall. [ABSTRACT FROM AUTHOR]

Published
2017
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44. Pneumococcal CbpD is a murein hydrolase that requires a dual cell envelope binding specificity to kill target cells during fratricide

Author

Research Council of Norway, Eldholm, Vegard, Johnsborg, Ola, Straume, Daniel, Ohnstad, Hilde Solheim, Berg, K. H., Hermoso, Juan A., Håvarstein, Leiv Sigve, Research Council of Norway, Eldholm, Vegard, Johnsborg, Ola, Straume, Daniel, Ohnstad, Hilde Solheim, Berg, K. H., Hermoso, Juan A., and Håvarstein, Leiv Sigve

Abstract

Pneumococci that are competent for natural genetic transformation express a number of proteins involved in binding, uptake, translocation and recombination of DNA. In addition, they attack and lyse non-competent sister cells present in the same environment. This phenomenon has been termed fratricide. The key effector of pneumococcal fratricide is CbpD, a secreted protein encompassing an N-terminal CHAP domain, two SH3b domains and a C-terminal choline-binding domain (CBD). CbpD is believed to degrade the cell wall of target cells, but experimental evidence supporting this hypothesis has been lacking. Here, we show that CbpD indeed has muralytic activity, and that this activity requires functional CBD and SH3b domains. To better understand the critical role played by the non-catalytic C-terminal region of CbpD, various translational fusions were constructed between the CBD and SH3b domains and green fluorescent protein (GFP). The results showed that the SH3b domains specifically recognize and bind peptidoglycan, while the CBD domain functions as a localization signal that directs CbpD to the septal region of the pneumococcal cell. Intriguingly, transmission electron microscopy analysis revealed that target cells attacked by CbpD ruptures at the septal region, in accordance with the binding specificity displayed by the CBD domain. © 2010 Blackwell Publishing Ltd.

Published
2010

50. Funksjonelle studier av SmdA : et nytt protein involvert i celledeling og varmetoleranse i Staphylococcus aureus

Author

Knutsen, Tiril Mathiesen, Kjos, Morten, and Straume, Daniel

Abstract

Staphylococcus aureus er et av de viktigste patogenene å studere i sammenheng med infeksjonssykdommer i samfunnet, da det de seneste årene er observert en betydelig økning av resistente stammer mot antibiotika. For å kunne utvikle nye samt forbedre eksisterende behandlingsmetoder mot S. aureus, er det helt nødvendig å få en større forståelse for essensielle cellulære mekanismer i arten. Celledeling kreves for overlevelse i S. aureus, og både proteinene og mekanismene involvert er derfor potensielle nye angrepspunkt for antibiotika. SmdA («staphylococcal morphology determinant A») er et membranprotein i S. aureus som ble identifisert blant konserverte stafylokokkproteiner med ukjent funksjon. Et tidligere studie av SmdA har vist at det er essensielt for rett utført celledeling og morfologi i S. aureus, og at SmdA deplesjon fører til økt sensitivitet mot celleveggangripende antibiotika. I dette arbeidet ble proteinstrukturen og funksjonen til SmdA nærmere studert for å få en større forståelse for hvordan proteinet er involvert i, eller påvirker, de ulike stegene under cellesyklus og deling. Selv om det i dette arbeidet ikke var mulig å bekrefte den predikerte membrantopologien til SmdA, ble det likevel vist at membranlokaliseringen samt det predikerte NERD-domenet og C-terminus er viktig for proteinfunksjon. Det ble innledningsvis observert at et nedregulert uttrykk av SmdA resulterer i celler med defekt cellemorfologi, forårsaket av flere aktive punkter med peptidoglykansyntese og dermed flere dannede septa. Sammenlignet viste et overuttrykk av SmdA tilsvarende defekter, men cellene ble observert med en lavere frekvens. Samtidig ble det også vist at det nedregulerte uttrykket av SmdA påvirker lokaliseringen av celledelingsproteinet EzrA, og dermed også den videre koordineringen av divisomet. Resultatene i dette arbeidet indikerer i tillegg at SmdA har en bredere rolle tilknyttet termosensitivitet og stresstoleranse. Vekstanalyser viste at S. aureus verken kan vokse ved høyere temperaturer eller indusere termotoleranse uten SmdA. Målt mengde proteinaggregater i celler uten SmdA indikerer også at fraværet av proteinet fører til mindre aggregatdannelse, mulig som følge av det oppregulerte uttrykket av Clp-proteiner med chaperon-aktivitet vist i en RNA-sekvensering. SmdA ble også bekreftet å ha en sammenheng med ica-operonet, da SmdA deplesjon fører til et nedregulert uttrykk av ica og signifikant mindre biofilmdannelse i S. aureus. Et av de store spørsmålene etter arbeidet er likevel hvorfor termostabiliteten reduseres ved økt temperatur uten SmdA, selv om mengden proteinaggregater samtidig reduseres og ekspresjonen av Clp-proteinene øker. Staphylococcus aureus is one of the most important pathogens to study in conjunction with infectious diseases in the community due to the increased observations of resistant strains against antibiotics. To develop new as well as improving existing treatment methods against S. aureus, it’s necessary to obtain a deeper knowledge of essential cellular mechanisms in the species. Cell division is required for S. aureus viability, and both proteins and mechanisms involved could be new potential targets for antibiotics. SmdA («staphylococcal morphology determinant A») is a membrane protein identified among conserved staphylococcal proteins with unknown function. A previous study of this protein has demonstrated that SmdA is essential for proper cell division and morphology in S. aureus, and that a depletion results in increased sensitivity against cell wall targeting antibiotics. In this work both protein structure and function of SmdA was studied to get a deeper insight into how the protein is involved, or affects, the different steps in the cell cycle and division. Even though we were not able to confirm the predicted membrane topology of SmdA, we were still able to show that the membrane localization as well as the predicted NERD domain and Cterminal part is important for protein function. It was initially observed that a downregulated expression of SmdA resulted in cells with morphological defects caused by several active sites with peptidoglycan synthesis thus multiple septa. Overexpression of SmdA led to similar defects, although the cells were observed with a lower frequency. At the same time a downregulated expression of SmdA was shown to affect the localization of the cell division protein EzrA, and as a result the further coordination of the divisome. The results obtained in this work also indicate that SmdA has a larger role related to thermosensitivity and stress tolerance. Growth analysis shows that S. aureus are not able to grow at higher temperatures nor induce thermotolerance without SmdA. The measured quantity of protein aggregates in cells without SmdA indicates that the absence of this proteins leads to less aggregates, possibly because of the upregulated expression of Clp-proteins with chaperon activity shown in an RNA sequencing. This work also confirmed a functional link between SmdA and the ica-operon where SmdA depletion leads to downregulation of ica and significant decreased biofilm formation in S. aureus. One of the big questions after this work is why the thermostability is reduced with increased temperature without SmdA even though the quantity of protein aggregates is reduced and the expression of Clp proteins increases. M-BIOTEK

Published
2022

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