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Bin Hafeez A, Sappati S, Krzemieniecki R, Worobo R, Szweda P. In Silico Functional Annotation and Structural Characterization of Hypothetical Proteins in Bacillus paralicheniformis and Bacillus subtilis Isolated from Honey. ACS OMEGA 2025; 10:8993-9006. [PMID: 40092810 PMCID: PMC11904672 DOI: 10.1021/acsomega.4c07105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 12/14/2024] [Accepted: 12/25/2024] [Indexed: 03/19/2025]
Abstract
Bacillus species are ubiquitous and survive in competitive microbial communities under adverse environmental conditions. Bacillus paralicheniformis and Bacillus subtilis obtained from honey revealed a significant proportion of proteins within their genomes as uncharacterized hypothetical proteins (HPs). A total of 1007 HP sequences were evaluated, resulting in the successful annotation of 56 HPs by assigning specific functions to them. A systematic in silico approach, integrating a range of bioinformatics tools and databases to annotate functions, characterize physicochemical properties, determine subcellular localization, and study protein-protein interactions, was used. Homology and de novo models were generated for the HPs, coupled with iterative remodeling and molecular dynamics (MD) simulations. HPs having significant roles in sporulation, biofilm formation, motility, ion transportation, regulation of metabolic processes, DNA repair, replication, and transcription were identified. Classical MD simulations of globular and transducer membrane proteins, along with postprocessing analyses, refined our structural predictions and provided deeper insights into the stability and functional dynamics of the protein structures under physiological conditions. Moreover, we observed a correlation between the percentage of α helix, β sheet, and coil structures in globular proteins and transducer membrane proteins. The integration of iterative loop modeling, MD simulations, and Dictionary of Secondary Structure in Proteins analysis further validated our predicted models and facilitated the identification of regions critical for protein function, thereby enhancing the overall reliability and robustness of our functional annotations. Furthermore, annotation of these hypothetical proteins aids in identifying novel proteins within bacterial cells, ultimately contributing to a deeper understanding of bacterial cell biology and their use for biotechnological purposes.
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Affiliation(s)
- Ahmer Bin Hafeez
- Department
of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Subrahmanyam Sappati
- Department
of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Radoslaw Krzemieniecki
- Department
of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Randy Worobo
- Department
of Food Science, Cornell University, Ithaca, New York 14853, United States
| | - Piotr Szweda
- Department
of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, ul. G. Narutowicza 11/12, Gdańsk 80-233, Poland
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Stefanović C, Legg MSG, Mateyko N, Ender JJ, Kuvek T, Oostenbrink C, Schäffer C, Evans SV, Hager-Mair FF. Insights into structure and activity of a UDP-GlcNAc 2-epimerase involved in secondary cell wall polymer biosynthesis in Paenibacillus alvei. Front Mol Biosci 2024; 11:1470989. [PMID: 39391870 PMCID: PMC11464976 DOI: 10.3389/fmolb.2024.1470989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 09/03/2024] [Indexed: 10/12/2024] Open
Abstract
Introduction S-layer anchoring in Paenibacillus alvei is enabled by a non-covalent interaction between an S-layer homology domain trimer and a secondary cell wall polymer (SCWP), ensuring the structural integrity of the bacterial cell wall. Within the SCWP repeat, pyruvylated ManNAc serves as the ligand and the UDP-GlcNAc-2-epimerase MnaA supplies UDP-ManNAc to SCWP biosynthesis. Methods To better understand SCWP biosynthesis and identify strategies for inhibiting pathogens with comparable cell wall architecture, like Bacillus anthracis, MnaA and rational variants were produced in E. coli and their kinetic constants determined. The effect of UDP-GlcNAc as a predicted allosteric activator and tunicamycin as a potential inhibitor of MnaA was tested in vitro supported by molecular docking experiments. Additionally, wild-type MnaA was crystallized. Results We present the crystal structure of unliganded P. alvei MnaA resolved at 2.20 Å. It adopts a GT-B fold consistent with other bacterial non-hydrolyzing UDP-GlcNAc 2-epimerases. A comparison of amino acid sequences reveals conservation of putative and known catalytic and allosteric-site residues in MnaA, which was confirmed through analysis of Q42A, Q69A, E135A and H241A MnaA variants. The kinetic parameters K M and k cat of MnaA were determined to be 3.91 mM and 33.44 s-1 for the forward, and 2.41 mM and 6.02 s-1 for the reverse reaction. While allosteric regulation by UDP-GlcNAc has been proposed as a mechanism for enzyme activation, UDP-GlcNAc was not found to be essential for UDP-ManNAc epimerization by P. alvei MnaA. However, the reaction rate doubled upon addition of 5% UDP-GlcNAc. Unexpectedly, the UDP-GlcNAc analog tunicamycin did not inhibit MnaA. Molecular docking experiments comparing tunicamycin binding of P. alvei MnaA and Staphylococcus aureus MnaA, which is inhibited by tunicamycin, revealed different residues exposed to the antibiotic excluding, those at the predicted allosteric site of P. alvei MnaA, corroborating tunicamycin resistance. Conclusion The unliganded crystal structure of P. alvei MnaA reveals an open conformation characterized by an accessible cleft between the N- and C-terminal domains. Despite the conservation of residues involved in binding the allosteric activator UDP-GlcNAc, the enzyme is not strictly regulated by the substrate. Unlike S. aureus MnaA, the activity of P. alvei MnaA remains unaffected by tunicamycin.
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Affiliation(s)
- Cordula Stefanović
- Department of Chemistry, Institute of Biochemistry, NanoGlycobiology Research Group, Universität für Bodenkultur Wien, Vienna, Austria
| | - Max S. G. Legg
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC, Canada
| | - Nick Mateyko
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC, Canada
| | - Jakob J. Ender
- Department of Chemistry, Institute of Biochemistry, NanoGlycobiology Research Group, Universität für Bodenkultur Wien, Vienna, Austria
| | - Tea Kuvek
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Universität für Bodenkultur Wien, Vienna, Austria
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Universität für Bodenkultur Wien, Vienna, Austria
| | - Christina Schäffer
- Department of Chemistry, Institute of Biochemistry, NanoGlycobiology Research Group, Universität für Bodenkultur Wien, Vienna, Austria
| | - Stephen V. Evans
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, BC, Canada
| | - Fiona F. Hager-Mair
- Department of Chemistry, Institute of Biochemistry, NanoGlycobiology Research Group, Universität für Bodenkultur Wien, Vienna, Austria
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Tomatsidou A, Krunic M, Missiakas D. Contribution of TagA-Like Glycosyltransferases to the Assembly of the Secondary Cell Wall Polysaccharide in Bacillus anthracis. J Bacteriol 2022; 204:e0025322. [PMID: 35997505 PMCID: PMC9487633 DOI: 10.1128/jb.00253-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/01/2022] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis elaborates a secondary cell wall polysaccharide (SCWP) made of 6 to 12 trisaccharide units. Pyruvyl and acetyl substitutions of the distal unit are prerequisites for the noncovalent retention of 22 secreted Bacillus S-layer (Bsl)-associated proteins bearing an S-layer homology (SLH) domain. Surface display of Bsl proteins contributes to cell separation as well as virulence. Earlier work suggested that TagO initiates the synthesis of SCWP while GneY and GneZ, two UDP-GlcNAc 2-epimerases, synthesize ManNAc that is later incorporated in the repeat unit (→4)-ManNAc-(β1→4)-GlcNAc-(β1→6)-GlcNAc-(α1→). In organisms that synthesize wall teichoic acid, TagA catalysts have been shown to form the glycosidic bond ManNAc-(β1→4)-GlcNAc. Here, we show that genes bas2675 and bas5272, predicted to encode glycosyltransferases of the WecB/TagA/CpsF family (PFAM03808; CAZy GT26), are required for B. anthracis SCWP synthesis and S-layer assembly. Similar to tagO or gneY gneZ mutants, B. anthracis strains depleted of tagA1 (bas5272) cannot maintain cell shape, support vegetative growth, or synthesize SCWP. Expression of tagA2 (bas2675), or Staphylococcus aureus tagA on a plasmid, rescues the nonviable tagA1 mutant. We propose that TagA1 and TagA2 fulfill overlapping and key glycosyltransferase functions for the synthesis of repeat units of the SCWP of B. anthracis. IMPORTANCE Glycosyltransferases (GTs) catalyze the transfer of sugar moieties from activated donor molecules to acceptor molecules to form glycosidic bonds using a retaining or inverting mechanism. Based on the structural relatedness of their catalytic and carbohydrate-binding modules, GTs have been grouped into 115 families in the Carbohydrate-Active EnZyme (CAZy) database. For complex products, the functional assignment of GTs remains highly challenging without the knowledge of the chemical structure of the assembled polymer. Here, we propose that two uncharacterized GTs of B. anthracis belonging to the WecB/TagA/CpsF family incorporate ManNAc in repeat units of the secondary cell wall polymer of bacilli species.
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Affiliation(s)
- Anastasia Tomatsidou
- Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA
| | - Maria Krunic
- Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA
| | - Dominique Missiakas
- Department of Microbiology, Howard Taylor Ricketts Laboratory, The University of Chicago, Lemont, Illinois, USA
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Boutonnet C, Lyonnais S, Alpha-Bazin B, Armengaud J, Château A, Duport C. Dynamic Profile of S-Layer Proteins Controls Surface Properties of Emetic Bacillus cereus AH187 Strain. Front Microbiol 2022; 13:937862. [PMID: 35847057 PMCID: PMC9277125 DOI: 10.3389/fmicb.2022.937862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Many prokaryotes are covered by a two-dimensional array of proteinaceous subunits. This surface layers (S-layer) is incompletely characterized for many microorganisms. Here, we studied Bacillus cereus AH187. A genome analysis identified two genes encoding the S-layer proteins SL2 and EA1, which we experimentally confirmed to encode the two protein components of the S-layer covering the surface of B. cereus. Shotgun proteomics analysis indicated that SL2 is the major component of the B. cereus S-layer at the beginning of exponential growth, whereas EA1 becomes more abundant than SL2 during later stages of stationary growth. Microscopy analysis revealed the spatial organization of SL2 and EA1 at the surface of B. cereus to depend on their temporal-dynamics during growth. Our results also show that a mutant strain lacking functional SL2 and EA1 proteins has distinct surface properties compared to its parental strain, in terms of stiffness and hydrophilicity during the stationary growth phase. Surface properties, self-aggregation capacity, and bacterial adhesion were observed to correlate. We conclude that the dynamics of SL2 and EA1 expression is a key determinant of the surface properties of B. cereus AH187, and that the S-layer could contribute to B. cereus survival in starvation conditions.
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Affiliation(s)
| | | | - Beatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Alice Château
- Avignon Université, INRAE, UMR SQPOV, Avignon, France
| | - Catherine Duport
- Avignon Université, INRAE, UMR SQPOV, Avignon, France
- *Correspondence: Catherine Duport,
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LytR-CpsA-Psr Glycopolymer Transferases: Essential Bricks in Gram-Positive Bacterial Cell Wall Assembly. Int J Mol Sci 2021; 22:ijms22020908. [PMID: 33477538 PMCID: PMC7831098 DOI: 10.3390/ijms22020908] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/28/2022] Open
Abstract
The cell walls of Gram-positive bacteria contain a variety of glycopolymers (CWGPs), a significant proportion of which are covalently linked to the peptidoglycan (PGN) scaffolding structure. Prominent CWGPs include wall teichoic acids of Staphylococcus aureus, streptococcal capsules, mycobacterial arabinogalactan, and rhamnose-containing polysaccharides of lactic acid bacteria. CWGPs serve important roles in bacterial cellular functions, morphology, and virulence. Despite evident differences in composition, structure and underlaying biosynthesis pathways, the final ligation step of CWGPs to the PGN backbone involves a conserved class of enzymes-the LytR-CpsA-Psr (LCP) transferases. Typically, the enzymes are present in multiple copies displaying partly functional redundancy and/or preference for a distinct CWGP type. LCP enzymes require a lipid-phosphate-linked glycan precursor substrate and catalyse, with a certain degree of promiscuity, CWGP transfer to PGN of different maturation stages, according to in vitro evidence. The prototype attachment mode is that to the C6-OH of N-acetylmuramic acid residues via installation of a phosphodiester bond. In some cases, attachment proceeds to N-acetylglucosamine residues of PGN-in the case of the Streptococcus agalactiae capsule, even without involvement of a phosphate bond. A novel aspect of LCP enzymes concerns a predicted role in protein glycosylation in Actinomyces oris. Available crystal structures provide further insight into the catalytic mechanism of this biologically important class of enzymes, which are gaining attention as new targets for antibacterial drug discovery to counteract the emergence of multidrug resistant bacteria.
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Chateau A, Oh SY, Tomatsidou A, Brockhausen I, Schneewind O, Missiakas D. Distinct Pathways Carry Out α and β Galactosylation of Secondary Cell Wall Polysaccharide in Bacillus anthracis. J Bacteriol 2020; 202:e00191-20. [PMID: 32457049 PMCID: PMC7348550 DOI: 10.1128/jb.00191-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 05/15/2020] [Indexed: 12/26/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax disease, elaborates a secondary cell wall polysaccharide (SCWP) that is required for the retention of surface layer (S-layer) and S-layer homology (SLH) domain proteins. Genetic disruption of the SCWP biosynthetic pathway impairs growth and cell division. B. anthracis SCWP is comprised of trisaccharide repeats composed of one ManNAc and two GlcNAc residues with O-3-α-Gal and O-4-β-Gal substitutions. UDP-Gal, synthesized by GalE1, is the substrate of galactosyltransferases that modify the SCWP repeat. Here, we show that the gtsE gene, which encodes a predicted glycosyltransferase with a GT-A fold, is required for O-4-β-Gal modification of trisaccharide repeats. We identify a DXD motif critical for GtsE activity. Three distinct genes, gtsA, gtsB, and gtsC, are required for O-3-α-Gal modification of trisaccharide repeats. Based on the similarity with other three-component glycosyltransferase systems, we propose that GtsA transfers Gal from cytosolic UDP-Gal to undecaprenyl phosphate (C55-P), GtsB flips the C55-P-Gal intermediate to the trans side of the membrane, and GtsC transfers Gal onto trisaccharide repeats. The deletion of galE1 does not affect growth in vitro, suggesting that galactosyl modifications are dispensable for the function of SCWP. The deletion of gtsA, gtsB, or gtsC leads to a loss of viability, yet gtsA and gtsC can be deleted in strains lacking galE1 or gtsE We propose that the loss of viability is caused by the accumulation of undecaprenol-bound precursors and present an updated model for SCWP assembly in B. anthracis to account for the galactosylation of repeat units.IMPORTANCE Peptidoglycan is a conserved extracellular macromolecule that protects bacterial cells from turgor pressure. Peptidoglycan of Gram-positive bacteria serves as a scaffold for the attachment of polymers that provide defined bacterial interactions with their environment. One such polymer, B. anthracis SCWP, is pyruvylated at its distal end to serve as a receptor for secreted proteins bearing the S-layer homology domain. Repeat units of SCWP carry three galactoses in B. anthracis Glycosylation is a recurring theme in nature and often represents a means to mask or alter conserved molecular signatures from intruders such as bacteriophages. Several glycosyltransferase families have been described based on bioinformatics prediction, but few have been studied. Here, we describe the glycosyltransferases that mediate the galactosylation of B. anthracis SCWP.
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Affiliation(s)
- Alice Chateau
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
| | - So Young Oh
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
| | - Anastasia Tomatsidou
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
| | - Inka Brockhausen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
| | - Dominique Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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Abstract
Bacillus anthracis, the anthrax agent, is a member of the Bacillus cereus sensu lato group, which includes invasive pathogens of mammals or insects as well as nonpathogenic environmental strains. The genes for anthrax pathogenesis are located on two large virulence plasmids. Similar virulence plasmids have been acquired by other B. cereus strains and enable the pathogenesis of anthrax-like diseases. Among the virulence factors of B. anthracis is the S-layer-associated protein BslA, which endows bacilli with invasive attributes for mammalian hosts. BslA surface display and function are dependent on the bacterial S-layer, whose constituents assemble by binding to the secondary cell wall polysaccharide (SCWP) via S-layer homology (SLH) domains. B. anthracis and other pathogenic B. cereus isolates harbor genes for the secretion of S-layer proteins, for S-layer assembly, and for synthesis of the SCWP. We review here recent insights into the assembly and function of the S-layer and the SCWP.
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Affiliation(s)
- Dominique Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois 60649.,Department of Microbiology, University of Chicago, Chicago, Illinois 60637;
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois 60649.,Department of Microbiology, University of Chicago, Chicago, Illinois 60637;
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Chateau A, Lunderberg JM, Oh SY, Abshire T, Friedlander A, Quinn CP, Missiakas DM, Schneewind O. Galactosylation of the Secondary Cell Wall Polysaccharide of Bacillus anthracis and Its Contribution to Anthrax Pathogenesis. J Bacteriol 2018; 200:e00562-17. [PMID: 29229702 PMCID: PMC5809694 DOI: 10.1128/jb.00562-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 12/05/2017] [Indexed: 12/13/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax disease, elaborates a secondary cell wall polysaccharide (SCWP) that is essential for bacterial growth and cell division. B. anthracis SCWP is comprised of trisaccharide repeats with the structure, [→4)-β-ManNAc-(1→4)-β-GlcNAc(O3-α-Gal)-(1→6)-α-GlcNAc(O3-α-Gal, O4-β-Gal)-(1→]6-12 The genes whose products promote the galactosylation of B. anthracis SCWP are not yet known. We show here that the expression of galE1, encoding a UDP-glucose 4-epimerase necessary for the synthesis of UDP-galactose, is required for B. anthracis SCWP galactosylation. The galE1 mutant assembles surface (S) layer and S layer-associated proteins that associate with ketal-pyruvylated SCWP via their S layer homology domains similarly to wild-type B. anthracis, but the mutant displays a defect in γ-phage murein hydrolase binding to SCWP. Furthermore, deletion of galE1 diminishes the capsulation of B. anthracis with poly-d-γ-glutamic acid (PDGA) and causes a reduction in bacterial virulence. These data suggest that SCWP galactosylation is required for the physiologic assembly of the B. anthracis cell wall envelope and for the pathogenesis of anthrax disease.IMPORTANCE Unlike virulent Bacillus anthracis isolates, B. anthracis strain CDC684 synthesizes secondary cell wall polysaccharide (SCWP) trisaccharide repeats without galactosyl modification, exhibits diminished growth in vitro in broth cultures, and is severely attenuated in an animal model of anthrax. To examine whether SCWP galactosylation is a requirement for anthrax disease, we generated variants of B. anthracis strains Sterne 34F2 and Ames lacking UDP-glucose 4-epimerase by mutating the genes galE1 and galE2 We identified galE1 as necessary for SCWP galactosylation. Deletion of galE1 decreased the poly-d-γ-glutamic acid (PDGA) capsulation of the vegetative form of B. anthracis and increased the bacterial inoculum required to produce lethal disease in mice, indicating that SCWP galactosylation is indeed a determinant of anthrax disease.
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Affiliation(s)
- Alice Chateau
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Justin Mark Lunderberg
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - So Young Oh
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Teresa Abshire
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Arthur Friedlander
- Headquarters, United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Conrad P Quinn
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dominique M Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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Liang X, Zhu J, Zhao Z, Zheng F, Zhang E, Wei J, Ji Y, Ji Y. A Single Nucleotide Polymorphism Is Involved in Regulation of Growth and Spore Formation of Bacillus anthracis Pasteur II Strain. Front Cell Infect Microbiol 2017; 7:270. [PMID: 28702375 PMCID: PMC5487402 DOI: 10.3389/fcimb.2017.00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/06/2017] [Indexed: 01/03/2023] Open
Abstract
Anthrax toxins and capsules, which are encoded by genes located on pXO1 and pXO2, respectively, are major virulence factors of Bacillus anthracis. Our previous studies demonstrated that exposure to high-temperatures is unable to abolish the pXO1 plasmid of the Pasteur II strain, but the growth of the strain was obviously slower than that of the Sterne strain and wild-type virulent strain. To elucidate a potential regulatory mechanism of slowing growth, we employed comparative genome and bioinformatic analysis and revealed a unique SNP (G to T) at the 143135 bp position in pXO1 that is possibly involved in the mediation of growth of Pasteur II. However, the T to G mutation in groR did not result in any change of the amino acid sequence. A predominant nucleotide G existed at the 143135 bp in pXO1 of 100 wild-type B. anthracis isolates and 9 isolates documented in GenBank, whereas T replaced G in pXO1 of the Pasteur II strain. Further analysis indicate that the SNP is located in a gene between 143042 and 143173 bp, and that it encodes a small protein of 43 amino acids and is termed as a growth regulator (GroR). Site-directed mutagenesis and gene deletion demonstrates that groR regulates the growth and spore formation of B. anthracis. Our results indicate that the pXO1 plasmid is involved in the regulation of growth and spore formation in B. anthracis.
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Affiliation(s)
- Xudong Liang
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and PreventionBeijing, China
| | - Jin Zhu
- Huadong Medical Institute of BiotechniquesNanjing, China
| | - Zhongzhi Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and PreventionBeijing, China
| | - Feng Zheng
- Huadong Medical Institute of BiotechniquesNanjing, China
| | - Enmin Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and PreventionBeijing, China
| | - Jianchun Wei
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and PreventionBeijing, China
| | - Yon Ji
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and PreventionBeijing, China
| | - Yinduo Ji
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. PaulMN, United States
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Genes Required for Bacillus anthracis Secondary Cell Wall Polysaccharide Synthesis. J Bacteriol 2016; 199:JB.00613-16. [PMID: 27795328 DOI: 10.1128/jb.00613-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/07/2016] [Indexed: 12/19/2022] Open
Abstract
The secondary cell wall polysaccharide (SCWP) is thought to be essential for vegetative growth and surface (S)-layer assembly in Bacillus anthracis; however, the genetic determinants for the assembly of its trisaccharide repeat structure are not known. Here, we report that WpaA (BAS0847) and WpaB (BAS5274) share features with membrane proteins involved in the assembly of O-antigen lipopolysaccharide in Gram-negative bacteria and propose that WpaA and WpaB contribute to the assembly of the SCWP in B. anthracis Vegetative forms of the B. anthracis wpaA mutant displayed increased lengths of cell chains, a cell separation defect that was attributed to mislocalization of the S-layer-associated murein hydrolases BslO, BslS, and BslT. The wpaB mutant was defective in vegetative replication during early logarithmic growth and formed smaller colonies. Deletion of both genes, wpaA and wpaB, did not yield viable bacilli, and when depleted of both wpaA and wpaB, B. anthracis could not maintain cell shape, support vegetative growth, or assemble SCWP. We propose that WpaA and WpaB fulfill overlapping glycosyltransferase functions of either polymerizing repeat units or transferring SCWP polymers to linkage units prior to LCP-mediated anchoring of the polysaccharide to peptidoglycan. IMPORTANCE The secondary cell wall polysaccharide (SCWP) is essential for Bacillus anthracis growth, cell shape, and division. SCWP is comprised of trisaccharide repeats (→4)-β-ManNAc-(1→4)-β-GlcNAc-(1→6)-α-GlcNAc-(1→) with α-Gal and β-Gal substitutions; however, the genetic determinants and enzymes for SCWP synthesis are not known. Here, we identify WpaA and WpaB and report that depletion of these factors affects vegetative growth, cell shape, and S-layer assembly. We hypothesize that WpaA and WpaB are involved in the assembly of SCWP prior to transfer of this polymer onto peptidoglycan.
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Mann PA, Müller A, Wolff KA, Fischmann T, Wang H, Reed P, Hou Y, Li W, Müller CE, Xiao J, Murgolo N, Sher X, Mayhood T, Sheth PR, Mirza A, Labroli M, Xiao L, McCoy M, Gill CJ, Pinho MG, Schneider T, Roemer T. Chemical Genetic Analysis and Functional Characterization of Staphylococcal Wall Teichoic Acid 2-Epimerases Reveals Unconventional Antibiotic Drug Targets. PLoS Pathog 2016; 12:e1005585. [PMID: 27144276 PMCID: PMC4856313 DOI: 10.1371/journal.ppat.1005585] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/29/2016] [Indexed: 11/18/2022] Open
Abstract
Here we describe a chemical biology strategy performed in Staphylococcus aureus and Staphylococcus epidermidis to identify MnaA, a 2-epimerase that we demonstrate interconverts UDP-GlcNAc and UDP-ManNAc to modulate substrate levels of TarO and TarA wall teichoic acid (WTA) biosynthesis enzymes. Genetic inactivation of mnaA results in complete loss of WTA and dramatic in vitro β-lactam hypersensitivity in methicillin-resistant S. aureus (MRSA) and S. epidermidis (MRSE). Likewise, the β-lactam antibiotic imipenem exhibits restored bactericidal activity against mnaA mutants in vitro and concomitant efficacy against 2-epimerase defective strains in a mouse thigh model of MRSA and MRSE infection. Interestingly, whereas MnaA serves as the sole 2-epimerase required for WTA biosynthesis in S. epidermidis, MnaA and Cap5P provide compensatory WTA functional roles in S. aureus. We also demonstrate that MnaA and other enzymes of WTA biosynthesis are required for biofilm formation in MRSA and MRSE. We further determine the 1.9Å crystal structure of S. aureus MnaA and identify critical residues for enzymatic dimerization, stability, and substrate binding. Finally, the natural product antibiotic tunicamycin is shown to physically bind MnaA and Cap5P and inhibit 2-epimerase activity, demonstrating that it inhibits a previously unanticipated step in WTA biosynthesis. In summary, MnaA serves as a new Staphylococcal antibiotic target with cognate inhibitors predicted to possess dual therapeutic benefit: as combination agents to restore β-lactam efficacy against MRSA and MRSE and as non-bioactive prophylactic agents to prevent Staphylococcal biofilm formation. Staphylococcus aureus and Staphylococcus epidermidis cause life-threatening infections that are commonly acquired in hospitals as well as the community and remain difficult to treat with current antibiotics. In part, this is due to the emergence of methicillin-resistant S. aureus and S. epidermidis (MRSA and MRSE), which exhibit broad resistance to β-lactams such as penicillin and other members of this important founding class of antibiotics. Compounding this problem, Staphylococci commonly colonize the surface of catheters and other medical devices, forming bacterial communities that are intrinsically resistant to antibiotics. Here we functionally characterize a family of 2-epimerases, named MnaA and Cap5P, that we demonstrate by genetic, biochemical, and X-ray crystallography means are essential for wall teichoic acid biosynthesis and that upon their genetic inactivation render methicillin-resistant Staphylococci unable to form biofilms as well as broadly hypersusceptible to β-lactam antibiotics both in vitro and in a host infection setting. WTA 2-epimerases therefore constitute a novel class of methicillin-resistant Staphylococcal drug targets.
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Affiliation(s)
- Paul A. Mann
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Anna Müller
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Kerstin A. Wolff
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Thierry Fischmann
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Hao Wang
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Patricia Reed
- Laboratory of Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Yan Hou
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Wenjin Li
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry, University of Bonn, Bonn, Germany
| | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry, University of Bonn, Bonn, Germany
| | - Jianying Xiao
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Nicholas Murgolo
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Xinwei Sher
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Todd Mayhood
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Payal R. Sheth
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Asra Mirza
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Marc Labroli
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Li Xiao
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Mark McCoy
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Charles J. Gill
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
| | - Mariana G. Pinho
- Laboratory of Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Bonn, Germany
| | - Terry Roemer
- Merck Research Laboratories, Kenilworth New Jersey, United States of America
- * E-mail:
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Lunderberg JM, Liszewski Zilla M, Missiakas D, Schneewind O. Bacillus anthracis tagO Is Required for Vegetative Growth and Secondary Cell Wall Polysaccharide Synthesis. J Bacteriol 2015; 197:3511-20. [PMID: 26324447 PMCID: PMC4621081 DOI: 10.1128/jb.00494-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/17/2015] [Indexed: 12/29/2022] Open
Abstract
UNLABELLED Bacillus anthracis elaborates a linear secondary cell wall polysaccharide (SCWP) that retains surface (S)-layer and associated proteins via their S-layer homology (SLH) domains. The SCWP is comprised of trisaccharide repeats [→4)-β-ManNAc-(1→4)-β-GlcNAc-(1→6)-α-GlcNAc-(1→] and tethered via acid-labile phosphodiester bonds to peptidoglycan. Earlier work identified UDP-GlcNAc 2-epimerases GneY (BAS5048) and GneZ (BAS5117), which act as catalysts of ManNAc synthesis, as well as a polysaccharide deacetylase (BAS5051), as factors contributing to SCWP synthesis. Here, we show that tagO (BAS5050), which encodes a UDP-N-acetylglucosamine:undecaprenyl-P N-acetylglucosaminyl 1-P transferase, the enzyme that initiates the synthesis of murein linkage units, is required for B. anthracis SCWP synthesis and S-layer assembly. Similar to gneY-gneZ mutants, B. anthracis strains lacking tagO cannot maintain cell shape or support vegetative growth. In contrast, mutations in BAS5051 do not affect B. anthracis cell shape, vegetative growth, SCWP synthesis, or S-layer assembly. These data suggest that TagO-mediated murein linkage unit assembly supports SCWP synthesis and attachment to the peptidoglycan via acid-labile phosphodiester bonds. Further, B. anthracis variants unable to synthesize SCWP trisaccharide repeats cannot sustain cell shape and vegetative growth. IMPORTANCE Bacillus anthracis elaborates an SCWP to support vegetative growth and envelope assembly. Here, we show that some, but not all, SCWP synthesis is dependent on tagO-derived murein linkage units and subsequent attachment of SCWP to peptidoglycan. The data implicate secondary polymer modifications of peptidoglycan and subcellular distributions as a key feature of the cell cycle in Gram-positive bacteria and establish foundations for work on the molecular functions of the SCWP and on inhibitors with antibiotic attributes.
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Affiliation(s)
- J Mark Lunderberg
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Megan Liszewski Zilla
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Dominique Missiakas
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Olaf Schneewind
- Howard Taylor Ricketts Laboratory, Argonne National Laboratory, Lemont, Illinois, USA Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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Bacillus anthracis lcp Genes Support Vegetative Growth, Envelope Assembly, and Spore Formation. J Bacteriol 2015; 197:3731-41. [PMID: 26391207 DOI: 10.1128/jb.00656-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/17/2015] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Bacillus anthracis, a spore-forming pathogen, replicates as chains of vegetative cells by regulating the separation of septal peptidoglycan. Surface (S)-layer proteins and B. anthracis S-layer-associated proteins (BSLs) function as chain length determinants and are assembled in the envelope by binding to the secondary cell wall polysaccharide (SCWP). B. anthracis expresses six different genes encoding LytR-CpsA-Psr (LCP) enzymes (lcpB1 to -4, lcpC, and lcpD), which when expressed in Staphylococcus aureus promote attachment of wall teichoic acid to peptidoglycan. Mutations in B. anthracis lcpB3 and lcpD cause aberrations in cell size and chain length that can be explained as discrete defects in SCWP assembly; however, the function of the other lcp genes is not known. By deleting combinations of lcp genes from the B. anthracis genome, we generated variants with single lcp genes. B. anthracis expressing lcpB3 alone displayed physiological cell size, vegetative growth, spore formation, and S-layer assembly. Strains expressing lcpB1 or lcpB4 displayed defects in cell size and shape, S-layer assembly, and spore formation yet sustained vegetative growth. In contrast, the lcpB2 strain was unable to grow unless the gene was expressed from a multicopy plasmid (lcpB2(++)), and variants expressing lcpC or lcpD displayed severe defects in growth and cell shape. The lcpB2(++), lcpC, or lcpD strains supported neither S-layer assembly nor spore formation. We propose a model whereby LCP enzymes fulfill partially overlapping functions in transferring SCWP molecules to discrete sites within the bacterial envelope. IMPORTANCE Products of genes essential for bacterial envelope assembly represent targets for antibiotic development. The LytR-CpsA-Psr (LCP) enzymes tether bactoprenol-linked intermediates of secondary cell wall polymers to the C6 hydroxyl of N-acetylmuramic acid in peptidoglycan; however, the role of LCPs as a target for antibiotic therapy is not defined. We show here that LCP enzymes are essential for the cell cycle, vegetative growth, and spore formation of Bacillus anthracis, the causative agent of anthrax disease. Furthermore, we assign functions for each of the six LCP enzymes, including cell size and shape, vegetative growth and sporulation, and S-layer and S-layer-associated protein assembly.
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LytR-CpsA-Psr enzymes as determinants of Bacillus anthracis secondary cell wall polysaccharide assembly. J Bacteriol 2014; 197:343-53. [PMID: 25384480 DOI: 10.1128/jb.02364-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, replicates as chains of vegetative cells by regulating the separation of septal peptidoglycan. Surface (S)-layer proteins and associated proteins (BSLs) function as chain length determinants and bind to the secondary cell wall polysaccharide (SCWP). In this study, we identified the B. anthracis lcpD mutant, which displays increased chain length and S-layer assembly defects due to diminished SCWP attachment to peptidoglycan. In contrast, the B. anthracis lcpB3 variant displayed reduced cell size and chain length, which could be attributed to increased deposition of BSLs. In other bacteria, LytR-CpsA-Psr (LCP) proteins attach wall teichoic acid (WTA) and polysaccharide capsule to peptidoglycan. B. anthracis does not synthesize these polymers, yet its genome encodes six LCP homologues, which, when expressed in S. aureus, promote WTA attachment. We propose a model whereby B. anthracis LCPs promote attachment of SCWP precursors to discrete locations in the peptidoglycan, enabling BSL assembly and regulated separation of septal peptidoglycan.
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