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Mishra AH, Mohan S, Gutti P, Krishna S, Sundaraman S, Chakraborti S, Jaiswal AK, Nambi Raj NA, Mishra D. Bioselective and Radiopaque Zinc-Biopolymeric Complex-Based Porous Biomaterials Promote Mammalian Tissue Ingrowth In Vivo While Inhibiting Microbial Biofilm Gene Expression and Biofilm Formation. ACS APPLIED BIO MATERIALS 2024; 7:3701-3713. [PMID: 38748449 DOI: 10.1021/acsabm.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Metal-organic complexes have shown astounding bioactive properties; however, they are rarely explored as biomaterials. Recent studies showed that carboxymethyl-chitosan (CMC) genipin-conjugated zinc biomimetic scaffolds have unique bioselective properties. The biomaterial was reported to be mammalian cell-friendly; at the same time, it was found to discourage microbial biofilm formation on its surface, which seemed to be a promising solution to addressing the problem of trauma-associated biofilm formation and development of antimicrobial resistance. However, the mechanically frail characteristics and zinc overload raise concerns and limit the potential of the said biomaterials. Hence, the present work is focused on improving the strength of the earlier scaffold formulations, testing its in vivo efficacy and reaffirming its action against biofilm-forming microbe Staphylococcus aureus. Scaling up of CMC proportion increased rigidity, and 8% CMC was found to be the ideal concentration for robust scaffold fabrication. Freeze-dried CMC scaffolds with or without genipin (GP) cross-linking were conjugated with zinc using 2 M zinc acetate solution. Characterization results indicated that the CMC-Zn scaffolds, without genipin, showed mechanical properties close to bone fillers, resist in vitro enzymatic degradation until 4 weeks, are porous in nature, and have radiopacity close to mandibular bones. Upon implantation in a subcutaneous pocket of Wistar rats, the scaffolds showed tissue in-growth with simultaneous degradation without any signs of toxicity past 28 days. Neither were there any signs of toxicity in any of the vital organs. Considering many superior properties among the other formulations, the CMC-Zn scaffolds were furthered for biofilm studies. CMC-Zn showed negligible S. aureus biofilm formation on its surface as revealed by an alamar blue-based study. RT-PCR analysis revealed that CMC-Zn downregulated the expression of pro-biofilm effector genes such as icaC and clfB. A protein docking study predicted the inhibitory mechanism of CMC-Zn. Although it binds strongly when alone, at high density, it may cause inactivation of the transmembrane upstream activators of the said genes, thereby preventing their dimerization and subsequent inactivation of the effector genes. In conclusion, zinc-conjugated carboxymethyl-chitosan scaffolds are mechanically robust, porous, yet biodegradable, harmless to the host in the long term, they are radiopaque and prevent biofilm gene expression in notorious microbes; hence, they could be a suitable candidate for bone filler applications.
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Affiliation(s)
- Arushi Hitendra Mishra
- Bioinspired Design Lab, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - Sanjukta Mohan
- Bioinspired Design Lab, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - Pavan Gutti
- Bioinspired Design Lab, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - Sreevatsan Krishna
- Bioinspired Design Lab, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - Sugunapriyadarshini Sundaraman
- Bioinspired Design Lab, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - Sourangshu Chakraborti
- Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - Amit Kumar Jaiswal
- Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - N Arunai Nambi Raj
- School of Advanced Sciences (SAS), Vellore Institute of Technology (VIT), Vellore Campus, Vellore, Tamil Nadu 632014, India
| | - Debasish Mishra
- Bioinspired Design Lab, School of Bio-Sciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore Campus, Vellore, Tamil Nadu 632014, India
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Rabaan AA, Garout M, Aljeldah M, Al Shammari BR, Alawfi A, Alshengeti A, Najim MA, Alrouji M, Almuhanna Y, Alissa M, Mashraqi MM, Alwashmi ASS, Alhajri M, Alateah SM, Farahat RA, Mohapatra RK. Anti-tubercular activity evaluation of natural compounds by targeting Mycobacterium tuberculosis resuscitation promoting factor B inhibition: An in silico study. Mol Divers 2023:10.1007/s11030-023-10632-8. [PMID: 36964456 DOI: 10.1007/s11030-023-10632-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/14/2023] [Indexed: 03/26/2023]
Abstract
Tuberculosis (TB), an infectious disease caused by the Mycobacterium tuberculosis (Mtb), has been responsible for the deaths of millions of individuals around the globe. A vital protein in viral pathogenesis known as resuscitation promoting factor (RpfB) has been identified as a potential therapeutic target of anti-tuberculosis drugs. This study offered an in silico process to examine possible RpfB inhibitors employing a computational drug design pipeline. In this study, a total of 1228 phytomolecules were virtually tested against the RpfB of Mtb. These phytomolecules were sourced from the NP-lib database of the MTi-OpenScreen server, and five top hits (ZINC000044404209, ZINC000059779788, ZINC000001562130, ZINC000014766825, and ZINC000043552589) were prioritized for compute intensive docking with dock score ≤ - 8.5 kcal/mole. Later, molecular dynamics (MD) simulation and principal component analysis (PCA) were used to validate these top five hits. In the list of these top five hits, the ligands ZINC000044404209, ZINC000059779788, and ZINC000043552589 showed hydrogen bond formation with the functional residue Glu292 of the RpfB protein suggesting biological significance of the binding. The RMSD study showed stable protein-ligand complexes and higher conformational consistency for the ligands ZINC000014766825, and ZINC000043552589 with RMSD 3-4 Å during 100 ns MD simulation. The overall analysis performed in the study suggested promising binding of these compounds with the RpfB protein of the Mtb at its functional site, further experimental investigation is needed to validate the computational finding.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia.
- College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan.
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, 39831, Saudi Arabia
| | - Basim R Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, 39831, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah41491, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah41491, Saudi Arabia
- Department of Infection prevention and control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah, 41491, Saudi Arabia
| | - Mustafa A Najim
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah, 41411, Saudi Arabia
| | - Mohammed Alrouji
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, 11961, Saudi Arabia
| | - Yasir Almuhanna
- Department of Medical Laboratories, College of Applied Medical Sciences, Shaqra University, Shaqra, 11961, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, 61441, Saudi Arabia
| | - Ameen S S Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Mashael Alhajri
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 34212, Saudi Arabia
| | - Souad Mohammed Alateah
- Microbiology laboratory, Central military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, 11159, Saudi Arabia
| | | | - Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, 758002, India.
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Penicillin-Binding Protein 1 (PBP1) of Staphylococcus aureus Has Multiple Essential Functions in Cell Division. mBio 2022; 13:e0066922. [PMID: 35703435 PMCID: PMC9426605 DOI: 10.1128/mbio.00669-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bacterial cell division is a complex process requiring the coordination of multiple components to allow the appropriate spatial and temporal control of septum formation and cell scission. Peptidoglycan (PG) is the major structural component of the septum, and our recent studies in the human pathogen Staphylococcus aureus have revealed a complex, multistage PG architecture that develops during septation. Penicillin-binding proteins (PBPs) are essential for the final steps of PG biosynthesis; their transpeptidase activity links the peptide side chains of nascent glycan strands. PBP1 is required for cell division in S. aureus, and here, we demonstrate that it has multiple essential functions associated with its enzymatic activity and as a regulator of division. Loss of PBP1, or just its C-terminal PASTA domains, results in cessation of division at the point of septal plate formation. The PASTA domains can bind PG and thereby potentially coordinate the cell division process. The transpeptidase activity of PBP1 is also essential, but its loss leads to a strikingly different phenotype of thickened and aberrant septa, which is phenocopied by the morphological effects of adding the PBP1-specific β-lactam, meropenem. Together, these results lead to a model for septal PG synthesis where PBP1 enzyme activity is required for the characteristic architecture of the septum and PBP1 protein molecules enable the formation of the septal plate.
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Martínez-Caballero S, Mahasenan KV, Kim C, Molina R, Feltzer R, Lee M, Bouley R, Hesek D, Fisher JF, Muñoz IG, Chang M, Mobashery S, Hermoso JA. Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus, an essential component of the divisome machinery. Comput Struct Biotechnol J 2021; 19:5392-5405. [PMID: 34667534 PMCID: PMC8493512 DOI: 10.1016/j.csbj.2021.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 12/18/2022] Open
Abstract
The penicillin-binding proteins are the enzyme catalysts of the critical transpeptidation crosslinking polymerization reaction of bacterial peptidoglycan synthesis and the molecular targets of the penicillin antibiotics. Here, we report a combined crystallographic, small-angle X-ray scattering (SAXS) in-solution structure, computational and biophysical analysis of PBP1 of Staphylococcus aureus (saPBP1), providing mechanistic clues about its function and regulation during cell division. The structure reveals the pedestal domain, the transpeptidase domain, and most of the linker connecting to the "penicillin-binding protein and serine/threonine kinase associated" (PASTA) domains, but not its two PASTA domains, despite their presence in the construct. To address this absence, the structure of the PASTA domains was determined at 1.5 Å resolution. Extensive molecular-dynamics simulations interpret the PASTA domains of saPBP1 as conformationally mobile and separated from the transpeptidase domain. This conclusion was confirmed by SAXS experiments on the full-length protein in solution. A series of crystallographic complexes with β-lactam antibiotics (as inhibitors) and penta-Gly (as a substrate mimetic) allowed the molecular characterization of both inhibition by antibiotics and binding for the donor and acceptor peptidoglycan strands. Mass-spectrometry experiments with synthetic peptidoglycan fragments revealed binding by PASTA domains in coordination with the remaining domains. The observed mobility of the PASTA domain in saPBP1 could play a crucial role for in vivo interaction with its glycosyltransferase partner in the membrane or with other components of the divisome machinery, as well as for coordination of transpeptidation and polymerization processes in the bacterial divisome.
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Affiliation(s)
- Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Choon Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
| | - Rhona Feltzer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Renee Bouley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Inés G Muñoz
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
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Fisher JF, Mobashery S. β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium. Chem Rev 2021; 121:3412-3463. [PMID: 33373523 PMCID: PMC8653850 DOI: 10.1021/acs.chemrev.0c01010] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
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Morales Angeles D, Macia-Valero A, Bohorquez LC, Scheffers DJ. The PASTA domains of Bacillus subtilis PBP2B strengthen the interaction of PBP2B with DivIB. MICROBIOLOGY (READING, ENGLAND) 2020; 166:826-836. [PMID: 32749956 PMCID: PMC7654742 DOI: 10.1099/mic.0.000957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022]
Abstract
Bacterial cell division is mediated by a protein complex known as the divisome. Many protein-protein interactions in the divisome have been characterized. In this report, we analyse the role of the PASTA (Penicillin-binding protein And Serine Threonine kinase Associated) domains of Bacillus subtilis PBP2B. PBP2B itself is essential and cannot be deleted, but removing the PBP2B PASTA domains results in impaired cell division and a heat-sensitive phenotype. This resembles the deletion of divIB, a known interaction partner of PBP2B. Bacterial two-hybrid and co-immunoprecipitation analyses show that the interaction between PBP2B and DivIB is weakened when the PBP2B PASTA domains are removed. Combined, our results show that the PBP2B PASTA domains are required to strengthen the interaction between PBP2B and DivIB.
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Affiliation(s)
- Danae Morales Angeles
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Present address: Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Alicia Macia-Valero
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Laura C. Bohorquez
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Present address: BluSense Diagnostics ApS, Carrera 63 100-49, Bogota 111121, Colombia
| | - Dirk-Jan Scheffers
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Elicitor and Receptor Molecules: Orchestrators of Plant Defense and Immunity. Int J Mol Sci 2020; 21:ijms21030963. [PMID: 32024003 PMCID: PMC7037962 DOI: 10.3390/ijms21030963] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Pathogen-associated molecular patterns (PAMPs), microbe-associated molecular patterns (MAMPs), herbivore-associated molecular patterns (HAMPs), and damage-associated molecular patterns (DAMPs) are molecules produced by microorganisms and insects in the event of infection, microbial priming, and insect predation. These molecules are then recognized by receptor molecules on or within the plant, which activates the defense signaling pathways, resulting in plant’s ability to overcome pathogenic invasion, induce systemic resistance, and protect against insect predation and damage. These small molecular motifs are conserved in all organisms. Fungi, bacteria, and insects have their own specific molecular patterns that induce defenses in plants. Most of the molecular patterns are either present as part of the pathogen’s structure or exudates (in bacteria and fungi), or insect saliva and honeydew. Since biotic stresses such as pathogens and insects can impair crop yield and production, understanding the interaction between these organisms and the host via the elicitor–receptor interaction is essential to equip us with the knowledge necessary to design durable resistance in plants. In addition, it is also important to look into the role played by beneficial microbes and synthetic elicitors in activating plants’ defense and protection against disease and predation. This review addresses receptors, elicitors, and the receptor–elicitor interactions where these components in fungi, bacteria, and insects will be elaborated, giving special emphasis to the molecules, responses, and mechanisms at play, variations between organisms where applicable, and applications and prospects.
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Squeglia F, Moreira M, Ruggiero A, Berisio R. The Cell Wall Hydrolytic NlpC/P60 Endopeptidases in Mycobacterial Cytokinesis: A Structural Perspective. Cells 2019; 8:cells8060609. [PMID: 31216697 PMCID: PMC6628586 DOI: 10.3390/cells8060609] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
In preparation for division, bacteria replicate their DNA and segregate the newly formed chromosomes. A division septum then assembles between the chromosomes, and the mother cell splits into two identical daughters due to septum degradation. A major constituent of bacterial septa and of the whole cell wall is peptidoglycan (PGN), an essential cell wall polymer, formed by glycan chains of β−(1-4)-linked-N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), cross-linked by short peptide stems. Depending on the amino acid located at the third position of the peptide stem, PGN is classified as either Lys-type or meso-diaminopimelic acid (DAP)-type. Hydrolytic enzymes play a crucial role in the degradation of bacterial septa to split the cell wall material shared by adjacent daughter cells to promote their separation. In mycobacteria, a key PGN hydrolase, belonging to the NlpC/P60 endopeptidase family and denoted as RipA, is responsible for the degradation of septa, as the deletion of the gene encoding for this enzyme generates abnormal bacteria with multiple septa. This review provides an update of structural and functional data highlighting the central role of RipA in mycobacterial cytokinesis and the fine regulation of its catalytic activity, which involves multiple molecular partners.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging (IBB), CNR, 80134 Naples, Italy.
| | - Miguel Moreira
- Institute of Biostructures and Bioimaging (IBB), CNR, 80134 Naples, Italy.
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging (IBB), CNR, 80134 Naples, Italy.
| | - Rita Berisio
- Institute of Biostructures and Bioimaging (IBB), CNR, 80134 Naples, Italy.
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Collagen degradation in tuberculosis pathogenesis: the biochemical consequences of hosting an undesired guest. Biochem J 2018; 475:3123-3140. [PMID: 30315001 DOI: 10.1042/bcj20180482] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022]
Abstract
The scenario of chemical reactions prompted by the infection by Mycobacterium tuberculosis is huge. The infection generates a localized inflammatory response, with the recruitment of neutrophils, monocytes, and T-lymphocytes. Consequences of this immune reaction can be the eradication or containment of the infection, but these events can be deleterious to the host inasmuch as lung tissue can be destroyed. Indeed, a hallmark of tuberculosis (TB) is the formation of lung cavities, which increase disease development and transmission, as they are sites of high mycobacterial burden. Pulmonary cavitation is associated with antibiotic failure and the emergence of antibiotic resistance. For cavities to form, M. tuberculosis induces the overexpression of host proteases, like matrix metalloproteinases and cathepsin, which are secreted from monocyte-derived cells, neutrophils, and stromal cells. These proteases destroy the lung parenchyma, in particular the collagen constituent of the extracellular matrix (ECM). Namely, in an attempt to destroy infected cells, the immune reactions prompted by mycobacterial infections induce the destruction of vital regions of the lung, in a process that can become fatal. Here, we review structure and function of the main molecular actors of ECM degradation due to M. tuberculosis infection and the proposed mechanisms of tissue destruction, mainly attacking fibrillar collagen. Importantly, enzymes responsible for collagen destruction are emerging as key targets for adjunctive therapies to limit immunopathology in TB.
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Calvanese L, Falcigno L, Squeglia F, Berisio R, D’Auria G. PASTA sequence composition is a predictive tool for protein class identification. Amino Acids 2018; 50:1441-1450. [DOI: 10.1007/s00726-018-2621-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/13/2018] [Indexed: 12/18/2022]
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Zucchini L, Mercy C, Garcia PS, Cluzel C, Gueguen-Chaignon V, Galisson F, Freton C, Guiral S, Brochier-Armanet C, Gouet P, Grangeasse C. PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae. Nat Microbiol 2018; 3:197-209. [PMID: 29203882 DOI: 10.1038/s41564-017-0069-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/23/2017] [Indexed: 11/09/2022]
Abstract
Eukaryotic-like serine/threonine kinases (eSTKs) with extracellular PASTA repeats are key membrane regulators of bacterial cell division. How PASTA repeats govern eSTK activation and function remains elusive. Using evolution- and structural-guided approaches combined with cell imaging, we disentangle the role of each PASTA repeat of the eSTK StkP from Streptococcus pneumoniae. While the three membrane-proximal PASTA repeats behave as interchangeable modules required for the activation of StkP independently of cell wall binding, they also control the septal cell wall thickness. In contrast, the fourth and membrane-distal PASTA repeat directs StkP localization at the division septum and encompasses a specific motif that is critical for final cell separation through interaction with the cell wall hydrolase LytB. We propose a model in which the extracellular four-PASTA domain of StkP plays a dual function in interconnecting the phosphorylation of StkP endogenous targets along with septal cell wall remodelling to allow cell division of the pneumococcus.
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Affiliation(s)
- Laure Zucchini
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Chryslène Mercy
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre Simon Garcia
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
- Laboratoire de Biométrie et Biologie Evolutive, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Caroline Cluzel
- Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Virginie Gueguen-Chaignon
- Protein Science Facility, Structure Fédérative de Recherche Biosciences/UMS3444/US8, Université Claude Bernard Lyon 1, Ecole Normale Supérieur de Lyon, INSERM, Centre National de la Recherche Scientifique, Lyon, France
| | - Frédéric Galisson
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Sébastien Guiral
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Céline Brochier-Armanet
- Laboratoire de Biométrie et Biologie Evolutive, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, Unité Mixte de Recherche, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Lyon, France.
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Pompeo F, Byrne D, Mengin-Lecreulx D, Galinier A. Dual regulation of activity and intracellular localization of the PASTA kinase PrkC during Bacillus subtilis growth. Sci Rep 2018; 8:1660. [PMID: 29374241 PMCID: PMC5786024 DOI: 10.1038/s41598-018-20145-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/15/2018] [Indexed: 12/13/2022] Open
Abstract
The activity of the PrkC protein kinase is regulated in a sophisticated manner in Bacillus subtilis cells. In spores, in the presence of muropeptides, PrkC stimulates dormancy exit. The extracellular region containing PASTA domains binds peptidoglycan fragments to probably enhance the intracellular kinase activity. During exponential growth, the cell division protein GpsB interacts with the intracellular domain of PrkC to stimulate its activity. In this paper, we have reinvestigated the regulation of PrkC during exponential and stationary phases. We observed that, during exponential growth, neither its septal localization nor its activity are influenced by the addition of peptidoglycan fragments or by the deletion of one or all PASTA domains. However, Dynamic Light Scattering experiments suggest that peptidoglycan fragments bind specifically to PrkC and induce its oligomerization. In addition, during stationary phase, PrkC appeared evenly distributed in the cell wall and the deletion of one or all PASTA domains led to a non-activated kinase. We conclude that PrkC activation is not as straightforward as previously suggested and that regulation of its kinase activity via the PASTA domains and peptidoglycan fragments binding occurs when PrkC is not concentrated to the bacterial septum, but all over the cell wall in non-dividing bacillus cells.
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Affiliation(s)
- Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13009, Marseille, France.
| | - Deborah Byrne
- Protein Expression Facility, IMM, CNRS, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13009, Marseille, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, UMR 7283, IMM, CNRS, Aix Marseille Univ, 31 Chemin Joseph Aiguier, 13009, Marseille, France
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Squeglia F, Ruggiero A, De Simone A, Berisio R. A structural overview of mycobacterial adhesins: Key biomarkers for diagnostics and therapeutics. Protein Sci 2017; 27:369-380. [PMID: 29139177 DOI: 10.1002/pro.3346] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/09/2017] [Accepted: 11/09/2017] [Indexed: 01/14/2023]
Abstract
Adherence, colonization, and survival of mycobacteria in host cells require surface adhesins, which are attractive pharmacotherapeutic targets. A large arsenal of pilus and non-pilus adhesins have been identified in mycobacteria. These adhesins are capable of interacting with host cells, including macrophages and epithelial cells and are essential to microbial pathogenesis. In the last decade, several structures of mycobacterial adhesins responsible for adhesion to either macrophages or extra cellular matrix proteins have been elucidated. In addition, key structural and functional information have emerged for the process of mycobacterial adhesion to epithelial cells, mediated by the Heparin-binding hemagglutinin (HBHA). In this review, we provide an overview of the structural and functional features of mycobacterial adhesins and discuss their role as important biomarkers for diagnostics and therapeutics. Based on the reported data, it appears clear that adhesins are endowed with a variety of different structures and functions. Most adhesins play important roles in the cell life of mycobacteria and are key virulence factors. However, they have adapted to an extracellular life to exert a role in host-pathogen interaction. The type of interactions they form with the host and the adhesin regions involved in binding is partly known and is described in this review.
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, I-80134, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, I-80134, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, SW7 2AZ, UK
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, I-80134, Italy
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Squeglia F, Ruggiero A, Berisio R. Chemistry of Peptidoglycan in Mycobacterium tuberculosis
Life Cycle: An off-the-wall Balance of Synthesis and Degradation. Chemistry 2017; 24:2533-2546. [DOI: 10.1002/chem.201702973] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16. 80134 Napoli Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16. 80134 Napoli Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging; CNR; Via Mezzocannone 16. 80134 Napoli Italy
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15
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Righino B, Galisson F, Pirolli D, Vitale S, Réty S, Gouet P, De Rosa MC. Structural model of the full-length Ser/Thr protein kinase StkP from S. pneumoniae and its recognition of peptidoglycan fragments. J Biomol Struct Dyn 2017; 36:3666-3679. [PMID: 29057709 DOI: 10.1080/07391102.2017.1395767] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The unique eukaryotic-like Ser/Thr protein kinases of Streptococcus pneumoniae, StkP, plays a primary role in the cell division process. It is composed of an intracellular kinase domain, a transmembrane helix and four extracellular PASTA subunits. PASTA domains were shown to interact with cell wall fragments but the key questions related to the molecular mechanism governing ligand recognition remain unclear. To address this issue, the full-length structural model of StkP was generated by combining small-angle X-ray scattering data with the results of computer simulations. Docking and molecular dynamics studies on the generated three-dimensional model structure reveal the possibility of peptidoglycan fragment binding at the hinge regions between PASTA subunits with a preference for a bent hinge between PASTA3 and PASTA4.
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Affiliation(s)
- Benedetta Righino
- a Istituto di Biochimica e Biochimica Clinica , Università Cattolica del Sacro Cuore , L.go F. Vito 1, Rome 00168 , Italy
| | - Frédéric Galisson
- b Molecular Microbiology and Structural Biochemistry Institute , UMR5086 CNRS Univ-Lyon , Cedex 7, Lyon F-69367 , France
| | - Davide Pirolli
- a Istituto di Biochimica e Biochimica Clinica , Università Cattolica del Sacro Cuore , L.go F. Vito 1, Rome 00168 , Italy.,c Istituto di Chimica del Riconoscimento Molecolare (ICRM) , CNR c/o Università Cattolica del Sacro Cuore L.go F , Vito 1, Rome 00168 , Italy
| | - Serena Vitale
- a Istituto di Biochimica e Biochimica Clinica , Università Cattolica del Sacro Cuore , L.go F. Vito 1, Rome 00168 , Italy
| | - Stéphane Réty
- b Molecular Microbiology and Structural Biochemistry Institute , UMR5086 CNRS Univ-Lyon , Cedex 7, Lyon F-69367 , France
| | - Patrice Gouet
- b Molecular Microbiology and Structural Biochemistry Institute , UMR5086 CNRS Univ-Lyon , Cedex 7, Lyon F-69367 , France
| | - Maria Cristina De Rosa
- c Istituto di Chimica del Riconoscimento Molecolare (ICRM) , CNR c/o Università Cattolica del Sacro Cuore L.go F , Vito 1, Rome 00168 , Italy
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16
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Growth- and Stress-Induced PASTA Kinase Phosphorylation in Enterococcus faecalis. J Bacteriol 2017; 199:JB.00363-17. [PMID: 28808126 DOI: 10.1128/jb.00363-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/04/2017] [Indexed: 12/22/2022] Open
Abstract
Transmembrane Ser/Thr kinases containing extracellular PASTA domains are ubiquitous among Actinobacteria and Firmicutes Such PASTA kinases regulate critical processes, including antibiotic resistance, cell division, toxin production, and virulence, and are essential for viability in certain organisms. Based on in vitro studies with purified extracellular and intracellular fragments of PASTA kinases, a model for signaling has been proposed, in which the extracellular PASTA domains bind currently undefined ligands (typically thought to be peptidoglycan, or fragments thereof) to drive kinase dimerization, which leads to enhanced kinase autophosphorylation and enhanced phosphorylation of substrates. However, this model has not been rigorously tested in vivoEnterococcus faecalis is a Gram-positive intestinal commensal and major antibiotic-resistant opportunistic pathogen. In E. faecalis, the PASTA kinase IreK drives intrinsic resistance to cell wall-active antimicrobials, suggesting that such antimicrobials may trigger IreK signaling. Here we show that IreK responds to cell wall stress in vivo by enhancing its phosphorylation and that of a downstream substrate. This response requires both the extracellular PASTA domains and specific phosphorylatable residues in the kinase domain. Thus, our results provide in vivo evidence, with an intact full-length PASTA kinase in its native physiological environment, that supports the prevailing model of PASTA kinase signaling. In addition, we show that IreK responds to a signal associated with growth and/or cell division, in the absence of cell wall-active antimicrobials. Surprisingly, the ability of IreK to respond to growth and/or division does not require the extracellular PASTA domains, suggesting that IreK monitors multiple parameters for sensory input in vivoIMPORTANCE Transmembrane Ser/Thr kinases containing extracellular PASTA domains are ubiquitous among Actinobacteria and Firmicutes and regulate critical processes. The prevailing model for signaling by PASTA kinases proposes that the extracellular PASTA domains bind ligands to drive kinase dimerization, enhanced autophosphorylation, and enhanced phosphorylation of substrates. However, this model has not been rigorously tested in vivo We show that the PASTA kinase IreK of Enterococcus faecalis responds to cell wall stress in vivo by enhancing its phosphorylation and that of a downstream substrate. This response requires the PASTA domains and phosphorylatable residues in the kinase domain. Thus, our results provide in vivo evidence, with an intact full-length PASTA kinase in its native physiological environment, that supports the prevailing model of PASTA kinase signaling.
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Pensinger DA, Schaenzer AJ, Sauer JD. Do Shoot the Messenger: PASTA Kinases as Virulence Determinants and Antibiotic Targets. Trends Microbiol 2017; 26:56-69. [PMID: 28734616 DOI: 10.1016/j.tim.2017.06.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/15/2017] [Accepted: 06/27/2017] [Indexed: 01/14/2023]
Abstract
All domains of life utilize protein phosphorylation as a mechanism of signal transduction. In bacteria, protein phosphorylation was classically thought to be mediated exclusively by histidine kinases as part of two-component signaling systems. However, it is now well appreciated that eukaryotic-like serine/threonine kinases (eSTKs) control essential processes in bacteria. A subset of eSTKs are single-pass transmembrane proteins that have extracellular penicillin-binding-protein and serine/threonine kinase-associated (PASTA) domains which bind muropeptides. In a variety of important pathogens, PASTA kinases have been implicated in regulating biofilms, antibiotic resistance, and ultimately virulence. Although there are limited examples of direct regulation of virulence factors, PASTA kinases are critical for virulence due to their roles in regulating bacterial physiology in the context of stress. This review focuses on the role of PASTA kinases in virulence for a variety of important Gram-positive pathogens and concludes with a discussion of current efforts to develop kinase inhibitors as novel antimicrobials.
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Affiliation(s)
- Daniel A Pensinger
- Microbiology Doctoral Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Adam J Schaenzer
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; Molecular and Cellular Pharmacology Doctoral Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John-Demian Sauer
- Microbiology Doctoral Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; Molecular and Cellular Pharmacology Doctoral Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA.
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18
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Nikitushkin VD, Demina GR, Kaprelyants AS. Rpf proteins are the factors of reactivation of the dormant forms of actinobacteria. BIOCHEMISTRY (MOSCOW) 2017; 81:1719-1734. [DOI: 10.1134/s0006297916130095] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Hardt P, Engels I, Rausch M, Gajdiss M, Ulm H, Sass P, Ohlsen K, Sahl HG, Bierbaum G, Schneider T, Grein F. The cell wall precursor lipid II acts as a molecular signal for the Ser/Thr kinase PknB of Staphylococcus aureus. Int J Med Microbiol 2016; 307:1-10. [PMID: 27989665 DOI: 10.1016/j.ijmm.2016.12.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/22/2016] [Accepted: 12/10/2016] [Indexed: 12/23/2022] Open
Abstract
The assembly of the bacterial cell wall requires synchronization of a multitude of biosynthetic machineries and regulatory networks. The eukaryotic-like serine/threonine kinase PknB has been implicated in coordinating cross-wall formation, autolysis and cell division in Staphylococcus aureus. However, the signal molecule sensed by this kinase remained elusive so far. Here, we provide compelling biochemical evidence that PknB interacts with the ultimate cell wall precursor lipid II, triggering kinase activity. Moreover, we observed crosstalk of PknB with the two component system WalKR and identified the early cell division protein FtsZ as another PknB phosphorylation substrate in S. aureus. In agreement with the implied role in regulation of cell envelope metabolism, we found PknB to preferentially localize to the septum of S. aureus and the PASTA domains to be crucial for recruitment to this site. The data provide a model for the contribution of PknB to control cell wall metabolism and cell division.
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Affiliation(s)
- Patrick Hardt
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Ina Engels
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Marvin Rausch
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Mike Gajdiss
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Hannah Ulm
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany
| | - Peter Sass
- Interfaculty Institute for Microbiology and Infection Medicine, Department for Microbial Bioactive Compounds, University of Tuebingen, Tuebingen, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Hans-Georg Sahl
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany; Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany.
| | - Fabian Grein
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany.
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20
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Prigozhin DM, Papavinasasundaram KG, Baer CE, Murphy KC, Moskaleva A, Chen TY, Alber T, Sassetti CM. Structural and Genetic Analyses of the Mycobacterium tuberculosis Protein Kinase B Sensor Domain Identify a Potential Ligand-binding Site. J Biol Chem 2016; 291:22961-22969. [PMID: 27601474 DOI: 10.1074/jbc.m116.731760] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Indexed: 11/06/2022] Open
Abstract
Monitoring the environment with serine/threonine protein kinases is critical for growth and survival of Mycobacterium tuberculosis, a devastating human pathogen. Protein kinase B (PknB) is a transmembrane serine/threonine protein kinase that acts as an essential regulator of mycobacterial growth and division. The PknB extracellular domain (ECD) consists of four repeats homologous to penicillin-binding protein and serine/threonine kinase associated (PASTA) domains, and binds fragments of peptidoglycan. These properties suggest that PknB activity is modulated by ECD binding to peptidoglycan substructures, however, the molecular mechanisms underpinning PknB regulation remain unclear. In this study, we report structural and genetic characterization of the PknB ECD. We determined the crystal structures of overlapping ECD fragments at near atomic resolution, built a model of the full ECD, and discovered a region on the C-terminal PASTA domain that has the properties of a ligand-binding site. Hydrophobic interaction between this surface and a bound molecule of citrate was observed in a crystal structure. Our genetic analyses in M. tuberculosis showed that nonfunctional alleles were produced either by deletion of any of single PASTA domain or by mutation of individual conserved residues lining the putative ligand-binding surface of the C-terminal PASTA repeat. These results define two distinct structural features necessary for PknB signal transduction, a fully extended ECD and a conserved, membrane-distal putative ligand-binding site.
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Affiliation(s)
- Daniil M Prigozhin
- From the Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, California 94720-3220 and
| | - Kadamba G Papavinasasundaram
- the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Christina E Baer
- the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Kenan C Murphy
- the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Alisa Moskaleva
- From the Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, California 94720-3220 and
| | - Tony Y Chen
- From the Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, California 94720-3220 and
| | - Tom Alber
- From the Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, California 94720-3220 and
| | - Christopher M Sassetti
- the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
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Calvanese L, Falcigno L, Squeglia F, D'Auria G, Berisio R. Structural and dynamic features of PASTA domains with different functional roles. J Biomol Struct Dyn 2016; 35:2293-2300. [PMID: 27568813 DOI: 10.1080/07391102.2016.1217274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Luisa Calvanese
- a CIRPeB , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy
| | - Lucia Falcigno
- a CIRPeB , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy.,b Department of Pharmacy , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy.,c Institute of Biostructures and Bioimaging-CNR , via Mezzocannone, 16, Naples 80134 , Italy
| | - Flavia Squeglia
- c Institute of Biostructures and Bioimaging-CNR , via Mezzocannone, 16, Naples 80134 , Italy
| | - Gabriella D'Auria
- a CIRPeB , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy.,b Department of Pharmacy , University of Naples "Federico II" , via Mezzocannone, 16, Naples 80134 , Italy.,c Institute of Biostructures and Bioimaging-CNR , via Mezzocannone, 16, Naples 80134 , Italy
| | - Rita Berisio
- c Institute of Biostructures and Bioimaging-CNR , via Mezzocannone, 16, Naples 80134 , Italy
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22
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Ruggiero A, Squeglia F, Romano M, Vitagliano L, De Simone A, Berisio R. Structure and dynamics of the multi-domain resuscitation promoting factor RpfB from Mycobacterium tuberculosis. J Biomol Struct Dyn 2016; 35:1322-1330. [PMID: 27420638 DOI: 10.1080/07391102.2016.1182947] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
RpfB is multidomain protein that is crucial for Mycobacterium tuberculosis resuscitation from dormancy. This protein cleaves cell wall peptidoglycan, an essential bacterial cell wall polymer formed by glycan chains of β-(1-4)-linked-N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) cross-linked by short peptide stems. RpfB is structurally complex being composed of five distinct domains, namely a catalytic, a G5 and three DUF348 domains. Here, we have undertaken a combined experimental and computation structural investigations on the entire protein to gain insights into its structure-function relationships. CD spectroscopy and light scattering experiments have provided insights into the protein fold stability and into its oligomeric state. Using the available structure information, we modeled the entire protein structure, which includes the two DUF348 domains whose structure is experimentally unknown, and we analyzed the dynamic behavior of RpfB using molecular dynamics simulations. Present results highlight an intricate mutual influence of the dynamics of the different protein domains. These data provide interesting clues on the functional role of non-catalytic domains of RpfB and on the mechanism of peptidoglycan degradation necessary to resuscitation of M. tuberculosis.
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Affiliation(s)
- Alessia Ruggiero
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
| | - Flavia Squeglia
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
| | - Maria Romano
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
| | - Luigi Vitagliano
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
| | - Alfonso De Simone
- b Division of Molecular Biosciences , Imperial College London , London , UK
| | - Rita Berisio
- a Institute of Biostructures and Bioimaging , CNR , Naples , Italy
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23
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Pompeo F, Foulquier E, Galinier A. Impact of Serine/Threonine Protein Kinases on the Regulation of Sporulation in Bacillus subtilis. Front Microbiol 2016; 7:568. [PMID: 27148245 PMCID: PMC4837961 DOI: 10.3389/fmicb.2016.00568] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
Bacteria possess many kinases that catalyze phosphorylation of proteins on diverse amino acids including arginine, cysteine, histidine, aspartate, serine, threonine, and tyrosine. These protein kinases regulate different physiological processes in response to environmental modifications. For example, in response to nutritional stresses, the Gram-positive bacterium Bacillus subtilis can differentiate into an endospore; the initiation of sporulation is controlled by the master regulator Spo0A, which is activated by phosphorylation. Spo0A phosphorylation is carried out by a multi-component phosphorelay system. These phosphorylation events on histidine and aspartate residues are labile, highly dynamic and permit a temporal control of the sporulation initiation decision. More recently, another kind of phosphorylation, more stable yet still dynamic, on serine or threonine residues, was proposed to play a role in spore maintenance and spore revival. Kinases that perform these phosphorylation events mainly belong to the Hanks family and could regulate spore dormancy and spore germination. The aim of this mini review is to focus on the regulation of sporulation in B. subtilis by these serine and threonine phosphorylation events and the kinases catalyzing them.
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Affiliation(s)
- Frédérique Pompeo
- Laboratoire de Chimie Bactérienne, CNRS, UMR 7283, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
| | - Elodie Foulquier
- Laboratoire de Chimie Bactérienne, CNRS, UMR 7283, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne, CNRS, UMR 7283, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
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24
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Distribution of PASTA domains in penicillin-binding proteins and serine/threonine kinases of Actinobacteria. J Antibiot (Tokyo) 2016; 69:660-85. [DOI: 10.1038/ja.2015.138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 11/15/2015] [Accepted: 11/25/2015] [Indexed: 01/25/2023]
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25
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Ruggiero A, Squeglia F, Romano M, Vitagliano L, De Simone A, Berisio R. The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains. Biochim Biophys Acta Gen Subj 2015; 1860:445-51. [PMID: 26549874 DOI: 10.1016/j.bbagen.2015.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/26/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND RpfB is a key factor in resuscitation from dormancy of Mycobacterium tuberculosis. This protein is a cell-wall glycosidase, which cleaves cell-wall peptidoglycan. RpfB is structurally complex and is composed of three types of domains, including a catalytic, a G5 and three DUF348 domains. Structural information is currently limited to a portion of the protein including only the catalytic and G5 domains. To gain insights into the structure and function of all domains we have undertaken structural investigations on a large protein fragment containing all three types of domains that constitute RpfB (RpfB3D). METHODS The structural features of RpfB3D have been investigated combining x-ray crystallography and biophysical studies. RESULTS AND CONCLUSIONS The crystal structure of RpfB3D provides the first structural characterization of a DUF348 domain and revealed an unexpected structural relationship with ubiquitin. The crystal structure also provides specific structural features of these domains explaining their frequent association with G5 domains. GENERAL SIGNIFICANCE Results provided novel insights into the mechanism of peptidoglycan degradation necessary to the resuscitation of M. tuberculosis. Features of the DUF348 domain add structural data to a large set of proteins embedding this domain. Based on its structural similarity to ubiquitin and frequent association to the G5 domain, we propose to name this domain as G5-linked-Ubiquitin-like domain, UBLG5.
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Affiliation(s)
- Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Maria Romano
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, SW7 2AZ, UK
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy.
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Manuse S, Fleurie A, Zucchini L, Lesterlin C, Grangeasse C. Role of eukaryotic-like serine/threonine kinases in bacterial cell division and morphogenesis. FEMS Microbiol Rev 2015; 40:41-56. [DOI: 10.1093/femsre/fuv041] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2015] [Indexed: 11/14/2022] Open
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27
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Venkateswara Prasad U, Vasu D, Yeswanth S, Swarupa V, Sunitha MM, Choudhary A, Sarma PVGK. Phosphorylation controls the functioning ofStaphylococcus aureusisocitrate dehydrogenase – favours biofilm formation. J Enzyme Inhib Med Chem 2015; 30:655-61. [DOI: 10.3109/14756366.2014.959945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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28
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Berisio R, Squeglia F, Ruggiero A, Petraccone L, Stellato MI, Del Vecchio P. Differential thermodynamic behaviours of the extra-cellular regions of two Ser/Thr PrkC kinases revealed by calorimetric studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:402-9. [PMID: 25668224 DOI: 10.1016/j.bbapap.2015.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/13/2015] [Accepted: 02/03/2015] [Indexed: 10/24/2022]
Abstract
Eukaryotic-type Ser/Thr protein-kinases are critical mediators of developmental changes and host pathogen interactions in bacteria. Although with lower abundance compared to their homologues from eukaryotes, Ser/Thr protein-kinases (STPK) are widespread in gram positive bacteria, where they regulate several cellular functions. STPKs belong to the protein kinase family named as one-component signal transduction systems, which combine both sensing and regulating properties. Thermodynamic investigations of sensing extra-cellular portions of two important Ser-Thr kinases, PrkC, from Staphylococcus aureus and Bacillus subtilis were conducted by differential scanning calorimetry (DSC) and circular dichroism (CD) melting measurements, coupled with modelling studies. The study of thermodynamic properties of the two domains is challenging since they share a modular domain organization. Consistently, DSC and CD data show that they present similar thermodynamic behaviours and that folding/unfolding transitions do not fit a two-state folding model. However, the thermal unfolding of the two proteins is differentially sensitive to pH. In particular, their unfolding is characteristic of modular structures at the neutral pH, with independent contributions of individual domains to folding. Differently, a cooperative unfolding is evidenced at acidic pH for the B. subtilis member, suggesting that a significant interaction between domains becomes valuable.
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Affiliation(s)
- Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy.
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Marco Ignazio Stellato
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy.
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29
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Calvanese L, Falcigno L, Maglione C, Marasco D, Ruggiero A, Squeglia F, Berisio R, D'Auria G. Structural and binding properties of the PASTA domain of PonA2, a key penicillin binding protein fromMycobacterium tuberculosis. Biopolymers 2014; 101:712-9. [DOI: 10.1002/bip.22447] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/08/2013] [Indexed: 12/18/2022]
Affiliation(s)
| | - Lucia Falcigno
- CIRPeB; University of Naples Federico II; Naples Italy
- Department of Pharmacy; University of Naples “Federico II,”; via Mezzocannone 16 80134 Naples Italy
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
| | - Cira Maglione
- Department of Chemical Sciences; University of Naples “Federico II,”; via Cintia 45 80126 Naples Italy
| | - Daniela Marasco
- Department of Pharmacy; University of Naples “Federico II,”; via Mezzocannone 16 80134 Naples Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
| | - Gabriella D'Auria
- CIRPeB; University of Naples Federico II; Naples Italy
- Department of Pharmacy; University of Naples “Federico II,”; via Mezzocannone 16 80134 Naples Italy
- Institute of Biostructures and Bioimaging-CNR; via Mezzocannone, 16 80134 Naples Italy
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Structure and function of RNase AS, a polyadenylate-specific exoribonuclease affecting mycobacterial virulence in vivo. Structure 2014; 22:719-30. [PMID: 24704253 DOI: 10.1016/j.str.2014.01.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/24/2014] [Accepted: 01/24/2014] [Indexed: 11/21/2022]
Abstract
The cell-envelope of Mycobacterium tuberculosis plays a key role in bacterial virulence and antibiotic resistance. Little is known about the molecular mechanisms of regulation of cell-envelope formation. Here, we elucidate functional and structural properties of RNase AS, which modulates M. tuberculosis cell-envelope properties and strongly impacts bacterial virulence in vivo. The structure of RNase AS reveals a resemblance to RNase T from Escherichia coli, an RNase of the DEDD family involved in RNA maturation. We show that RNase AS acts as a 3'-5'-exoribonuclease that specifically hydrolyzes adenylate-containing RNA sequences. Also, crystal structures of complexes with AMP and UMP reveal the structural basis for the observed enzyme specificity. Notably, RNase AS shows a mechanism of substrate recruitment, based on the recognition of the hydrogen bond donor NH2 group of adenine. Our work opens a field for the design of drugs able to reduce bacterial virulence in vivo.
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Squeglia F, Bachert B, De Simone A, Lukomski S, Berisio R. The crystal structure of the streptococcal collagen-like protein 2 globular domain from invasive M3-type group A Streptococcus shows significant similarity to immunomodulatory HIV protein gp41. J Biol Chem 2013; 289:5122-33. [PMID: 24356966 DOI: 10.1074/jbc.m113.523597] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The arsenal of virulence factors deployed by streptococci includes streptococcal collagen-like (Scl) proteins. These proteins, which are characterized by a globular domain and a collagen-like domain, play key roles in host adhesion, host immune defense evasion, and biofilm formation. In this work, we demonstrate that the Scl2.3 protein is expressed on the surface of invasive M3-type strain MGAS315 of Streptococcus pyogenes. We report the crystal structure of Scl2.3 globular domain, the first of any Scl. This structure shows a novel fold among collagen trimerization domains of either bacterial or human origin. Despite there being low sequence identity, we observed that Scl2.3 globular domain structurally resembles the gp41 subunit of the envelope glycoprotein from human immunodeficiency virus type 1, an essential subunit for viral fusion to human T cells. We combined crystallographic data with modeling and molecular dynamics techniques to gather information on the entire lollipop-like Scl2.3 structure. Molecular dynamics data evidence a high flexibility of Scl2.3 with remarkable interdomain motions that are likely instrumental to the protein biological function in mediating adhesive or immune-modulatory functions in host-pathogen interactions. Altogether, our results provide molecular tools for the understanding of Scl-mediated streptococcal pathogenesis and important structural insights for the future design of small molecular inhibitors of streptococcal invasion.
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Affiliation(s)
- Flavia Squeglia
- From the Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, I-80134 Napoli, Italy
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32
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Ruggiero A, De Simone P, Smaldone G, Squeglia F, Berisio R. Bacterial cell division regulation by Ser/Thr kinases: a structural perspective. Curr Protein Pept Sci 2013; 13:756-66. [PMID: 23305362 PMCID: PMC3601408 DOI: 10.2174/138920312804871201] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/16/2012] [Accepted: 08/03/2012] [Indexed: 12/17/2022]
Abstract
Recent genetic, biochemical and structural studies have established that eukaryotic-like Ser/Thr protein-kinases are critical mediators of developmental changes and host pathogen interactions in bacteria. Although with lower abundance compared to their homologues from eukaryotes, Ser/Thr protein-kinases are widespread in gram-positive bacteria. These data underline a key role of reversible Ser/Thr phosphorylation in bacterial physiology and virulence. Numerous studies have revealed how phosphorylation/dephosphorylation of Ser/Thr protein-kinases governs cell division and cell wall biosynthesis and that Ser/Thr protein kinases are responsible for distinct phenotypes, dependent on different environmental signals. In this review we discuss the current understandings of Ser/Thr protein-kinases functional processes based on structural data.
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Affiliation(s)
- Alessia Ruggiero
- Institute of Biostructure and Bioimaging, CNR, Via Mezzocannone, 16. I-80134, Napoli, Italy.
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33
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Squeglia F, Bachert B, Romano M, Lukomski S, Berisio R. Crystallization and preliminary X-ray crystallographic analysis of the variable domain of Scl2.3, a streptococcal collagen-like protein from invasive M3-type Streptococcus pyogenes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1023-5. [PMID: 23989154 PMCID: PMC3758154 DOI: 10.1107/s174430911302068x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/25/2013] [Indexed: 11/11/2022]
Abstract
Streptococcal collagen-like proteins (Scls) are widely expressed by the well recognized human pathogen Streptococcus pyogenes. These surface proteins contain a signature central collagen-like region and an amino-terminal globular domain, termed the variable domain, which is protruded away from the cell surface by the collagen-like domain. Despite their recognized importance in bacterial pathogenicity, no structural information is presently available on proteins of the Scl class. The variable domain of Scl2 from invasive M3-type S. pyogenes has successfully been crystallized using vapour-diffusion methods. The crystals diffracted to 1.5 Å resolution and belonged to space group H32, with unit-cell parameters a = 44.23, b = 44.23, c = 227.83 Å. The crystal structure was solved by single-wavelength anomalous dispersion using anomalous signal from a europium chloride derivative.|
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Beth Bachert
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, 2095 Health Sciences North, Morgantown, WV 26506, USA
| | - Maria Romano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Slawomir Lukomski
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, 2095 Health Sciences North, Morgantown, WV 26506, USA
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy
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Correale S, Ruggiero A, Capparelli R, Pedone E, Berisio R. Structures of free and inhibited forms of theL,D-transpeptidase LdtMt1fromMycobacterium tuberculosis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1697-706. [DOI: 10.1107/s0907444913013085] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/13/2013] [Indexed: 11/10/2022]
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Zinc regulates the activity of kinase-phosphatase pair (BasPrkC/BasPrpC) in Bacillus anthracis. Biometals 2013; 26:715-30. [PMID: 23793375 DOI: 10.1007/s10534-013-9646-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 06/09/2013] [Indexed: 01/02/2023]
Abstract
Bacillus anthracis Ser/Thr protein kinase PrkC (BasPrkC) is important for virulence of the bacterium within the host. Homologs of PrkC and its cognate phosphatase PrpC (BasPrpC) are the most conserved mediators of signaling events in diverse bacteria. BasPrkC homolog in Bacillus subtilis regulates critical processes like spore germination and BasPrpC modulates the activity of BasPrkC by dephosphorylation. So far, biochemical and genetic studies have provided important insights into the roles of BasPrkC and BasPrpC; however, regulation of their activities is not known. We studied the regulation of BasPrkC/BasPrpC pair and observed that Zn(2+) metal ions can alter their activities. Zn(2+) promotes BasPrkC kinase activity while inhibits the BasPrpC phosphatase activity. Concentration of Zn(2+) in growing B. anthracis cells was found to vary with growth phase. Zn(2+) was found to be lowest in log phase cells while it was highest in spores. This variation in Zn(2+) concentration is significant for understanding the antagonistic activities of BasPrkC/BasPrpC pair. Our results also show that BasPrkC activity is modulated by temperature changes and kinase inhibitors. Additionally, we identified Elongation Factor Tu (BasEf-Tu) as a substrate of BasPrkC/BasPrpC pair and assessed the impact of their regulation on BasEf-Tu phosphorylation. Based on these results, we propose Zn(2+) as an important regulator of BasPrkC/BasPrpC mediated phosphorylation cascades. Thus, this study reveals additional means by which BasPrkC can be activated leading to autophosphorylation and substrate phosphorylation.
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36
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Squeglia F, Romano M, Ruggiero A, Vitagliano L, De Simone A, Berisio R. Carbohydrate recognition by RpfB from Mycobacterium tuberculosis unveiled by crystallographic and molecular dynamics analyses. Biophys J 2013; 104:2530-9. [PMID: 23746526 PMCID: PMC3672874 DOI: 10.1016/j.bpj.2013.04.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 12/24/2022] Open
Abstract
Resuscitation of Mtb is crucial to the etiology of Tuberculosis, because latent tuberculosis is estimated to affect one-third of the world population. The resuscitation-promoting factor RpfB is mainly responsible for Mtb resuscitation from dormancy. Given the impact of latent Tuberculosis, RpfB represents an interesting target for tuberculosis drug discovery. However, no molecular models of substrate binding and catalysis are hitherto available for this enzyme. Here, we identified key interactions involved in substrate binding to RpfB by combining x-ray diffraction studies and computational approaches. The crystal structure of RpfB catalytic domain in complex with N,N',N"-triacetyl-chitotriose, as described here, provides the first, to our knowledge, atomic representation of ligand recognition by RpfB and demonstrates that the strongest interactions are established by the N-acetylglucosamine moiety in the central region of the enzyme binding cleft. Molecular dynamics analyses provided information on the dynamic behavior of protein-substrate interactions and on the role played by the solvent in RpfB function. These data combined with sequence conservation analysis suggest that Glu-292 is the sole residue crucial for catalysis, implying that RpfB acts via the formation of an oxocarbenium ion rather than a covalent intermediate. Present data represent a solid base for the design of effective drug inhibitors of RpfB. Moreover, homology models were generated for the catalytic domains of all members of the Mtb Rpf family (RpfA-E). The analysis of these models unveiled analogies and differences among the different members of the Rpf protein family.
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Key Words
- mtb, mycobacterium tuberculosis
- rpfb, resuscitation promoting factor b
- pdb, protein data bank
- rpfbc, catalytic domain of rpfb
- nag3, n,n',n"-triacetyl-chitotriose
- nag6, hexa-n- acetylchitohexaose
- md, molecular dynamics
- rmsf, root mean-square fluctuation
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Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
- Department of Chemistry, University of Naples Federico II, Napoli, Italy
| | - Maria Romano
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
- Seconda Università di Napoli, Caserta, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, United Kingdom
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, C.N.R., Naples, Italy
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37
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Correale S, Ruggiero A, Pedone E, Berisio R. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the L,D-transpeptidase LdtMt1 from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:253-6. [PMID: 23519798 PMCID: PMC3606568 DOI: 10.1107/s1744309112052141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 12/31/2012] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis is capable of adapting to prolonged periods of dormancy, a state which is resistant to killing by antimycobacterial agents. The L,D-transpeptidation reaction catalysed by the L,D-transpeptidase LdtMt1 is likely to play an essential role in the adaptation of M. tuberculosis to its dormant state. LdtMt1 has been successfully crystallized using vapour-diffusion methods. The crystals of this protein belonged to space group P6₅22, with unit-cell parameters a=57.25, b=57.25, c=257.96 Å, α=90, β=90, γ=120°. Diffraction data have also been collected from a selenomethionine derivative to 2.9 Å resolution. Model building using the phases derived from the multiwavelength anomalous dispersion experiment is in progress.
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Affiliation(s)
- Stefania Correale
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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38
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Vijayakumar B, Velmurugan D. Use of europium ions for SAD phasing of lysozyme at the Cu Kα wavelength. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:20-4. [PMID: 23295480 PMCID: PMC3539697 DOI: 10.1107/s1744309112047562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 11/19/2012] [Indexed: 11/10/2022]
Abstract
Europium is shown to be a good anomalous scatterer in SAD phasing for solving the structure of biological macromolecules. The large value of the anomalous contribution of europium, f'' = 11.17 e(-), at the Cu Kα wavelength is an advantage in de novo phasing and automated model building. Tetragonal crystals of hen egg-white lysozyme (HEWL) incorporating europium(III) chloride (50 mM) were obtained which diffracted to a resolution of 2.3 Å at a wavelength of 1.54 Å (Cu Kα). The master data set (360° frames) was split and analyzed for anomalous signal-to-noise ratio, multiplicity, completeness, SAD phasing and automated building. The structure solution and model building of the split data sets were carried out using phenix.autosol and phenix.autobuild. The contributions of the Eu ions to SAD phasing using in-house data collection are discussed. This study revealed successful lysozyme phasing by SAD using laboratory-source data involving Eu ions, which are mainly coordinated by the side chains of Asn46, Asp52 and Asp101 together with some water molecules.
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Affiliation(s)
- Balakrishnan Vijayakumar
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai (Guindy) Campus, Chennai 600 025, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Maraimalai (Guindy) Campus, Chennai 600 025, India
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39
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Peptidoglycan fragments stimulate resuscitation of “non-culturable” mycobacteria. Antonie van Leeuwenhoek 2012; 103:37-46. [DOI: 10.1007/s10482-012-9784-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/23/2012] [Indexed: 01/08/2023]
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40
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Rakette S, Donat S, Ohlsen K, Stehle T. Structural analysis of Staphylococcus aureus serine/threonine kinase PknB. PLoS One 2012; 7:e39136. [PMID: 22701750 PMCID: PMC3372466 DOI: 10.1371/journal.pone.0039136] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 05/18/2012] [Indexed: 11/29/2022] Open
Abstract
Effective treatment of infections caused by the bacterium Staphylococcus aureus remains a worldwide challenge, in part due to the constant emergence of new strains that are resistant to antibiotics. The serine/threonine kinase PknB is of particular relevance to the life cycle of S. aureus as it is involved in the regulation of purine biosynthesis, autolysis, and other central metabolic processes of the bacterium. We have determined the crystal structure of the kinase domain of PknB in complex with a non-hydrolyzable analog of the substrate ATP at 3.0 Å resolution. Although the purified PknB kinase is active in solution, it crystallized in an inactive, autoinhibited state. Comparison with other bacterial kinases provides insights into the determinants of catalysis, interactions of PknB with ligands, and the pathway of activation.
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Affiliation(s)
- Sonja Rakette
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Stefanie Donat
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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41
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Boudreau MA, Fisher JF, Mobashery S. Messenger functions of the bacterial cell wall-derived muropeptides. Biochemistry 2012; 51:2974-90. [PMID: 22409164 DOI: 10.1021/bi300174x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacterial muropeptides are soluble peptidoglycan structures central to recycling of the bacterial cell wall and messengers in diverse cell signaling events. Bacteria sense muropeptides as signals that antibiotics targeting cell-wall biosynthesis are present, and eukaryotes detect muropeptides during the innate immune response to bacterial infection. This review summarizes the roles of bacterial muropeptides as messengers, with a special emphasis on bacterial muropeptide structures and the relationship of structure to the biochemical events that the muropeptides elicit. Muropeptide sensing and recycling in both Gram-positive and Gram-negative bacteria are discussed, followed by muropeptide sensing by eukaryotes as a crucial event in the innate immune response of insects (via peptidoglycan-recognition proteins) and mammals (through Nod-like receptors) to bacterial invasion.
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Affiliation(s)
- Marc A Boudreau
- Department of Chemistry and Biochemistry, Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556, USA
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42
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Squeglia F, Marchetti R, Ruggiero A, Lanzetta R, Marasco D, Dworkin J, Petoukhov M, Molinaro A, Berisio R, Silipo A. Chemical Basis of Peptidoglycan Discrimination by PrkC, a Key Kinase Involved in Bacterial Resuscitation from Dormancy. J Am Chem Soc 2011; 133:20676-9. [DOI: 10.1021/ja208080r] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Flavia Squeglia
- Institute of Biostructures and
Bioimaging, Consiglio Nazionale delle Ricerche (CNR), Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Roberta Marchetti
- Department of Organic and Biological
Chemistry, University of Naples “Federico II”, Via Cinthia 4, I-80126 Napoli, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and
Bioimaging, Consiglio Nazionale delle Ricerche (CNR), Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Rosa Lanzetta
- Department of Organic and Biological
Chemistry, University of Naples “Federico II”, Via Cinthia 4, I-80126 Napoli, Italy
| | - Daniela Marasco
- Institute of Biostructures and
Bioimaging, Consiglio Nazionale delle Ricerche (CNR), Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Jonathan Dworkin
- Department of Microbiology, College
of Physicians and Surgeons, Columbia University, New York, New York 10032, United States
| | - Maxim Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse
85, 22607 Hamburg, Germany
| | - Antonio Molinaro
- Department of Organic and Biological
Chemistry, University of Naples “Federico II”, Via Cinthia 4, I-80126 Napoli, Italy
| | - Rita Berisio
- Institute of Biostructures and
Bioimaging, Consiglio Nazionale delle Ricerche (CNR), Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Alba Silipo
- Department of Organic and Biological
Chemistry, University of Naples “Federico II”, Via Cinthia 4, I-80126 Napoli, Italy
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