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Patel Y, Soni V, Rhee KY, Helmann JD. Mutations in rpoB That Confer Rifampicin Resistance Can Alter Levels of Peptidoglycan Precursors and Affect β-Lactam Susceptibility. mBio 2023; 14:e0316822. [PMID: 36779708 PMCID: PMC10128067 DOI: 10.1128/mbio.03168-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/23/2023] [Indexed: 02/14/2023] Open
Abstract
Bacteria can adapt to stressful conditions through mutations affecting the RNA polymerase core subunits that lead to beneficial changes in transcription. In response to selection with rifampicin (RIF), mutations arise in the RIF resistance-determining region (RRDR) of rpoB that reduce antibiotic binding. These changes can also alter transcription and thereby have pleiotropic effects on bacterial fitness. Here, we studied the evolution of resistance in Bacillus subtilis to the synergistic combination of RIF and the β-lactam cefuroxime (CEF). Two independent evolution experiments led to the recovery of a single rpoB allele (S487L) that was able to confer resistance to RIF and CEF through a single mutation. Two other common RRDR mutations made the cells 32 times more sensitive to CEF (H482Y) or led to only modest CEF resistance (Q469R). The diverse effects of these three mutations on CEF resistance are correlated with differences in the expression of peptidoglycan (PG) synthesis genes and in the levels of two metabolites crucial in regulating PG synthesis, glucosamine-6-phosphate (GlcN-6-P) and UDP-N-acetylglucosamine (UDP-GlcNAc). We conclude that RRDR mutations can have widely varying effects on pathways important for cell wall biosynthesis, and this may restrict the spectrum of mutations that arise during combination therapy. IMPORTANCE Rifampicin (RIF) is one of the most valued drugs in the treatment of tuberculosis. TB treatment relies on a combination therapy and for multidrug-resistant strains may include β-lactams. Mutations in rpoB present a common route for emergence of resistance to RIF. In this study, using B. subtilis as a model, we evaluate the emergence of resistance for the synergistic combination of RIF and the β-lactam cefuroxime (CEF). One clinically relevant rpoB mutation conferred resistance to both RIF and CEF, whereas one other increased CEF sensitivity. We were able to link these CEF sensitivity phenotypes to accumulation of UDP-N-acetylglucosamine (UDP-GlcNAc), which feedback regulates GlmS activity and thereby peptidoglycan synthesis. Further, we found that higher CEF concentrations precluded the emergence of high RIF resistance. Collectively, these results suggest that multidrug treatment regimens may limit the available pathways for the evolution of antibiotic resistance.
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Affiliation(s)
- Yesha Patel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Vijay Soni
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Kyu Y. Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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2
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Optimized Fast Filtration-Based Sampling and Extraction Enables Precise and Absolute Quantification of the Escherichia coli Central Carbon Metabolome. Metabolites 2023; 13:metabo13020150. [PMID: 36837769 PMCID: PMC9965072 DOI: 10.3390/metabo13020150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/07/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
Precise and accurate quantification is a prerequisite for interpretation of targeted metabolomics data, but this task is challenged by the inherent instability of the analytes. The sampling, quenching, extraction, and sample purification conditions required to recover and stabilize metabolites in representative extracts have also been proven highly dependent on species-specific properties. For Escherichia coli, unspecific leakage has been demonstrated for conventional microbial metabolomics sampling protocols. We herein present a fast filtration-based sampling protocol for this widely applied model organism, focusing on pitfalls such as inefficient filtration, selective loss of biomass, matrix contamination, and membrane permeabilization and leakage. We evaluate the effect of and need for removal of extracellular components and demonstrate how residual salts can challenge analytical accuracy of hyphenated mass spectrometric analyses, even when sophisticated correction strategies are applied. Laborious extraction procedures are bypassed by direct extraction in cold acetonitrile:water:methanol (3:5:2, v/v%), ensuring compatibility with sample concentration and thus, any downstream analysis. By applying this protocol, we achieve and demonstrate high precision and low metabolite turnover, and, followingly, minimal perturbation of the inherent metabolic state. This allows us to herein report absolute intracellular concentrations in E. coli and explore its central carbon metabolome at several commonly applied cultivation conditions.
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3
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Guo C, Zhou B, Liu Y, Niu H, Lv L, Li M. Simulation analysis and physiological and biochemical evaluation of Sophora flavescens aboveground against aphids using network pharmacology. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 189:105308. [PMID: 36549815 DOI: 10.1016/j.pestbp.2022.105308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/19/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Pests cause substantial damage to human environments; therefore, studying insecticidal mechanisms is crucial for improving pest control. However, the use of chemical pesticides can cause irreversible secondary damage. In this study, we used network pharmacology to investigate the effect of Sophora flavescens Alt., as a biological pest control agent, on glucose-6-phosphate 1-dehydrogenase, thymidylate synthase, and a translocation protein in aphids. The stability and reliability of target proteins was analyzed using molecular docking and molecular dynamic simulations. Enzyme activity assays validated the feasibility of network pharmacology to obtain actionable targets. We used interdisciplinary integration to study pest control and network pharmacology to identify how Sophora flavescens Alt. resists aphid attacks. The results show that the use of network pharmacology can increase the accuracy and specificity of our predictions for the molecules targeted by insecticides. This approach will facilitate improved, environmentally friendly pest control development in the future.
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Affiliation(s)
- Chunyan Guo
- College of Pharmacy, Qiqihar Medical University, Qiqihar, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China
| | - Baochang Zhou
- Inner Mongolia Medical University, Hohhot, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China
| | - Yibo Liu
- Inner Mongolia Medical University, Hohhot, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China
| | - Hui Niu
- Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, Baotou Medical College, Baotou, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China
| | - Lijuan Lv
- Department of Basic Science, Tianjin Agricultural University, Tianjin, China.
| | - Minhui Li
- College of Pharmacy, Qiqihar Medical University, Qiqihar, China; Inner Mongolia Medical University, Hohhot, China; Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, Baotou Medical College, Baotou, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China.
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4
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Bhayani J, Iglesias MJ, Minen RI, Cereijo AE, Ballicora MA, Iglesias AA, Asencion Diez MD. Carbohydrate Metabolism in Bacteria: Alternative Specificities in ADP-Glucose Pyrophosphorylases Open Novel Metabolic Scenarios and Biotechnological Tools. Front Microbiol 2022; 13:867384. [PMID: 35572620 PMCID: PMC9093745 DOI: 10.3389/fmicb.2022.867384] [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] [Received: 02/01/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
We explored the ability of ADP-glucose pyrophosphorylase (ADP-Glc PPase) from different bacteria to use glucosamine (GlcN) metabolites as a substrate or allosteric effectors. The enzyme from the actinobacteria Kocuria rhizophila exhibited marked and distinctive sensitivity to allosteric activation by GlcN-6P when producing ADP-Glc from glucose-1-phosphate (Glc-1P) and ATP. This behavior is also seen in the enzyme from Rhodococcus spp., the only one known so far to portray this activation. GlcN-6P had a more modest effect on the enzyme from other Actinobacteria (Streptomyces coelicolor), Firmicutes (Ruminococcus albus), and Proteobacteria (Agrobacterium tumefaciens) groups. In addition, we studied the catalytic capacity of ADP-Glc PPases from the different sources using GlcN-1P as a substrate when assayed in the presence of their respective allosteric activators. In all cases, the catalytic efficiency of Glc-1P was 1-2 orders of magnitude higher than GlcN-1P, except for the unregulated heterotetrameric protein (GlgC/GgD) from Geobacillus stearothermophilus. The Glc-1P substrate preference is explained using a model of ADP-Glc PPase from A. tumefaciens based on the crystallographic structure of the enzyme from potato tuber. The substrate-binding domain localizes near the N-terminal of an α-helix, which has a partial positive charge, thus favoring the interaction with a hydroxyl rather than a charged primary amine group. Results support the scenario where the ability of ADP-Glc PPases to use GlcN-1P as an alternative occurred during evolution despite the enzyme being selected to use Glc-1P and ATP for α-glucans synthesis. As an associated consequence in such a process, certain bacteria could have improved their ability to metabolize GlcN. The work also provides insights in designing molecular tools for producing oligo and polysaccharides with amino moieties.
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Affiliation(s)
- Jaina Bhayani
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Maria Josefina Iglesias
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Romina I Minen
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Antonela E Cereijo
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Miguel A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Alberto A Iglesias
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
| | - Matias D Asencion Diez
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, Santa Fe, Argentina
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Sugita T, Koketsu K. Transporter Engineering Enables the Efficient Production of Lacto- N-triose II and Lacto- N-tetraose in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5106-5114. [PMID: 35426313 DOI: 10.1021/acs.jafc.2c01369] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lacto-N-triose (LNT II) and lacto-N-tetraose (LNT) are human milk oligosaccharides (HMOs) with various potential functions for infants. HMO production by Escherichia coli fermentation has attracted attention in recent years. However, little is known about the cellular export of HMOs. In this study, we identified four endogenous E. coli transporter genes (setA, setB, ydeA, and mdfA), overexpression of which significantly increased the efficiency of LNT II production. The setA-enhanced strain accumulated 34.2 g/L LNT II in a 3 L bioreactor. In the production of LNT, which uses LNT II as an intermediate, disruption of setA remarkably decreased the LNT II accumulation and enhanced the titer of LNT. Furthermore, by heterologous expression of extracellular β-1,3-N-acetylglucosaminidase from Bifidobacterium bifidum, which degrades LNT II, we eliminated LNT II completely. This study shows that regulation of sugar efflux transporters in E. coli can increase the production of HMOs and decrease the amounts of undesired byproducts.
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Affiliation(s)
- Tomotoshi Sugita
- Kirin Central Research Institute, Kirin Holdings Company Limited, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Kanagawa, Japan
| | - Kento Koketsu
- Kirin Central Research Institute, Kirin Holdings Company Limited, 2-26-1, Muraoka-Higashi, Fujisawa 251-8555, Kanagawa, Japan
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6
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Aroonsri A, Kongsee J, Gunawan JD, Aubry DA, Shaw PJ. A cell-based ribozyme reporter system employing a chromosomally-integrated 5' exonuclease gene. BMC Mol Cell Biol 2021; 22:20. [PMID: 33726662 PMCID: PMC7967978 DOI: 10.1186/s12860-021-00357-7] [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] [Received: 06/26/2020] [Accepted: 02/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background Bioinformatic genome surveys indicate that self-cleaving ribonucleic acids (ribozymes) appear to be widespread among all domains of life, although the functions of only a small number have been validated by biochemical methods. Alternatively, cell-based reporter gene assays can be used to validate ribozyme function. However, reporter activity can be confounded by phenomena unrelated to ribozyme-mediated cleavage of RNA. Results We established a ribozyme reporter system in Escherichia coli in which a significant reduction of reporter activity is manifest when an active ribozyme sequence is fused to the reporter gene and the expression of a foreign Bacillus subtilis RNaseJ1 5′ exonuclease is induced from a chromosomally-integrated gene in the same cell. Conclusions The reporter system could be useful for validating ribozyme function in candidate sequences identified from bioinformatics. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00357-7.
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Affiliation(s)
- Aiyada Aroonsri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Jindaporn Kongsee
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Jeremy David Gunawan
- School of Life Science, Indonesia International Institute for Life Sciences (i3L), Jakarta, 13210, Indonesia
| | - Daniel Abidin Aubry
- School of Life Science, Indonesia International Institute for Life Sciences (i3L), Jakarta, 13210, Indonesia
| | - Philip James Shaw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
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7
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Cereijo AE, Kuhn ML, Hernández MA, Ballicora MA, Iglesias AA, Alvarez HM, Asencion Diez MD. Study of duplicated galU genes in Rhodococcus jostii and a putative new metabolic node for glucosamine-1P in rhodococci. Biochim Biophys Acta Gen Subj 2020; 1865:129727. [PMID: 32890704 DOI: 10.1016/j.bbagen.2020.129727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/11/2020] [Accepted: 08/30/2020] [Indexed: 01/10/2023]
Abstract
BACKGOUND Studying enzymes that determine glucose-1P fate in carbohydrate metabolism is important to better understand microorganisms as biotechnological tools. One example ripe for discovery is the UDP-glucose pyrophosphorylase enzyme from Rhodococcus spp. In the R. jostii genome, this gene is duplicated, whereas R. fascians contains only one copy. METHODS We report the molecular cloning of galU genes from R. jostii and R. fascians to produce recombinant proteins RjoGalU1, RjoGalU2, and RfaGalU. Substrate saturation curves were conducted, kinetic parameters were obtained and the catalytic efficiency (kcat/Km) was used to analyze enzyme promiscuity. We also investigated the response of R. jostii GlmU pyrophosphorylase activity with different sugar-1Ps, which may compete for substrates with RjoGalU2. RESULTS All enzymes were active as pyrophosphorylases and exhibited substrate promiscuity toward sugar-1Ps. Remarkably, RjoGalU2 exhibited one order of magnitude higher activity with glucosamine-1P than glucose-1P, the canonical substrate. Glucosamine-1P activity was also significant in RfaGalU. The efficient use of the phospho-amino-sugar suggests the feasibility of the reaction to occur in vivo. Also, RjoGalU2 and RfaGalU represent enzymatic tools for the production of (amino)glucosyl precursors for the putative synthesis of novel molecules. CONCLUSIONS Results support the hypothesis that partitioning of glucosamine-1P includes an uncharacterized metabolic node in Rhodococcus spp., which could be important for producing diverse alternatives for carbohydrate metabolism in biotechnological applications. GENERAL SIGNIFICANCE Results presented here provide a model to study evolutionary enzyme promiscuity, which could be used as a tool to expand an organism's metabolic repertoire by incorporating non-canonical substrates into novel metabolic pathways.
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Affiliation(s)
- A E Cereijo
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Ave., San Francisco, CA, United States
| | - M A Hernández
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina
| | - M A Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Rd., Chicago, IL 60660, United States
| | - A A Iglesias
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina
| | - H M Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP), Universidad Nacional de la Patagonia San Juan Bosco y CONICET, Km 4-Ciudad Universitaria 9000, Comodoro Rivadavia, Chubut, Argentina.
| | - M D Asencion Diez
- Instituto de Agrobiotecnología del Litoral (UNL-CONICET), Facultad de Bioquímica y Ciencias Biológicas, CCT-Santa Fe, Colectora Ruta Nac 168 km 0, 3000 Santa Fe, Argentina.
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8
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Manjunath L, Coombes D, Davies J, Dhurandhar M, Tiwari VR, Dobson RCJ, Sowdhamini R, Ramaswamy S, Bose S. Quaternary variations in the structural assembly of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella multocida. Proteins 2020; 89:81-93. [PMID: 32865821 DOI: 10.1002/prot.25996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/14/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
N-acetylglucosamine 6-phosphate deacetylase (NagA) catalyzes the conversion of N-acetylglucosamine-6-phosphate to glucosamine-6-phosphate in amino sugar catabolism. This conversion is an essential step in the catabolism of sialic acid in several pathogenic bacteria, including Pasteurella multocida, and thus NagA is identified as a potential drug target. Here, we report the unique structural features of NagA from P. multocida (PmNagA) resolved to 1.95 Å. PmNagA displays an altered quaternary architecture with unique interface interactions compared to its close homolog, the Escherichia coli NagA (EcNagA). We confirmed that the altered quaternary structure is not a crystallographic artifact using single particle electron cryo-microscopy. Analysis of the determined crystal structure reveals a set of hot-spot residues involved in novel interactions at the dimer-dimer interface. PmNagA binds to one Zn2+ ion in the active site and demonstrates kinetic parameters comparable to other bacterial homologs. Kinetic studies reveal that at high substrate concentrations (~10-fold the KM ), the tetrameric PmNagA displays hysteresis similar to its distant neighbor, the dimeric Staphylococcus aureus NagA (SaNagA). Our findings provide key information on structural and functional properties of NagA in P. multocida that could be utilized to design novel antibacterials.
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Affiliation(s)
- Lavanyaa Manjunath
- Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Tiger Circle, Manipal, Karnataka, India
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mugdha Dhurandhar
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
| | - Vikas R Tiwari
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - R Sowdhamini
- National Centre for Biological Sciences, GKVK Campus, Bangalore, Karnataka, India
| | - S Ramaswamy
- Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India
- Department of Biological Sciences and Department of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, NCBS, GKVK Campus, Bangalore, Karnataka, India
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Khan MA, Durica‐Mitic S, Göpel Y, Heermann R, Görke B. Small RNA-binding protein RapZ mediates cell envelope precursor sensing and signaling in Escherichia coli. EMBO J 2020; 39:e103848. [PMID: 32065419 PMCID: PMC7073468 DOI: 10.15252/embj.2019103848] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 11/24/2022] Open
Abstract
The RNA-binding protein RapZ cooperates with small RNAs (sRNAs) GlmY and GlmZ to regulate the glmS mRNA in Escherichia coli. Enzyme GlmS synthesizes glucosamine-6-phosphate (GlcN6P), initiating cell envelope biosynthesis. GlmZ activates glmS expression by base-pairing. When GlcN6P is ample, GlmZ is bound by RapZ and degraded through ribonuclease recruitment. Upon GlcN6P depletion, the decoy sRNA GlmY accumulates through a previously unknown mechanism and sequesters RapZ, suppressing GlmZ decay. This circuit ensures GlcN6P homeostasis and thereby envelope integrity. In this work, we identify RapZ as GlcN6P receptor. GlcN6P-free RapZ stimulates phosphorylation of the two-component system QseE/QseF by interaction, which in turn activates glmY expression. Elevated GlmY levels sequester RapZ into stable complexes, which prevents GlmZ decay, promoting glmS expression. Binding of GlmY also prevents RapZ from activating QseE/QseF, generating a negative feedback loop limiting the response. When GlcN6P is replenished, GlmY is released from RapZ and rapidly degraded. We reveal a multifunctional sRNA-binding protein that dynamically engages into higher-order complexes for metabolite signaling.
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Affiliation(s)
- Muna A Khan
- Department of Microbiology, Immunobiology and GeneticsMax Perutz LabsVienna Biocenter (VBC)University of ViennaViennaAustria
| | - Svetlana Durica‐Mitic
- Department of Microbiology, Immunobiology and GeneticsMax Perutz LabsVienna Biocenter (VBC)University of ViennaViennaAustria
| | - Yvonne Göpel
- Department of Microbiology, Immunobiology and GeneticsMax Perutz LabsVienna Biocenter (VBC)University of ViennaViennaAustria
| | - Ralf Heermann
- Microbiology and Wine ResearchInstitute for Molecular PhysiologyJohannes Gutenberg‐University MainzMainzGermany
| | - Boris Görke
- Department of Microbiology, Immunobiology and GeneticsMax Perutz LabsVienna Biocenter (VBC)University of ViennaViennaAustria
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10
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Adewumi AT, Ramharack P, Soremekun OS, Soliman MES. Delving into the Characteristic Features of "Menace" Mycobacterium tuberculosis Homologs: A Structural Dynamics and Proteomics Perspectives. Protein J 2020; 39:118-132. [PMID: 32162114 DOI: 10.1007/s10930-020-09890-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The global increase in the morbidity/mortality rate of Mycobacterial infections, predominantly renascent tuberculosis, leprosy, and Buruli ulcers have become worrisome over the years. More challenging is the incidence of resistance mediated by mutant Mycobacterium strains against front-line antitubercular drugs. Homologous to all Mycobacteria species is the GlcNAc-6-phosphate deacetylase (NagA) which catalyzes essential amino sugars synthesis required for cell wall architecture, hence, metamorphosing into an important pharmacological target for curtailing virulence and drug-resistance. This study used integrated bioinformatics methods, MD simulations, and DynaMut and PolyPhen2 to; explore unique features, monitor dynamics, and analyze the functional impact of non-synonymous single-nucleotide polymorphisms of the six NagA of most ruinous Mycobacterium species; tuberculosis (Mtb), smegmatis (MS), marinum (MM), ulcerans, africanum, and microti respectively. This approach is essential for multi-targeting and could result in the identification of potential polypharmacological antitubercular compounds. Comparative sequential analyses revealed ≤ 50% of the overall structure, including the catalytic Asp267 and reactive Cys131, remained conserved. Interestingly, MS-NagA and MM-NagA possess unique hydrophobic isoleucine (Ile) residues at their active sites in contrast to leucine (Leu) found in other variants. More so, unique to the active sites of the NagA is a 'subunit loop' that covers the active site; probably crucial in binding (entry and exit) mechanisms of targeted NagA inhibitors. Relatively, nsSNP mutations exerted a destabilizing effect on the native NagA conformation. Structural and dynamical insights provided, basically pin-pointed the "Achilles' heel" explorable for the rational drug design of target-specific 'NagA' inhibitors potent against a wide range of mycobacterial diseases.
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Affiliation(s)
- Adeniyi T Adewumi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Pritika Ramharack
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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11
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Fernandez M, Plumbridge J. Complex synergistic amino acid-nucleotide interactions contribute to the specificity of NagC operator recognition and induction. MICROBIOLOGY-SGM 2019; 165:792-803. [PMID: 31107208 DOI: 10.1099/mic.0.000814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
NagC is a transcription factor that represses genes involved in N-acetylglucosamine catabolism in Escherichia coli. Repression by NagC is relieved by interaction with GlcNAc6P, the product of transport of GlcNAc into the cell. The DNA-binding domain of NagC contains a classic helix-turn-helix (HTH) motif, but specific operator recognition requires, in addition, an adjacent linker sequence, which is thought to form an extended wing. Sequences in the linker region are required to distinguish NagC-binding sites from those of its paralogue, Mlc. In investigating the contribution of the HTH to operator recognition, we have identified mutations in the first two positions of the recognition helix of the DNA-binding motif of NagC, which change NagC from being a repressor, which binds in the absence of the inducing signal (GlcNAc6P), to one whose binding is enhanced by GlcNAc6P. In this case GlcNAc6P behaves as a co-repressor rather than an inducer for NagC. The NagC mutants exhibiting this paradoxical behaviour have basic amino acids, arginine or lysine, at two critical positions of the recognition helix. Introducing a third amino acid change converts NagC back to a protein, which represses in the absence of GlcNAc6P. The triple mutant also effectively represses a modified NagC operator that is not repressed by wild-type NagC, showing that this form of NagC is a more promiscuous DNA binder. Specific recognition of the NagC operator thus involves a modulation of basic amino acid-DNA interactions, which affects the ability to discriminate against other permissive sites.
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Affiliation(s)
- Marion Fernandez
- UMR8261,CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13, rue P. et M. Curie, 75005 Paris, France
| | - Jacqueline Plumbridge
- UMR8261,CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13, rue P. et M. Curie, 75005 Paris, France
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12
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Davies JS, Coombes D, Horne CR, Pearce FG, Friemann R, North RA, Dobson RCJ. Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus. FEBS Lett 2018; 593:52-66. [PMID: 30411345 DOI: 10.1002/1873-3468.13289] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/13/2022]
Abstract
N-Acetylglucosamine-6-phosphate deacetylase (NagA) and glucosamine-6-phosphate deaminase (NagB) are branch point enzymes that direct amino sugars into different pathways. For Staphylococcus aureus NagA, analytical ultracentrifugation and small-angle X-ray scattering data demonstrate that it is an asymmetric dimer in solution. Initial rate experiments show hysteresis, which may be related to pathway regulation, and kinetic parameters similar to other bacterial isozymes. The enzyme binds two Zn2+ ions and is not substrate inhibited, unlike the Escherichia coli isozyme. S. aureus NagB adopts a novel dimeric structure in solution and shows kinetic parameters comparable to other Gram-positive isozymes. In summary, these functional data and solution structures are of use for understanding amino sugar metabolism in S. aureus, and will inform the design of inhibitory molecules.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - David Coombes
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rosmarie Friemann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Sweden
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Chemistry and Molecular Biology, University of Gothenburg, Sweden
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
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13
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van der Ark KCH, Aalvink S, Suarez-Diez M, Schaap PJ, de Vos WM, Belzer C. Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation. Microb Biotechnol 2018; 11:476-485. [PMID: 29377524 PMCID: PMC5902328 DOI: 10.1111/1751-7915.13033] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 02/04/2023] Open
Abstract
The abundance of the human intestinal symbiont Akkermansia muciniphila has found to be inversely correlated with several diseases, including metabolic syndrome and obesity. A. muciniphila is known to use mucin as sole carbon and nitrogen source. To study the physiology and the potential for therapeutic applications of this bacterium, we designed a defined minimal medium. The composition of the medium was based on the genome‐scale metabolic model of A. muciniphila and the composition of mucin. Our results indicate that A. muciniphila does not code for GlmS, the enzyme that mediates the conversion of fructose‐6‐phosphate (Fru6P) to glucosamine‐6‐phosphate (GlcN6P), which is essential in peptidoglycan formation. The only annotated enzyme that could mediate this conversion is Amuc‐NagB on locus Amuc_1822. We found that Amuc‐NagB was unable to form GlcN6P from Fru6P at physiological conditions, while it efficiently catalyzed the reverse reaction. To overcome this inability, N‐acetylglucosamine needs to be present in the medium for A. muciniphila growth. With these findings, the genome‐scale metabolic model was updated and used to accurately predict growth of A. muciniphila on synthetic media. The finding that A. muciniphila has a necessity for GlcNAc, which is present in mucin further prompts the adaptation to its mucosal niche.
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Affiliation(s)
- Kees C H van der Ark
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Department of Bacteriology and Immunology, RPU Immunobiology, University of Helsinki, Haartmanikatu 4, 002940, Helsinki, Finland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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14
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Rodionova IA, Zhang Z, Mehla J, Goodacre N, Babu M, Emili A, Uetz P, Saier MH. The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli. J Biol Chem 2017. [PMID: 28634232 DOI: 10.1074/jbc.m117.795294] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The histidine-phosphorylatable phosphocarrier protein (HPr) is an essential component of the sugar-transporting phosphotransferase system (PTS) in many bacteria. Recent interactome findings suggested that HPr interacts with several carbohydrate-metabolizing enzymes, but whether HPr plays a regulatory role was unclear. Here, we provide evidence that HPr interacts with a large number of proteins in Escherichia coli We demonstrate HPr-dependent allosteric regulation of the activities of pyruvate kinase (PykF, but not PykA), phosphofructokinase (PfkB, but not PfkA), glucosamine-6-phosphate deaminase (NagB), and adenylate kinase (Adk). HPr is either phosphorylated on a histidyl residue (HPr-P) or non-phosphorylated (HPr). PykF is activated only by non-phosphorylated HPr, which decreases the PykF Khalf for phosphoenolpyruvate by 10-fold (from 3.5 to 0.36 mm), thus influencing glycolysis. PfkB activation by HPr, but not by HPr-P, resulted from a decrease in the Khalf for fructose-6-P, which likely influences both gluconeogenesis and glycolysis. Moreover, NagB activation by HPr was important for the utilization of amino sugars, and allosteric inhibition of Adk activity by HPr-P, but not by HPr, allows HPr to regulate the cellular energy charge coordinately with glycolysis. These observations suggest that HPr serves as a directly interacting global regulator of carbon and energy metabolism and probably of other physiological processes in enteric bacteria.
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Affiliation(s)
- Irina A Rodionova
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116
| | - Zhongge Zhang
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116
| | - Jitender Mehla
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Norman Goodacre
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Andrew Emili
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Milton H Saier
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116,.
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15
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Skarbek K, Gabriel I, Szweda P, Wojciechowski M, Khan MA, Görke B, Milewski S, Milewska MJ. Synthesis and antimicrobial activity of 6-sulfo-6-deoxy-D-glucosamine and its derivatives. Carbohydr Res 2017. [PMID: 28628891 DOI: 10.1016/j.carres.2017.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
6-Sulfo-6-deoxy-D-glucosamine (GlcN6S), 6-sulfo-6-deoxy-D-glucosaminitol (ADGS) and their N-acetyl and methyl ester derivatives have been synthesized and tested as inhibitors of enzymes catalyzing reactions of the UDP-GlcNAc pathway in bacteria and yeasts. GlcN6S and ADGS at micromolar concentrations inhibited glucosamine-6-phosphate (GlcN6P) synthase of microbial origin. The former was also inhibitory towards fungal GlcN6P N-acetyl transferase, but at millimolar concentrations. Both compounds and their N-acetyl derivatives exhibited antimicrobial in vitro activity, with MICs in the 0.125-2.0 mg mL-1 range. Antibacterial but not antifungal activity of GlcN6S was potentiated by D-glucosamine and a synergistic antibacterial effect was observed for combination of ADGP and a dipeptide Nva-FMDP.
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Affiliation(s)
- Kornelia Skarbek
- Department of Organic Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Iwona Gabriel
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Marek Wojciechowski
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Muna A Khan
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Sławomir Milewski
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland.
| | - Maria J Milewska
- Department of Organic Chemistry, Gdańsk University of Technology, Gdańsk, Poland
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