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Li H, Chen S, Wang M, Shi S, Zhao W, Xiong G, Zhou J, Qu J. Phosphate solubilization and plant growth properties are promoted by a lactic acid bacterium in calcareous soil. Appl Microbiol Biotechnol 2024; 108:24. [PMID: 38159115 DOI: 10.1007/s00253-023-12850-4] [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: 05/04/2023] [Revised: 09/19/2023] [Accepted: 10/03/2023] [Indexed: 01/03/2024]
Abstract
On the basis of good phosphate solubilization ability of a lactic acid bacteria (LAB) strain Limosilactobacillus sp. LF-17, bacterial agent was prepared and applied to calcareous soil to solubilize phosphate and promote the growth of maize seedlings in this study. A pot experiment showed that the plant growth indicators, phosphorus content, and related enzyme activity of the maize rhizospheric soils in the LF treatment (treated with LAB) were the highest compared with those of the JP treatment (treated with phosphate solubilizing bacteria, PSB) and the blank control (CK). The types of organic acids in maize rhizospheric soil were determined through LC-MS, and 12 acids were detected in all the treatments. The abundant microbes belonged to the genera of Lysobacter, Massilia, Methylbacillus, Brevundimonas, and Limosilactobacillus, and they were beneficial to dissolving phosphate or secreting growth-promoting phytohormones, which were obviously higher in the LF and JP treatments than in CK as analyzed by high-throughput metagenomic sequencing methods. In addition, the abundance values of several enzymes, Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology, and Carbohydrate-Active Enzymes (CAZys), which were related to substrate assimilation and metabolism, were the highest in the LF treatment. Therefore, aside from phosphate-solubilizing microorganisms, LAB can be used as environmentally friendly crop growth promoters in agriculture and provide another viable option for microbial fertilizers. KEY POINTS: • The inoculation of LAB strain effectively promoted the growth and chlorophyll synthesis of maize seedlings. • The inoculation of LAB strain significantly increased the TP content of maize seedlings and the AP concentration of the rhizosphere soil. • The inoculation of LAB strain increased the abundances of the dominant beneficial functional microbes in the rhizosphere soil.
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Affiliation(s)
- Haifeng Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China.
| | - Siyuan Chen
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Mengyu Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Shuoshuo Shi
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Wenjian Zhao
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Guoyang Xiong
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Jia Zhou
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Jianhang Qu
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
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2
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Ichioka R, Kitazawa Y, Taguchi G, Shimosaka M. A novel N-acetylglucosamine-6-phosphate deacetylase that is essential for chitin utilization in the chitinolytic bacterium, Chitiniphilus shinanonensis. J Appl Microbiol 2024; 135:lxae117. [PMID: 38724455 DOI: 10.1093/jambio/lxae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
AIMS We aimed to investigate the function of an unidentified gene annotated as a PIG-L domain deacetylase (cspld) in Chitiniphilus shinanonensis SAY3. cspld was identified using transposon mutagenesis, followed by negatively selecting a mutant incapable of growing on chitin, a polysaccharide consisting of N-acetyl-d-glucosamine (GlcNAc). We focused on the physiological role of CsPLD protein in chitin utilization. METHODS AND RESULTS Recombinant CsPLD expressed in Escherichia coli exhibited GlcNAc-6-phosphate deacetylase (GPD) activity, which is involved in the metabolism of amino sugars. However, SAY3 possesses two genes (csnagA1 and csnagA2) in its genome that code for proteins whose primary sequences are homologous to those of typical GPDs. Recombinant CsNagA1 and CsNagA2 also exhibited GPD activity with 23 and 1.6% of catalytic efficiency (kcat/Km), respectively, compared to CsPLD. The gene-disrupted mutant, Δcspld was unable to grow on chitin or GlcNAc, whereas the three mutants, ΔcsnagA1, ΔcsnagA2, and ΔcsnagA1ΔcsnagA2 grew similarly to SAY3. The determination of GPD activity in the crude extracts of each mutant revealed that CsPLD is a major enzyme that accounts for almost all cellular activities. CONCLUSIONS Deacetylation of GlcNAc-6P catalyzed by CsPLD (but not by typical GPDs) is essential for the assimilation of chitin and its constituent monosaccharide, GlcNAc, as a carbon and energy source in C. shinanonensis.
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Affiliation(s)
- Ryotaro Ichioka
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano 386-8567, Japan
| | - Yuri Kitazawa
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano 386-8567, Japan
| | - Goro Taguchi
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano 386-8567, Japan
| | - Makoto Shimosaka
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano 386-8567, Japan
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3
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Mycroft-West CJ, Abdelkarim S, Duyvesteyn HME, Gandhi NS, Skidmore MA, Owens RJ, Wu L. Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1. Nat Commun 2024; 15:1326. [PMID: 38351061 PMCID: PMC10864358 DOI: 10.1038/s41467-024-45419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Heparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, non-templated patterns of sulfation and epimerization, which mediate interactions with diverse protein partners. Complex HS modifications form around initial clusters of glucosamine-N-sulfate (GlcNS) on nascent polysaccharide chains, but the mechanistic basis underpinning incorporation of GlcNS itself into HS remains unclear. Here, we determine cryo-electron microscopy structures of human N-deacetylase-N-sulfotransferase (NDST)1, the bifunctional enzyme primarily responsible for initial GlcNS modification of HS. Our structures reveal the architecture of both NDST1 deacetylase and sulfotransferase catalytic domains, alongside a non-catalytic N-terminal domain. The two catalytic domains of NDST1 adopt a distinct back-to-back topology that limits direct cooperativity. Binding analyses, aided by activity-modulating nanobodies, suggest that anchoring of the substrate at the sulfotransferase domain initiates the NDST1 catalytic cycle, providing a plausible mechanism for cooperativity despite spatial domain separation. Our data shed light on key determinants of NDST1 activity, and describe tools to probe NDST1 function in vitro and in vivo.
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Affiliation(s)
| | - Sahar Abdelkarim
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK
| | - Neha S Gandhi
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- School of Chemistry and Physics, Queensland University of Technology, QLD 4000, Brisbane, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Mark A Skidmore
- Centre for Glycoscience Research and Training, Keele University, ST5 5BG, Newcastle-Under-Lyme, UK
| | - Raymond J Owens
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK
| | - Liang Wu
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK.
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4
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Kamal El-Sagheir AM, Abdelmesseh Nekhala I, Abd El-Gaber MK, Aboraia AS, Persson J, Schäfer AB, Wenzel M, Omar FA. Rational design, synthesis, molecular modeling, biological activity, and mechanism of action of polypharmacological norfloxacin hydroxamic acid derivatives. RSC Med Chem 2023; 14:2593-2610. [PMID: 38099058 PMCID: PMC10718593 DOI: 10.1039/d3md00309d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 12/17/2023] Open
Abstract
Fluoroquinolones are broad-spectrum antibiotics that target gyrase and topoisomerase IV, involved in DNA compaction and segregation. We synthesized 28 novel norfloxacin hydroxamic acid derivatives with additional metal-chelating and hydrophobic pharmacophores, designed to enable interactions with additional drug targets. Several compounds showed equal or better activity than norfloxacin against Gram-positive, Gram-negative, and mycobacteria, with MICs as low as 0.18 μM. The most interesting derivatives were selected for in silico, in vitro, and in vivo mode of action studies. Molecular docking, enzyme inhibition, and bacterial cytological profiling confirmed inhibition of gyrase and topoisomerase IV for all except two tested derivatives (10f and 11f). Further phenotypic analysis revealed polypharmacological effects on peptidoglycan synthesis for four derivatives (16a, 17a, 17b, 20b). Interestingly, compounds 17a, 17b, and 20b, showed never seen before effects on cell wall synthetic enzymes, including MreB, MurG, and PonA, suggesting a novel mechanism of action, possibly impairing the lipid II cycle.
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Affiliation(s)
| | - Ireny Abdelmesseh Nekhala
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
| | | | - Ahmed S Aboraia
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
| | - Jonatan Persson
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Ann-Britt Schäfer
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Farghaly A Omar
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
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5
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Kamal El-sagheir A, Abdelmesseh Nekhala I, Abd El-Gaber MK, Aboraia AS, Persson J, Schäfer AB, Wenzel M, Omar FA. Design, Synthesis, Molecular Modeling, Biological Activity, and Mechanism of Action of Novel Amino Acid Derivatives of Norfloxacin. ACS OMEGA 2023; 8:43271-43284. [PMID: 38024743 PMCID: PMC10653056 DOI: 10.1021/acsomega.3c07221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Two series of N4-substituted piperazinyl amino acid derivatives of norfloxacin (24 new compounds) were designed and synthesized to attain structural surrogates with additional binding sites and enhanced antibacterial activity. Synthesized derivatives showed increased antibacterial and antimycobacterial activity compared to their lead structure, norfloxacin. Molecular modeling studies supported the notion that the derivatives can establish additional bonds with the target enzymes gyrase and topoisomerase IV. In vitro enzyme inhibition assays confirmed that the tested compounds were significant inhibitors of these enzymes. Inhibition of gyrase and topoisomerase IV was then confirmed in living bacterial cells using bacterial cytological profiling of both Gram-negative Escherichia coli and Gram-positive Bacillus subtilis, revealing a typical topoisomerase inhibition phenotype characterized by severe nucleoid packing defects. Several derivatives exhibited additional effects on the Gram-positive cell wall synthesis machinery and/or the cytoplasmic membrane, which likely contributed to their increased antibacterial activity. While we could not identify specific cell wall or membrane targets, membrane depolarization was not observed. Our experiments further suggest that cell wall synthesis inhibition most likely occurs outside the membrane-bound lipid II cycle.
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Affiliation(s)
| | - Ireny Abdelmesseh Nekhala
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | | | - Ahmed S. Aboraia
- Medicinal
Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Jonatan Persson
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg 405 30, Sweden
| | - Ann-Britt Schäfer
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg 405 30, Sweden
| | - Michaela Wenzel
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Center
for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg 405 30, Sweden
| | - Farghaly A. Omar
- Medicinal
Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
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6
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Peng Y, Xu P, Tao F. Production of N-acetylglucosamine with Vibrio alginolyticus FA2, an emerging platform for economical unsterile open fermentation. Synth Syst Biotechnol 2023; 8:546-554. [PMID: 37637200 PMCID: PMC10457514 DOI: 10.1016/j.synbio.2023.08.003] [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: 06/20/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Members of the Vibrionaceae family are predominantly fast-growing and halophilic microorganisms that have captured the attention of researchers owing to their potential applications in rapid biotechnology. Among them, Vibrio alginolyticus FA2 is a particularly noteworthy halophilic bacterium that exhibits superior growth capability. It has the potential to serve as a biotechnological platform for sustainable and eco-friendly open fermentation with seawater. To evaluate this hypothesis, we integrated the N-acetylglucosamine (GlcNAc) pathway into V. alginolyticus FA2. Seven nag genes were knocked out to obstruct the utilization of GlcNAc, and then 16 exogenous gna1s co-expressing with EcglmS were introduced to strengthen the flux of GlcNAc pathway, respectively. To further enhance GlcNAc production, we fine-tuned promoter strength of the two genes and inactivated two genes alsS and alsD to prevent the production of acetoin. Furthermore, unsterile open fermentation was carried out using simulated seawater and a chemically defined medium, resulting in the production of 9.2 g/L GlcNAc in 14 h. This is the first report for de-novo synthesizing GlcNAc with a Vibrio strain, facilitated by an unsterile open fermentation process employing seawater as a substitute for fresh water. This development establishes a basis for production of diverse valuable chemicals using Vibrio strains and provides insights into biomanufacture.
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Affiliation(s)
- Yuan Peng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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7
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Qi L, Shi M, Zhu FC, Lian CA, He LS. Genomic evidence for the first symbiotic Deferribacterota, a novel gut symbiont from the deep-sea hydrothermal vent shrimp Rimicaris kairei. Front Microbiol 2023; 14:1179935. [PMID: 37455748 PMCID: PMC10344455 DOI: 10.3389/fmicb.2023.1179935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
The genus Rimicaris is the dominant organism living in hydrothermal vents. However, little research has been done on the functions of their intestinal flora. Here, we investigated the potential functions of Deferribacterota, which is dominant in the intestine of Rimicaris kairei from the Central Indian Ridge. In total, six metagenome-assembled genomes (MAGs) of Deferribacterota were obtained using the metagenomic approach. The six Deferribacterota MAGs (Def-MAGs) were clustered into a new branch in the phylogenetic tree. The six Def-MAGs were further classified into three species, including one new order and two new genera, based on the results of phylogenetic analysis, relative evolutionary divergence (RED), average nucleotide identity (ANI), average amino acid identity (AAI) and DNA-DNA hybridization (DDH) values. The results of the energy metabolism study showed that these bacteria can use a variety of carbon sources, such as glycogen, sucrose, salicin, arbutin, glucose, cellobiose, and maltose. These bacteria have a type II secretion system and effector proteins that can transport some intracellular toxins to the extracellular compartment and a type V CRISPR-Cas system that can defend against various invasions. In addition, cofactors such as biotin, riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) synthesized by R. kairei gut Deferribacterota may also assist their host in surviving under extreme conditions. Taken together, the potential function of Deferribacterota in the hydrothermal R. kairei gut suggests its long-term coevolution with the host.
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Affiliation(s)
- Li Qi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengke Shi
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fang-Chao Zhu
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Chun-Ang Lian
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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8
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Zeng H, Cheng M, Liu J, Hu C, Lin S, Cui R, Li H, Ye W, Wang L, Huang W. Pyrimirhodomyrtone inhibits Staphylococcus aureus by affecting the activity of NagA. Biochem Pharmacol 2023; 210:115455. [PMID: 36780990 DOI: 10.1016/j.bcp.2023.115455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]
Abstract
The epidemic of methicillin-resistant Staphylococcus aureus (MRSA) infections has created a critical health threat. The drug resistance of MRSA makes the development of drugs with new modes of action particularly urgent. In this study, we found that a natural product derivative pyrimirhodomyrtone (PRM) exerted antibacterial activity against S. aureus, including MRSA, both in vitro and in vivo. Genetic and biochemical studies revealed the interaction between PRM and N-acetylglucosamine-6-phosphate deacetylase (NagA) and the inhibitory effect of PRM on its deacetylation activity. We also found that PRM causes depolarization and destroys the integrity of the cell membrane. The elucidation of the antibacterial mechanism will inspire the subsequent development of new anti-MRSA drugs based on PRM.
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Affiliation(s)
- Huan Zeng
- Center for Bioactive Natural Molecules and Innovative Drugs Research, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 511443, Guangdong, China; Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Minjing Cheng
- Center for Bioactive Natural Molecules and Innovative Drugs Research, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 511443, Guangdong, China
| | - Jingyi Liu
- Department of Microbiology and Biochemical Pharmacy, National Engineering Research Center of Immunological Products, College of Pharmacy, Third Military Medical University, Chongqing 400038, China
| | - Chunxia Hu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Shilin Lin
- Center for Bioactive Natural Molecules and Innovative Drugs Research, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 511443, Guangdong, China
| | - Ruiqin Cui
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China
| | - Haibo Li
- Department of Microbiology and Biochemical Pharmacy, National Engineering Research Center of Immunological Products, College of Pharmacy, Third Military Medical University, Chongqing 400038, China.
| | - Wencai Ye
- Center for Bioactive Natural Molecules and Innovative Drugs Research, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 511443, Guangdong, China.
| | - Lei Wang
- Center for Bioactive Natural Molecules and Innovative Drugs Research, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 511443, Guangdong, China.
| | - Wei Huang
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China; Department of Clinical Microbiology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China.
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9
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Grāve K, Bennett MD, Högbom M. High-throughput strategy for identification of Mycobacterium tuberculosis membrane protein expression conditions using folding reporter GFP. Protein Expr Purif 2022; 198:106132. [PMID: 35750296 DOI: 10.1016/j.pep.2022.106132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 10/18/2022]
Abstract
Mycobacterium tuberculosis membrane protein biochemistry and structural biology studies are often hampered by challenges in protein expression and selection for well-expressing protein candidates, suitable for further investigation. Here we present a folding reporter GFP (frGFP) assay, adapted for M. tuberculosis membrane protein screening in Escherichia coli Rosetta 2 (DE3) and Mycobacterium smegmatis mc [2]4517. This method allows protein expression condition screening for multiple protein targets simultaneously by monitoring frGFP fluorescence in growing cells. We discuss the impact of common protein expression conditions on 42 essential M. tuberculosis H37Rv helical transmembrane proteins and establish the grounds for their further analysis. We have found that the basal expression of the lac operon in the T7-promoter expression system generally leads to high recombinant protein yield in M. smegmatis, and we suggest that a screening condition without the inducer is included in routine protein expression tests. In addition to the general observations, we describe conditions allowing high-level expression of more than 25 essential M. tuberculosis membrane proteins, containing 2 to 13 transmembrane helices. We hope that these findings will stimulate M. tuberculosis membrane protein research and aid the efforts in drug development against tuberculosis.
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Affiliation(s)
- Kristīne Grāve
- Department of Biochemistry and Biophysics, Stockholm University. Svante Arrhenius väg 16C, SE-10691, Stockholm, Sweden
| | - Matthew D Bennett
- Department of Biochemistry and Biophysics, Stockholm University. Svante Arrhenius väg 16C, SE-10691, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University. Svante Arrhenius väg 16C, SE-10691, Stockholm, Sweden.
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10
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Kumar S, Bansal K, Sethi SK. Comparative genomics analysis of genus Leuconostoc resolves its taxonomy and elucidates its biotechnological importance. Food Microbiol 2022; 106:104039. [DOI: 10.1016/j.fm.2022.104039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 04/04/2022] [Accepted: 04/12/2022] [Indexed: 11/27/2022]
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11
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Kroef V, Ruegenberg S, Horn M, Allmeroth K, Ebert L, Bozkus S, Miethe S, Elling U, Schermer B, Baumann U, Denzel MS. GFPT2/GFAT2 and AMDHD2 act in tandem to control the hexosamine pathway. eLife 2022; 11:69223. [PMID: 35229715 PMCID: PMC8970586 DOI: 10.7554/elife.69223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 02/28/2022] [Indexed: 11/25/2022] Open
Abstract
The hexosamine biosynthetic pathway (HBP) produces the essential metabolite UDP-GlcNAc and plays a key role in metabolism, health, and aging. The HBP is controlled by its rate-limiting enzyme glutamine fructose-6-phosphate amidotransferase (GFPT/GFAT) that is directly inhibited by UDP-GlcNAc in a feedback loop. HBP regulation by GFPT is well studied but other HBP regulators have remained obscure. Elevated UDP-GlcNAc levels counteract the glycosylation toxin tunicamycin (TM), and thus we screened for TM resistance in haploid mouse embryonic stem cells (mESCs) using random chemical mutagenesis to determine alternative HBP regulation. We identified the N-acetylglucosamine deacetylase AMDHD2 that catalyzes a reverse reaction in the HBP and its loss strongly elevated UDP-GlcNAc. To better understand AMDHD2, we solved the crystal structure and found that loss-of-function (LOF) is caused by protein destabilization or interference with its catalytic activity. Finally, we show that mESCs express AMDHD2 together with GFPT2 instead of the more common paralog GFPT1. Compared with GFPT1, GFPT2 had a much lower sensitivity to UDP-GlcNAc inhibition, explaining how AMDHD2 LOF resulted in HBP activation. This HBP configuration in which AMDHD2 serves to balance GFPT2 activity was also observed in other mESCs and, consistently, the GFPT2:GFPT1 ratio decreased with differentiation of human embryonic stem cells. Taken together, our data reveal a critical function of AMDHD2 in limiting UDP-GlcNAc production in cells that use GFPT2 for metabolite entry into the HBP.
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Affiliation(s)
- Virginia Kroef
- Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Sabine Ruegenberg
- Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Kira Allmeroth
- Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | | | - Stephan Miethe
- Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ulrich Elling
- Vienna Biocenter, Austrian Academy of Sciences, Vienna, Austria
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12
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Graham CLB, Newman H, Gillett FN, Smart K, Briggs N, Banzhaf M, Roper DI. A Dynamic Network of Proteins Facilitate Cell Envelope Biogenesis in Gram-Negative Bacteria. Int J Mol Sci 2021; 22:12831. [PMID: 34884635 PMCID: PMC8657477 DOI: 10.3390/ijms222312831] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteria must maintain the ability to modify and repair the peptidoglycan layer without jeopardising its essential functions in cell shape, cellular integrity and intermolecular interactions. A range of new experimental techniques is bringing an advanced understanding of how bacteria regulate and achieve peptidoglycan synthesis, particularly in respect of the central role played by complexes of Sporulation, Elongation or Division (SEDs) and class B penicillin-binding proteins required for cell division, growth and shape. In this review we highlight relationships implicated by a bioinformatic approach between the outer membrane, cytoskeletal components, periplasmic control proteins, and cell elongation/division proteins to provide further perspective on the interactions of these cell division, growth and shape complexes. We detail the network of protein interactions that assist in the formation of peptidoglycan and highlight the increasingly dynamic and connected set of protein machinery and macrostructures that assist in creating the cell envelope layers in Gram-negative bacteria.
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Affiliation(s)
- Chris L. B. Graham
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Hector Newman
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Francesca N. Gillett
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - Katie Smart
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Nicholas Briggs
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
| | - Manuel Banzhaf
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK;
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; (C.L.B.G.); (H.N.); (F.N.G.); (K.S.); (N.B.)
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13
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Synthesis and recycling of the mycobacterial cell envelope. Curr Opin Microbiol 2021; 60:58-65. [PMID: 33610125 PMCID: PMC8035080 DOI: 10.1016/j.mib.2021.01.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 02/07/2023]
Abstract
The unique mycobacterial cell wall is a layered structure of carbohydrates and lipids. The architecture and biosynthesis of the cell wall have largely been elucidated. Increasing evidence indicates that each cell wall layer is remodelled and recycled. There are opportunities to discover new essential enzymes in cell wall metabolism. Cell wall metabolism is a validated source of targets for tuberculosis drug discovery.
Mycobacterium tuberculosis (Mtb), the causative agent of the disease tuberculosis, is a recognised global health concern. The efficacy of the current treatment regime is under threat due to the emergence of antibiotic resistance, directing an urgent requirement for the discovery of new anti-tubercular agents and drug targets. The mycobacterial cell wall is a well-validated drug target for Mtb and is composed of three adaptive macromolecular structures, peptidoglycan, arabinogalactan and mycolic acids, an array of complex lipids and carbohydrates. The majority of the enzymes involved in cell wall synthesis have been established, whilst studies directed towards the mechanisms of remodelling and recycling have been neglected. This review briefly describes mycobacterial cell wall synthesis, and focuses on aspects of remodelling and recycling, thus highlighting opportunities for future research.
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14
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Adewumi AT, Elrashedy A, Soremekun OS, Ajadi MB, Soliman MES. Weak spots inhibition in the Mycobacterium tuberculosis antigen 85C target for antitubercular drug design through selective irreversible covalent inhibitor-SER124. J Biomol Struct Dyn 2020; 40:2934-2954. [PMID: 33155529 DOI: 10.1080/07391102.2020.1844061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis (Mtb) encoded secreted antigen 85 enzymes (Ag85A/Ag85B/Ag85C) play that critical roles in the virulence, survival and drug-resistant TB of the pathogen. Ag85 proteins are potential antitubercular drug targets because they are essential in the catalytic synthesis of trehalose moieties and mycolic acid attachment to the Mtb cell wall. Recently, experimental protocols led to the discovery of a selective covalent Ag85 inhibitor, β-isomer monocyclic enolphosphorus Cycliphostin (CyC8β) compound, which targets the Ag85 serine 124 to exhibit a promising therapeutic activity. For the first time, our study unravelled the structural features among Mtb Ag85C homologs and motions and dynamics of Ag85C when the CyC8β bound covalently and in open model conformations to the protein using bioinformatics tools and integrated Molecular dynamics simulations. Comparative Ag85C sequence analysis revealed conserved regions; 70% active site, 90% Adeniyi loop L1 and 50% loop L2, which acts as a switch between open and closed conformations. The average C-α atoms RMSD (2.05 Å) and RMSF (0.9 Å) revealed instability and high induced flexibility in the CyC8β covalent-bound compared to the apo and open model systems, which displayed more stability and lower fluctuations. DSSP showed structural transitions of α-helices to bend and loops to 310-helices in the bound systems. SASA of CyC8β covalent bound showed active site hydrophobic residues exposure to huge solvent. Therefore, these findings present the potential opportunity hotspots in Ag85C protein that would aid the structure-based design of novel chemical entities capable of resulting in potent antitubercular drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adeniyi T Adewumi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ahmed Elrashedy
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mary B Ajadi
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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15
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Pascual S, Planas A. Carbohydrate de-N-acetylases acting on structural polysaccharides and glycoconjugates. Curr Opin Chem Biol 2020; 61:9-18. [PMID: 33075728 DOI: 10.1016/j.cbpa.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022]
Abstract
Deacetylation of N-acetylhexosamine residues in structural polysaccharides and glycoconjugates is catalyzed by different families of carbohydrate esterases that, despite different structural folds, share a common metal-assisted acid/base mechanism with the metal cation coordinated with a conserved Asp-His-His triad. These enzymes serve diverse biological functions in the modification of cell-surface polysaccharides in bacteria and fungi as well as in the metabolism of hexosamines in the biosynthesis of cellular glycoconjugates. Focusing on carbohydrate de-N-acetylases, this article summarizes the background of the different families from a structural and functional viewpoint and covers advances in the characterization of novel enzymes over the last 2-3 years. Current research is addressed to the identification of new deacetylases and unravel their biological functions as they are candidate targets for the design of antimicrobials against pathogenic bacteria and fungi. Likewise, some families are also used as biocatalysts for the production of defined glycostructures with diverse applications.
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Affiliation(s)
- Sergi Pascual
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017, Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017, Barcelona, Spain.
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16
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Beckham KSH, Staack S, Wilmanns M, Parret AHA. The pMy vector series: A versatile cloning platform for the recombinant production of mycobacterial proteins in Mycobacterium smegmatis. Protein Sci 2020; 29:2528-2537. [PMID: 33006405 PMCID: PMC7679961 DOI: 10.1002/pro.3962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 12/16/2022]
Abstract
Structural and biophysical characterization of molecular mechanisms of disease‐causing pathogens, such as Mycobacterium tuberculosis, often requires recombinant expression of large amounts highly pure protein. For the production of mycobacterial proteins, overexpression in the fast‐growing and non‐pathogenic species Mycobacterium smegmatis has several benefits over the standard Escherichia coli expression strains. However, unlike for E. coli, the range of expression vectors currently available is limited. Here we describe the development of the pMy vector series, a set of expression plasmids for recombinant production of single proteins and protein complexes in M. smegmatis. By incorporating an alternative selection marker, we show that these plasmids can also be used for co‐expression studies. All vectors in the pMy vector series are available in the Addgene repository (www.addgene.com).
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Affiliation(s)
| | - Sonja Staack
- Hamburg Unit, European Molecular Biology Laboratory, Hamburg, Germany
| | - Matthias Wilmanns
- Hamburg Unit, European Molecular Biology Laboratory, Hamburg, Germany.,University Hamburg Clinical Centre Hamburg-Eppendorf, Hamburg, Germany
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17
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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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18
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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19
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Shaku M, Ealand C, Matlhabe O, Lala R, Kana BD. Peptidoglycan biosynthesis and remodeling revisited. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:67-103. [PMID: 32762868 DOI: 10.1016/bs.aambs.2020.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The bacterial peptidoglycan layer forms a complex mesh-like structure that surrounds the cell, imparting rigidity to withstand cytoplasmic turgor and the ability to tolerate stress. As peptidoglycan has been the target of numerous clinically successful antimicrobials such as penicillin, the biosynthesis, remodeling and recycling of this polymer has been the subject of much interest. Herein, we review recent advances in the understanding of peptidoglycan biosynthesis and remodeling in a variety of different organisms. In order for bacterial cells to grow and divide, remodeling of cross-linked peptidoglycan is essential hence, we also summarize the activity of important peptidoglycan hydrolases and how their functions differ in various species. There is a growing body of evidence highlighting complex regulatory mechanisms for peptidoglycan metabolism including protein interactions, phosphorylation and protein degradation and we summarize key recent findings in this regard. Finally, we provide an overview of peptidoglycan recycling and how components of this pathway mediate resistance to drugs. In the face of growing antimicrobial resistance, these recent advances are expected to uncover new drug targets in peptidoglycan metabolism, which can be used to develop novel therapies.
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Affiliation(s)
- Moagi Shaku
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Christopher Ealand
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Ofentse Matlhabe
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Rushil Lala
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bavesh D Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa.
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20
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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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21
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The hydrolase LpqI primes mycobacterial peptidoglycan recycling. Nat Commun 2019; 10:2647. [PMID: 31201321 PMCID: PMC6572805 DOI: 10.1038/s41467-019-10586-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Growth and division by most bacteria requires remodelling and cleavage of their cell wall. A byproduct of this process is the generation of free peptidoglycan (PG) fragments known as muropeptides, which are recycled in many model organisms. Bacteria and hosts can harness the unique nature of muropeptides as a signal for cell wall damage and infection, respectively. Despite this critical role for muropeptides, it has long been thought that pathogenic mycobacteria such as Mycobacterium tuberculosis do not recycle their PG. Herein we show that M. tuberculosis and Mycobacterium bovis BCG are able to recycle components of their PG. We demonstrate that the core mycobacterial gene lpqI, encodes an authentic NagZ β-N-acetylglucosaminidase and that it is essential for PG-derived amino sugar recycling via an unusual pathway. Together these data provide a critical first step in understanding how mycobacteria recycle their peptidoglycan. Bacterial growth and division require remodelling of the cell wall, which generates free peptidoglycan fragments. Here, Moynihan et al. show that Mycobacterium tuberculosis can recycle components of their peptidoglycan, and characterise a crucial enzyme required for this process.
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22
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Molecular Fingerprints for a Novel Enzyme Family in Actinobacteria with Glucosamine Kinase Activity. mBio 2019; 10:mBio.00239-19. [PMID: 31088917 PMCID: PMC6520443 DOI: 10.1128/mbio.00239-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The discovery of novel enzymes involved in antibiotic biosynthesis pathways is currently a topic of utmost importance. The high levels of antibiotic resistance detected worldwide threaten our ability to combat infections and other 20th-century medical achievements, namely, organ transplantation or cancer chemotherapy. We have identified and characterized a unique family of enzymes capable of phosphorylating glucosamine to glucosamine-6-phosphate, a crucial molecule directly involved in the activation of antibiotic production pathways in Actinobacteria, nature’s main source of antimicrobials. The consensus sequence identified for these glucosamine kinases will help establish a molecular fingerprint to reveal yet-uncharacterized sequences in antibiotic producers, which should have an important impact in biotechnological and biomedical applications, including the enhancement and optimization of antibiotic production. Actinobacteria have long been the main source of antibiotics, secondary metabolites with tightly controlled biosynthesis by environmental and physiological factors. Phosphorylation of exogenous glucosamine has been suggested as a mechanism for incorporation of this extracellular material into secondary metabolite biosynthesis, but experimental evidence of specific glucosamine kinases in Actinobacteria is lacking. Here, we present the molecular fingerprints for the identification of a unique family of actinobacterial glucosamine kinases. Structural and biochemical studies on a distinctive kinase from the soil bacterium Streptacidiphilus jiangxiensis unveiled its preference for glucosamine and provided structural evidence of a phosphoryl transfer to this substrate. Conservation of glucosamine-contacting residues across a large number of uncharacterized actinobacterial proteins unveiled a specific glucosamine binding sequence motif. This family of kinases and their genetic context may represent the missing link for the incorporation of environmental glucosamine into the antibiotic biosynthesis pathways in Actinobacteria and can be explored to enhance antibiotic production.
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23
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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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24
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Radhakrishnan A, Furze CM, Ahangar MS, Fullam E. A GFP-strategy for efficient recombinant protein overexpression and purification in Mycobacterium smegmatis. RSC Adv 2018; 8:33087-33095. [PMID: 30319771 PMCID: PMC6180428 DOI: 10.1039/c8ra06237d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/14/2018] [Indexed: 12/02/2022] Open
Abstract
One of the major obstacles to obtaining a complete structural and functional understanding of proteins encoded by the Mycobacterium tuberculosis (Mtb) pathogen is due to significant difficulties in producing recombinant mycobacterial proteins. Recent advances that have utilised the closely related Mycobacterium smegmatis species as a native host have been effective. Here we have developed a method for the rapid screening of both protein production and purification strategies of mycobacterial proteins in whole M. smegmatis cells following green fluorescent protein (GFP) fluorescence as an indicator. We have adapted the inducible T7-promoter based pYUB1062 shuttle vector by the addition of a tobacco etch virus (TEV) cleavable C-terminal GFP enabling the target protein to be produced as a GFP-fusion with a poly-histidine tag for affinity purification. We illustrate the advantages of a fluorescent monitoring approach with the production and purification of the mycobacterial N-acetylglucosamine-6-phosphate deacetylase (NagA)-GFP fusion protein. The GFP system described here will accelerate the production of mycobacterial proteins that can be used to understand the molecular mechanisms of Mtb proteins and facilitate drug discovery efforts. A GFP-strategy to monitor protein expression and purification in Mycobacterium smegmatis to overcome the obstacle of producing recombinant mycobacterial proteins.![]()
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Affiliation(s)
- Anjana Radhakrishnan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. ; Tel: +44 (0)2476 574239
| | - Christopher M Furze
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. ; Tel: +44 (0)2476 574239
| | - Mohd Syed Ahangar
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. ; Tel: +44 (0)2476 574239
| | - Elizabeth Fullam
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK. ; Tel: +44 (0)2476 574239
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