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Wojtyś MI, Maksymiuk W, Narczyk M, Bubić A, Ašler IL, Krzyżek P, Gościniak G, Jagusztyn-Krynicka EK, Bzowska A. Vitamin B6 inhibits activity of Helicobacter pylori adenylosuccinate synthetase and growth of reference and clinical, antibiotic-resistant H. pylori strains. J Enzyme Inhib Med Chem 2024; 39:2372734. [PMID: 39149761 DOI: 10.1080/14756366.2024.2372734] [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: 12/20/2023] [Revised: 06/07/2024] [Accepted: 06/20/2024] [Indexed: 08/17/2024] Open
Abstract
The current therapies against gastric pathogen Helicobacter pylori are ineffective in over 20% of patients. Enzymes belonging to the purine salvage pathway are considered as novel drug targets in this pathogen. Therefore, the main aim of the current study was to determine the antibacterial activity of pyridoxal 5'-phosphate (PLP), an active form of vitamin B6, against reference and clinical strains of H. pylori. Using a broad set of microbiological, physicochemical (UV absorption, LC-MS, X-ray analysis) and in silico experiments, we were able to prove that PLP inhibits adenylosuccinate synthetase (AdSS) from H. pylori by the competition with GTP (IC50eq ∼30 nM). This behaviour was attributed to formation of a Schiff base with a lysine residue (a covalent bond with Lys322 in the GTP binding site of AdSS) and was potentiated by the presence of vitamin C. This antibacterial activity of PLP gives hope for its future use against H. pylori.
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Affiliation(s)
- Marta Ilona Wojtyś
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Weronika Maksymiuk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Marta Narczyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Ante Bubić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivana Leščić Ašler
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Paweł Krzyżek
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Grażyna Gościniak
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, Wroclaw, Poland
| | | | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
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Roy PK, Paul A, Lalchhuanawmi S, Babu NK, Singh S. Pyridoxal kinase gene deletion leads to impaired growth, deranged redox metabolism and cell cycle arrest in Leishmania donovani. Biochimie 2024; 222:72-86. [PMID: 38403043 DOI: 10.1016/j.biochi.2024.02.009] [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: 09/14/2023] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Pyridoxal kinase (PdxK) is a vitamin B6 salvage pathway enzyme which produces pyridoxal phosphate. We have investigated the impact of PdxK deletion in Leishmania donovani on parasite survivability, infectivity and cellular metabolism. LdPdxK mutants were generated by gene replacement strategy. All mutants showed significant reduction in growth in comparison to wild type. For PdxK mediated biochemical perturbations, only heterozygous mutants and complementation mutants were used as the growth of null mutants were compromised. Heterozygous mutant showed reduction invitro infectivity and higher cytosolic and mitochondrial ROS levels. Glutathione levels decreased significantly in heterozygous mutant indicating its involvement in cellular oxidative metabolism. Pyridoxal kinase gene deletion resulted in reduced ATP levels in parasites and arrest at G0/G1 phase of cell cycle. All these perturbations were rescued by PdxK gene complementation. This is the first report to confirm that LdPdxK plays an indispensable role in cell survival, pathogenicity, redox metabolism and cell cycle progression of L. donovani parasites. These results provide substantial evidence supporting PdxK as a therapeutic target for the development of specific antileishmanial drug candidates.
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Affiliation(s)
- Pradyot Kumar Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India
| | - Anindita Paul
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India
| | - Sandra Lalchhuanawmi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India
| | - Neerupudi Kishore Babu
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India
| | - Sushma Singh
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, 160062, Punjab, India.
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Rosli NA, Al-Maleki AR, Loke MF, Tay ST, Rofiee MS, Teh LK, Salleh MZ, Vadivelu J. Exposure of Helicobacter pylori to clarithromycin in vitro resulting in the development of resistance and triggers metabolic reprogramming associated with virulence and pathogenicity. PLoS One 2024; 19:e0298434. [PMID: 38446753 PMCID: PMC10917248 DOI: 10.1371/journal.pone.0298434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/23/2024] [Indexed: 03/08/2024] Open
Abstract
In H. pylori infection, antibiotic-resistance is one of the most common causes of treatment failure. Bacterial metabolic activities, such as energy production, bacterial growth, cell wall construction, and cell-cell communication, all play important roles in antimicrobial resistance mechanisms. Identification of microbial metabolites may result in the discovery of novel antimicrobial therapeutic targets and treatments. The purpose of this work is to assess H. pylori metabolomic reprogramming in order to reveal the underlying mechanisms associated with the development of clarithromycin resistance. Previously, four H. pylori isolates were induced to become resistant to clarithromycin in vitro by incrementally increasing the concentrations of clarithromycin. Bacterial metabolites were extracted using the Bligh and Dyer technique and analyzed using metabolomic fingerprinting based on Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry (LC-Q-ToF-MS). The data was processed and analyzed using the MassHunter Qualitative Analysis and Mass Profiler Professional software. In parental sensitivity (S), breakpoint isolates (B), and induced resistance isolates (R) H. pylori isolates, 982 metabolites were found. Furthermore, based on accurate mass, isotope ratios, abundances, and spacing, 292 metabolites matched the metabolites in the Agilent METLIN precise Mass-Personal Metabolite Database and Library (AM-PCDL). Several metabolites associated with bacterial virulence, pathogenicity, survival, and proliferation (L-leucine, Pyridoxone [Vitamine B6], D-Mannitol, Sphingolipids, Indoleacrylic acid, Dulcitol, and D-Proline) were found to be elevated in generated resistant H. pylori isolates when compared to parental sensitive isolates. The elevated metabolites could be part of antibiotics resistance mechanisms. Understanding the fundamental metabolome changes in the course of progressing from clarithromycin-sensitive to breakpoint to resistant in H. pylori clinical isolates may be a promising strategy for discovering novel alternatives therapeutic targets.
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Affiliation(s)
- Naim Asyraf Rosli
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Anis Rageh Al-Maleki
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
- Faculty of Medicine and Health Sciences, Department of Medical Microbiology, Sana’a University, Sana’a, Yemen
| | - Mun Fai Loke
- Camtech Biomedical Pte Ltd, Singapore, Singapore
| | - Sun Tee Tay
- Faculty of Medicine, Department of Medical Microbiology, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Mohd Salleh Rofiee
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Selangor, Malaysia
| | - Jamuna Vadivelu
- Faculty of Medicine, Medical Education Research and Development Unit (MERDU), Universiti Malaya, Kuala Lumpur, Malaysia
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Chen P, Chen M, Peng C, Yan J, Shen X, Zhang W, Yuan Y, Gan G, Luo X, Zhu W, Yao M. In vitro anti-bactrical activity and its preliminary mechanism of action of the non-medicinal parts of Sanguisorba officinalis L. against Helicobacter pylori infection. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:116981. [PMID: 37574016 DOI: 10.1016/j.jep.2023.116981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/20/2023] [Accepted: 07/29/2023] [Indexed: 08/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Sanguisorba officinalis L. (S. officinalis L.), known as Di Yu (DY) in Traditional Chinese Medicine (TCM), are used to treat burns, vomiting of blood, asthma, intestinal infections, and dermatitis. It has been reported that the root of DY has a significant inhibitory effect on Helicobacter pylori (H. pylori). However, there is currently little research on the composition analysis and anti-H. pylori infection properties of the non-medicinal parts of DY, such as its stems, leaves, and flowers. AIM OF STUDY The commonly used eradication therapies for H. pylori infection are antibiotic-based therapies. With the increasing antibiotic resistance of H. pylori, it is urgent to find effective alternative therapies. To find alternative therapies and increase the utilization of DY, this study aims to investigate the phytochemistry profile, in vitro anti-H. pylori activity, and preliminary antibacterial mechanism of the non-medicinal parts of DY. MATERIALS AND METHODS The non-medicinal parts of DY extracts were obtained by using hot water reflux method. The chemical composition of these extracts was analyzed using colorimetric method, high-performance liquid chromatography (HPLC), and ultra-high-performance liquid chromatography-electrospray ionization-mass spectrometry (UPLC-ESI-MS). The in vitro anti-H. pylori activity was investigated using broth microdilution method, checkerboard dilution method, time-kill curve, time-inhibition curve, scanning electron microscopy, and transmission electron microscopy. Transcriptional sequencing technology was used to study the effect of DY stems and flowers on the gene expression of H. pylori and explore possible antibacterial mechanisms. RESULTS The non-medicinal parts of DY contain abundant phytochemicals, such as total phenols and total flavonoids, and possess strong inhibitory and bactericidal activity against both standard and clinical strains of H. pylori in vitro. The MIC was 80-1280 μg/mL and the MBC was 80-2560 μg/mL, and the strength of the antibacterial effects was dependent on the concentration of phytochemicals (total polyphenols, gallic acid and ellagic acid). In addition, the combination of non-medicinal parts of DY with antibiotics, such as amoxicillin, metronidazole, levofloxacin, and clarithromycin, did not result in any antagonistic effects. All of them could disrupt the morphology, internal microscopic and cell wall structures of H. pylori thereby acting as an inhibitor. The mechanism of action was found to be the disruption of H. pylori morphology, internal microstructure, and cell wall. Transcriptomic analysis showed that the non-medicinal parts of DY significantly regulated the gene expression of H. pylori, especially the metabolic pathway. CONCLUSIONS This study analyzed the chemical composition of the non-medicinal parts of DY and confirmed its inhibitory and bactericidal activities against H. pylori, both standard and clinical strains. Additional, the mechanism of inhibition involves disrupting the structure of H. pylori cells, altering gene expression, and interfering with bacterial metabolic pathways. This study provides a reference for further resource utilization and the development of H. pylori drugs using the non-medicinal parts of DY.
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Affiliation(s)
- Pengting Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Meiyun Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China.
| | - Chang Peng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China.
| | - Jiahui Yan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Xue Shen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Weijia Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Yuemei Yuan
- School of Earth Sciences and Engineering, Sun Yat-sen University, Zhuhai 519080, China.
| | - Guoxing Gan
- Qingyuan Hospital of Traditional Chinese Medicine, Qingyuan 511500, China.
| | - Xiaojun Luo
- Lianzhou Hospital of Traditional Chinese Medicine, Qingyuan 513400, China.
| | - Weixing Zhu
- Qingyuan Hospital of Traditional Chinese Medicine, Qingyuan 511500, China.
| | - Meicun Yao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China.
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Tramonti A, Donkor AK, Parroni A, Musayev FN, Barile A, Ghatge MS, Graziani C, Alkhairi M, AlAwadh M, di Salvo ML, Safo MK, Contestabile R. Functional and structural properties of pyridoxal reductase (PdxI) from Escherichia coli: a pivotal enzyme in the vitamin B6 salvage pathway. FEBS J 2023; 290:5628-5651. [PMID: 37734924 PMCID: PMC10872706 DOI: 10.1111/febs.16962] [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: 07/19/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/23/2023]
Abstract
Pyridoxine 4-dehydrogenase (PdxI), a NADPH-dependent pyridoxal reductase, is one of the key players in the Escherichia coli pyridoxal 5'-phosphate (PLP) salvage pathway. This enzyme, which catalyses the reduction of pyridoxal into pyridoxine, causes pyridoxal to be converted into PLP via the formation of pyridoxine and pyridoxine phosphate. The structural and functional properties of PdxI were hitherto unknown, preventing a rational explanation of how and why this longer, detoured pathway occurs, given that, in E. coli, two pyridoxal kinases (PdxK and PdxY) exist that could convert pyridoxal directly into PLP. Here, we report a detailed characterisation of E. coli PdxI that explains this behaviour. The enzyme efficiently catalyses the reversible transformation of pyridoxal into pyridoxine, although the reduction direction is thermodynamically strongly favoured, following a compulsory-order ternary-complex mechanism. In vitro, the enzyme is also able to catalyse PLP reduction and use NADH as an electron donor, although with lower efficiency. As with all members of the aldo-keto reductase (AKR) superfamily, the enzyme has a TIM barrel fold; however, it shows some specific features, the most important of which is the presence of an Arg residue that replaces the catalytic tetrad His residue that is present in all AKRs and appears to be involved in substrate specificity. The above results, in conjunction with kinetic and static measurements of vitamins B6 in cell extracts of E. coli wild-type and knockout strains, shed light on the role of PdxI and both kinases in determining the pathway followed by pyridoxal in its conversion to PLP, which has a precise regulatory function.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Akua K. Donkor
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Alessia Parroni
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Faik N. Musayev
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Anna Barile
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Mohini. S. Ghatge
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Claudio Graziani
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Roma, Italy
| | - Mona Alkhairi
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohammed AlAwadh
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Martino Luigi di Salvo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Roma, Italy
| | - Martin K. Safo
- Institute for Structural Biology, Drug Discovery and Development, Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
| | - Roberto Contestabile
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Roma, Italy
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Denise R, Babor J, Gerlt JA, de Crécy-Lagard V. Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes. Microb Genom 2023; 9:mgen000926. [PMID: 36729913 PMCID: PMC9997740 DOI: 10.1099/mgen.0.000926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Pyridoxal 5’-phosphate or PLP is a cofactor derived from B6 vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B6 transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis. Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B6 vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come.
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Affiliation(s)
- Rémi Denise
- Department of Microbiology and Cell Sciences, Gainesville, USA.,Present address: APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jill Babor
- Department of Microbiology and Cell Sciences, Gainesville, USA
| | | | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, Gainesville, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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Bista PK, Pillai D, Roy C, Scaria J, Narayanan SK. Comparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes. Microbiol Spectr 2022; 10:e0029722. [PMID: 36219094 PMCID: PMC9769765 DOI: 10.1128/spectrum.00297-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 09/16/2022] [Indexed: 01/05/2023] Open
Abstract
Fusobacterium necrophorum is a Gram-negative, filamentous anaerobe prevalent in the mucosal flora of animals and humans. It causes necrotic infections in cattle, resulting in a substantial economic impact on the cattle industry. Although infection severity and management differ within F. necrophorum species, little is known about F. necrophorum speciation and the genetic virulence determinants between strains. To characterize the clinical isolates, we performed whole-genome sequencing of four bovine isolates (8L1, 212, B17, and SM1216) and one human isolate (MK12). To determine the phylogenetic relationship and evolution pattern and investigate the presence of antimicrobial resistance genes (ARGs) and potential virulence genes of F. necrophorum, we also performed comparative genomics with publicly available Fusobacterium genomes. Using up-to-date bacterial core gene (UBCG) set analysis, we uncovered distinct Fusobacterium species and F. necrophorum subspecies clades. Pangenome analyses revealed a high level of diversity among Fusobacterium strains down to species levels. The output also identified 14 and 26 genes specific to F. necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme, respectively, which could be essential for bacterial survival under different environmental conditions. ClonalFrameML-based recombination analysis suggested that extensive recombination among accessory genes led to species divergence. Furthermore, the only strain of F. necrophorum with ARGs was F. necrophorum subsp. funduliforme B35, with acquired macrolide and tetracycline resistance genes. Our custom search revealed common virulence genes, including toxins, adhesion proteins, outer membrane proteins, cell envelope, type IV secretion system, ABC (ATP-binding cassette) transporters, and transporter proteins. A focused study on these genes could help identify major virulence genes and inform effective vaccination strategies against fusobacterial infections. IMPORTANCE Fusobacterium necrophorum is an anaerobic bacterium that causes liver abscesses in cattle with an annual incidence rate of 10% to 20%, resulting in a substantial economic impact on the cattle industry. The lack of definite biochemical tests makes it difficult to distinguish F. necrophorum subspecies phenotypically, where genomic characterization plays a significant role. However, due to the lack of a good reference genome for comparison, F. necrophorum subspecies-level identification represents a significant challenge. To overcome this challenge, we used comparative genomics to validate clinical test strains for subspecies-level identification. The findings of our study help predict specific clades of previously uncharacterized strains of F. necrophorum. Our study identifies both general and subspecies-specific virulence genes through a custom search-based analysis. The virulence genes identified in this study can be the focus of future studies aimed at evaluating their potential as vaccine targets to prevent fusobacterial infections in cattle.
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Affiliation(s)
- Prabha K. Bista
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, USA
| | - Deepti Pillai
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, USA
- Indiana Animal Disease and Diagnostic Laboratory, Purdue University, West Lafayette, Indiana, USA
| | - Chayan Roy
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
- Environment Microbial Genomics, Plant and Environmental Microbiology, Copenhagen University, Copenhagen, Denmark
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Sanjeev K. Narayanan
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana, USA
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Wang Y, Zhao Y, Xia L, Chen L, Liao Y, Chen B, Liu Y, Gong W, Tian Y, Hu B. yggS Encoding Pyridoxal 5'-Phosphate Binding Protein Is Required for Acidovorax citrulli Virulence. Front Microbiol 2022; 12:783862. [PMID: 35087487 PMCID: PMC8787154 DOI: 10.3389/fmicb.2021.783862] [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: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 11/26/2022] Open
Abstract
Bacterial fruit blotch, caused by seed-borne pathogen Acidovorax citrulli, poses a serious threat to the production of cucurbits globally. Although the disease can cause substantial economic losses, limited information is available about the molecular mechanisms of virulence. This study identified that, a random transposon insertion mutant impaired in the ability to elicit a hypersensitive response on tobacco. The disrupted gene in this mutant was determined to be Aave_0638, which is predicted to encode a YggS family pyridoxal phosphate-dependent enzyme. YggS is a highly conserved protein among multiple organisms, and is responsible for maintaining the homeostasis of pyridoxal 5′-phosphate and amino acids in cells. yggS deletion mutant of A. citrulli strain XjL12 displayed attenuated virulence, delayed hypersensitive response, less tolerance to H2O2 and pyridoxine, increased sensitivity to antibiotic β-chloro-D-alanine, and reduced swimming. In addition, RNA-Seq analysis demonstrated that yggS was involved in regulating the expression of certain pathogenicity-associated genes related to secretion, motility, quorum sensing and oxidative stress response. Importantly, YggS significantly affected type III secretion system and its effectors in vitro. Collectively, our results suggest that YggS is indispensable for A.citrulli virulence and expands the role of YggS in the biological processes.
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Affiliation(s)
- Yuanjie Wang
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Yuqiang Zhao
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-sen), Nanjing, China
| | - Liming Xia
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Lin Chen
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Yajie Liao
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Baohui Chen
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Yiyang Liu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Weirong Gong
- Plant Protection and Quarantine Station of Province, Nanjing, China
| | - Yanli Tian
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Baishi Hu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
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9
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Pan C, Zimmer A, Shah M, Huynh MS, Lai CCL, Sit B, Hooda Y, Curran DM, Moraes TF. Actinobacillus utilizes a binding protein-dependent ABC transporter to acquire the active form of vitamin B 6. J Biol Chem 2021; 297:101046. [PMID: 34358566 PMCID: PMC8427247 DOI: 10.1016/j.jbc.2021.101046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 12/02/2022] Open
Abstract
Bacteria require high-efficiency uptake systems to survive and proliferate in nutrient-limiting environments, such as those found in host organisms. ABC transporters in the bacterial plasma membrane provide a mechanism for transport of many substrates. In this study, we examine an operon containing a periplasmic binding protein in Actinobacillus for its potential role in nutrient acquisition. The electron density map of 1.76 Å resolution obtained from the crystal structure of the periplasmic binding protein was best fit with a molecular model containing a pyridoxal-5'-phosphate (P5P/pyridoxal phosphate/the active form of vitamin B6) ligand within the protein's binding site. The identity of the P5P bound to this periplasmic binding protein was verified by isothermal titration calorimetry, microscale thermophoresis, and mass spectrometry, leading us to name the protein P5PA and the operon P5PAB. To illustrate the functional utility of this uptake system, we introduced the P5PAB operon from Actinobacillus pleuropneumoniae into an Escherichia coli K-12 strain that was devoid of a key enzyme required for P5P synthesis. The growth of this strain at low levels of P5P supports the functional role of this operon in P5P uptake. This is the first report of a dedicated P5P bacterial uptake system, but through bioinformatics, we discovered homologs mainly within pathogenic representatives of the Pasteurellaceae family, suggesting that this operon exists more widely outside the Actinobacillus genus.
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Affiliation(s)
- Chuxi Pan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alexandra Zimmer
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Megha Shah
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Minh Sang Huynh
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Brandon Sit
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yogesh Hooda
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David M Curran
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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10
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Tarique KF, Devi S, Tomar P, Ali MF, Rehman SAA, Gourinath S. Characterization and functional insights into the Entamoeba histolytica pyridoxal kinase, an enzyme essential for its survival. J Struct Biol 2020; 212:107645. [PMID: 33045383 DOI: 10.1016/j.jsb.2020.107645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 01/18/2023]
Abstract
Pyridoxal 5'-phosphate (PLP) is the active form of vitamin B6 and a cofactor for more than 140 enzymes. This coenzyme plays a pivotal role in catalysis of various enzymatic reactions that are critical for the survival of organisms. Entamoeba histolytica depends on the uptake of pyridoxal (PL), a B6 vitamer from the external environment which is then phosphorylated by pyridoxal kinase (EhPLK) to form PLP via the salvage pathway. E. histolytica cannot synthesise vitamin B6de-novo, and also lacks pyridoxine 5'-phosphate oxidase, a salvage pathway enzyme required to produce PLP from pyridoxine phosphate (PNP) and pyridoxamine phosphate (PMP). Analysing the importance of PLK in E. histolytica, we have determined the high-resolution crystal structures of the dimeric pyridoxal kinase in apo, ADP-bound, and PLP-bound states. These structures provided a snapshot of the transition state and help in understanding the reaction mechanism in greater detail. The EhPLK structure significantly differed from the human homologue at its PLP binding site, and the phylogenetic study also revealed its divergence from human PLK. Further, gene regulation of EhPLK using sense and antisense RNA showed that any change in optimal level is harmful to the pathogen. Biochemical and in vivo studies unveiled EhPLK to be essential for this pathogen, while the molecular differences with human PLK structure can be exploited for the structure-guided design of EhPLK inhibitors.
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Affiliation(s)
- Khaja Faisal Tarique
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Suneeta Devi
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priya Tomar
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohammad Farhan Ali
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Syed Arif Abdul Rehman
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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11
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Contestabile R, di Salvo ML, Bunik V, Tramonti A, Vernì F. The multifaceted role of vitamin B 6 in cancer: Drosophila as a model system to investigate DNA damage. Open Biol 2020; 10:200034. [PMID: 32208818 PMCID: PMC7125957 DOI: 10.1098/rsob.200034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A perturbed uptake of micronutrients, such as minerals and vitamins, impacts on different human diseases, including cancer and neurological disorders. Several data converge towards a crucial role played by many micronutrients in genome integrity maintenance and in the establishment of a correct DNA methylation pattern. Failure in the proper accomplishment of these processes accelerates senescence and increases the risk of developing cancer, by promoting the formation of chromosome aberrations and deregulating the expression of oncogenes. Here, the main recent evidence regarding the impact of some B vitamins on DNA damage and cancer is summarized, providing an integrated and updated analysis, mainly centred on vitamin B6. In many cases, it is difficult to finely predict the optimal vitamin rate that is able to protect against DNA damage, as this can be influenced by a given individual's genotype. For this purpose, a precious resort is represented by model organisms which allow limitations imposed by more complex systems to be overcome. In this review, we show that Drosophila can be a useful model to deeply understand mechanisms underlying the relationship between vitamin B6 and genome integrity.
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Affiliation(s)
- Roberto Contestabile
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro, 5, 00185, Roma, Italy
| | - Martino Luigi di Salvo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro, 5, 00185, Roma, Italy
| | - Victoria Bunik
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia.,Sechenov Medical University, Sechenov University, 119048 Moscow, Russia
| | - Angela Tramonti
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, P.le A. Moro, 5, 00185, Roma, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Pl.e A. Moro, 5, 00185 Roma, Italy
| | - Fiammetta Vernì
- Dipartimento di Biologia e Biotecnologie 'Charles Darwin', Sapienza Università di Roma, Pl.e A. Moro, 5, 00185 Roma, Italy
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12
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Frame LA, Costa E, Jackson SA. Current explorations of nutrition and the gut microbiome: a comprehensive evaluation of the review literature. Nutr Rev 2020; 78:798-812. [DOI: 10.1093/nutrit/nuz106] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abstract
Context
The ability to measure the gut microbiome led to a surge in understanding and knowledge of its role in health and disease. The diet is a source of fuel for and influencer of composition of the microbiome.
Objective
To assess the understanding of the interactions between nutrition and the gut microbiome in healthy adults.
Data Sources
PubMed and Google Scholar searches were conducted in March and August 2018 and were limited to the following: English, 2010–2018, healthy adults, and reviews.
Data Extraction
A total of 86 articles were independently screened for duplicates and relevance, based on preidentified inclusion criteria.
Data Analysis
Research has focused on dietary fiber – microbiota fuel. The benefits of fiber center on short-chain fatty acids, which are required by colonocytes, improve absorption, and reduce intestinal transit time. Contrastingly, protein promotes microbial protein metabolism and potentially harmful by-products that can stagnate in the gut. The microbiota utilize and produce micronutrients; the bidirectional relationship between micronutrition and the gut microbiome is emerging.
Conclusions
Nutrition has profound effects on microbial composition, in turn affecting wide-ranging metabolic, hormonal, and neurological processes. There is no consensus on what defines a “healthy” gut microbiome. Future research must consider individual responses to diet.
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Affiliation(s)
- Leigh A Frame
- The George Washington School of Medicine and Health Sciences, Washington, USA
| | - Elise Costa
- The George Washington School of Medicine and Health Sciences, Washington, USA
| | - Scott A Jackson
- The George Washington School of Medicine and Health Sciences, Washington, USA
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
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13
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Barra ALC, Dantas LDOC, Morão LG, Gutierrez RF, Polikarpov I, Wrenger C, Nascimento AS. Essential Metabolic Routes as a Way to ESKAPE From Antibiotic Resistance. Front Public Health 2020; 8:26. [PMID: 32257985 PMCID: PMC7093009 DOI: 10.3389/fpubh.2020.00026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/27/2020] [Indexed: 02/03/2023] Open
Abstract
Antibiotic resistance is a worldwide concern that requires a concerted action from physicians, patients, governmental agencies, and academia to prevent infections and the spread of resistance, track resistant bacteria, improve the use of current antibiotics, and develop new antibiotics. Despite the efforts spent so far, the current antibiotics in the market are restricted to only five general targets/pathways highlighting the need for basic research focusing on the discovery and evaluation of new potential targets. Here we interrogate two biosynthetic pathways as potentially druggable pathways in bacteria. The biosynthesis pathway for thiamine (vitamin B1), absent in humans, but found in many bacteria, including organisms in the group of the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter sp.) and the biosynthesis pathway for pyridoxal 5'-phosphate and its vitamers (vitamin B6), found in S. aureus. Using current genomic data, we discuss the possibilities of inhibition of enzymes in the pathway and review the current state of the art in the scientific literature.
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Affiliation(s)
| | | | - Luana Galvão Morão
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Raíssa F. Gutierrez
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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14
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Barile A, Tramonti A, di Salvo ML, Nogués I, Nardella C, Malatesta F, Contestabile R. Allosteric feedback inhibition of pyridoxine 5'-phosphate oxidase from Escherichia coli. J Biol Chem 2019; 294:15593-15603. [PMID: 31484724 DOI: 10.1074/jbc.ra119.009697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/02/2019] [Indexed: 11/06/2022] Open
Abstract
In Escherichia coli, the synthesis of pyridoxal 5'-phosphate (PLP), the catalytically active form of vitamin B6, takes place through the so-called deoxyxylulose 5-phosphate-dependent pathway, whose last step is pyridoxine 5'-phosphate (PNP) oxidation to PLP, catalyzed by the FMN-dependent enzyme PNP oxidase (PNPOx). This enzyme plays a pivotal role in controlling intracellular homeostasis and bioavailability of PLP. PNPOx has been proposed to undergo product inhibition resulting from PLP binding at the active site. PLP has also been reported to bind tightly at a secondary site, apparently without causing PNPOx inhibition. The possible location of this secondary site has been indicated by crystallographic studies as two symmetric surface pockets present on the PNPOx homodimer, but this site has never been verified by other experimental means. Here, we demonstrate, through kinetic measurements, that PLP inhibition is actually of a mixed-type nature and results from binding of this vitamer at an allosteric site. This interpretation was confirmed by the characterization of a mutated PNPOx form, in which substrate binding at the active site is heavily hampered but PLP binding is preserved. Structural and functional connections between the active site and the allosteric site were indicated by equilibrium binding experiments, which revealed different PLP-binding stoichiometries with WT and mutant PNPOx forms. These observations open up new horizons on the mechanisms that regulate E. coli PNPOx, which may have commonalities with the mechanisms regulating human PNPOx, whose crucial role in vitamin B6 metabolism and epilepsy is well-known.
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Affiliation(s)
- Anna Barile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Angela Tramonti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy.,Istituto di Biologia e Patologia Molecolari, CNR, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Martino Luigi di Salvo
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Isabel Nogués
- Istituto di Ricerca sugli Ecosistemi Terrestri, CNR, Via G. Marconi 2, 05010 Porano (TR), Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Francesco Malatesta
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Laboratory affiliated with Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Piazzale Aldo Moro 5, 00185 Roma, Italy
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15
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Parra M, Stahl S, Hellmann H. Vitamin B₆ and Its Role in Cell Metabolism and Physiology. Cells 2018; 7:cells7070084. [PMID: 30037155 PMCID: PMC6071262 DOI: 10.3390/cells7070084] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/11/2022] Open
Abstract
Vitamin B6 is one of the most central molecules in cells of living organisms. It is a critical co-factor for a diverse range of biochemical reactions that regulate basic cellular metabolism, which impact overall physiology. In the last several years, major progress has been accomplished on various aspects of vitamin B6 biology. Consequently, this review goes beyond the classical role of vitamin B6 as a cofactor to highlight new structural and regulatory information that further defines how the vitamin is synthesized and controlled in the cell. We also discuss broader applications of the vitamin related to human health, pathogen resistance, and abiotic stress tolerance. Overall, the information assembled shall provide helpful insight on top of what is currently known about the vitamin, along with addressing currently open questions in the field to highlight possible approaches vitamin B6 research may take in the future.
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Affiliation(s)
- Marcelina Parra
- Hellmann Lab, School of Biological Sciences, College of Liberal Arts and Sciences, Washington State University, Pullman, 99164-6234 WA, USA.
| | - Seth Stahl
- Hellmann Lab, School of Biological Sciences, College of Liberal Arts and Sciences, Washington State University, Pullman, 99164-6234 WA, USA.
| | - Hanjo Hellmann
- Hellmann Lab, School of Biological Sciences, College of Liberal Arts and Sciences, Washington State University, Pullman, 99164-6234 WA, USA.
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16
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Meir Z, Osherov N. Vitamin Biosynthesis as an Antifungal Target. J Fungi (Basel) 2018; 4:E72. [PMID: 29914189 PMCID: PMC6023522 DOI: 10.3390/jof4020072] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022] Open
Abstract
The large increase in the population of immunosuppressed patients, coupled with the limited efficacy of existing antifungals and rising resistance toward them, have dramatically highlighted the need to develop novel drugs for the treatment of invasive fungal infections. An attractive possibility is the identification of possible drug targets within essential fungal metabolic pathways not shared with humans. Here, we review the vitamin biosynthetic pathways (vitamins A⁻E, K) as candidates for the development of antifungals. We present a set of ranking criteria that identify the vitamin B2 (riboflavin), B5 (pantothenic acid), and B9 (folate) biosynthesis pathways as being particularly rich in new antifungal targets. We propose that recent scientific advances in the fields of drug design and fungal genomics have developed sufficiently to merit a renewed look at these pathways as promising sources for the development of novel classes of antifungals.
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Affiliation(s)
- Zohar Meir
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel.
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel.
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17
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Sanders S, Bartee D, Harrison MJ, Phillips PD, Koppisch AT, Freel Meyers CL. Growth medium-dependent antimicrobial activity of early stage MEP pathway inhibitors. PLoS One 2018; 13:e0197638. [PMID: 29771999 PMCID: PMC5957436 DOI: 10.1371/journal.pone.0197638] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/04/2018] [Indexed: 01/01/2023] Open
Abstract
The in vivo microenvironment of bacterial pathogens is often characterized by nutrient limitation. Consequently, conventional rich in vitro culture conditions used widely to evaluate antibacterial agents are often poorly predictive of in vivo activity, especially for agents targeting metabolic pathways. In one such pathway, the methylerythritol phosphate (MEP) pathway, which is essential for production of isoprenoids in bacterial pathogens, relatively little is known about the influence of growth environment on antibacterial properties of inhibitors targeting enzymes in this pathway. The early steps of the MEP pathway are catalyzed by 1-deoxy-d-xylulose 5-phosphate (DXP) synthase and reductoisomerase (IspC). The in vitro antibacterial efficacy of the DXP synthase inhibitor butylacetylphosphonate (BAP) was recently reported to be strongly dependent upon growth medium, with high potency observed under nutrient limitation and exceedingly weak activity in nutrient-rich conditions. In contrast, the well-known IspC inhibitor fosmidomycin has potent antibacterial activity in nutrient-rich conditions, but to date, its efficacy had not been explored under more relevant nutrient-limited conditions. The goal of this work was to thoroughly characterize the effects of BAP and fosmidomycin on bacterial cells under varied growth conditions. In this work, we show that activities of both inhibitors, alone and in combination, are strongly dependent upon growth medium, with differences in cellular uptake contributing to variance in potency of both agents. Fosmidomycin is dissimilar to BAP in that it displays relatively weaker activity in nutrient-limited compared to nutrient-rich conditions. Interestingly, while it has been generally accepted that fosmidomycin activity depends upon expression of the GlpT transporter, our results indicate for the first time that fosmidomycin can enter cells by an alternative mechanism under nutrient limitation. Finally, we show that the potency and relationship of the BAP-fosmidomycin combination also depends upon the growth medium, revealing a striking loss of BAP-fosmidomycin synergy under nutrient limitation. This change in BAP-fosmidomycin relationship suggests a shift in the metabolic and/or regulatory networks surrounding DXP accompanying the change in growth medium, the understanding of which could significantly impact targeting strategies against this pathway. More generally, our findings emphasize the importance of considering physiologically relevant growth conditions for predicting the antibacterial potential MEP pathway inhibitors and for studies of their intracellular targets.
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Affiliation(s)
- Sara Sanders
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - David Bartee
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Mackenzie J. Harrison
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Paul D. Phillips
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Andrew T. Koppisch
- Department of Chemistry, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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18
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Biesalski HK. Nutrition meets the microbiome: micronutrients and the microbiota. Ann N Y Acad Sci 2017; 1372:53-64. [PMID: 27362360 DOI: 10.1111/nyas.13145] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 01/19/2023]
Abstract
There is increasing evidence that food is an important factor that influences and shapes the composition and configuration of the gut microbiota. Most studies have focused on macronutrients (fat, carbohydrate, protein) in particular and their effects on the gut microbiota. Although the microbiota can synthesize different water-soluble vitamins, the effects of vitamins synthesized within the microbiota on systemic vitamin status are unclear. Few studies exist on the shuttling of vitamins between the microbiota and intestine and the impact of luminal vitamins on the microbiota. Studying the interactions between vitamins and the microbiota may help to understand the effects of vitamins on the barrier function and immune system of the intestinal tract. Furthermore, understanding the impact of malnutrition, particularly low micronutrient supply, on microbiota development, composition, and metabolism may help in implementing new strategies to overcome the deleterious effects of malnutrition on child development. This article reviews data on the synthesis of different micronutrients and their effects on the human microbiota, and further discusses the consequences of malnutrition on microbiota composition.
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Affiliation(s)
- Hans K Biesalski
- Department of Biological Chemistry and Nutrition, University of Hohenheim, Stuttgart, Germany
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19
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Hutton ML, D'Costa K, Rossiter AE, Wang L, Turner L, Steer DL, Masters SL, Croker BA, Kaparakis-Liaskos M, Ferrero RL. A Helicobacter pylori Homolog of Eukaryotic Flotillin Is Involved in Cholesterol Accumulation, Epithelial Cell Responses and Host Colonization. Front Cell Infect Microbiol 2017; 7:219. [PMID: 28634572 PMCID: PMC5460342 DOI: 10.3389/fcimb.2017.00219] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 05/11/2017] [Indexed: 12/12/2022] Open
Abstract
The human pathogen Helicobacter pylori acquires cholesterol from membrane raft domains in eukaryotic cells, commonly known as "lipid rafts." Incorporation of this cholesterol into the H. pylori cell membrane allows the bacterium to avoid clearance by the host immune system and to resist the effects of antibiotics and antimicrobial peptides. The presence of cholesterol in H. pylori bacteria suggested that this pathogen may have cholesterol-enriched domains within its membrane. Consistent with this suggestion, we identified a hypothetical H. pylori protein (HP0248) with homology to the flotillin proteins normally found in the cholesterol-enriched domains of eukaryotic cells. As shown for eukaryotic flotillin proteins, HP0248 was detected in detergent-resistant membrane fractions of H. pylori. Importantly, H. pylori HP0248 mutants contained lower levels of cholesterol than wild-type bacteria (P < 0.01). HP0248 mutant bacteria also exhibited defects in type IV secretion functions, as indicated by reduced IL-8 responses and CagA translocation in epithelial cells (P < 0.05), and were less able to establish a chronic infection in mice than wild-type bacteria (P < 0.05). Thus, we have identified an H. pylori flotillin protein and shown its importance for bacterial virulence. Taken together, the data demonstrate important roles for H. pylori flotillin in host-pathogen interactions. We propose that H. pylori flotillin may be required for the organization of virulence proteins into membrane raft-like structures in this pathogen.
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Affiliation(s)
- Melanie L. Hutton
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical ResearchMelbourne, VIC, Australia
| | - Kimberley D'Costa
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical ResearchMelbourne, VIC, Australia
| | - Amanda E. Rossiter
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical ResearchMelbourne, VIC, Australia
| | - Lin Wang
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical ResearchMelbourne, VIC, Australia
| | - Lorinda Turner
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical ResearchMelbourne, VIC, Australia
| | - David L. Steer
- Monash Biomedical Proteomics Facility, Monash UniversityMelbourne, VIC, Australia
| | - Seth L. Masters
- Inflammation Division, The Walter and Eliza Hall InstituteMelbourne, VIC, Australia
| | - Ben A. Croker
- Inflammation Division, The Walter and Eliza Hall InstituteMelbourne, VIC, Australia
| | - Maria Kaparakis-Liaskos
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical ResearchMelbourne, VIC, Australia
| | - Richard L. Ferrero
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical ResearchMelbourne, VIC, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash UniversityMelbourne, VIC, Australia
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20
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Xie F, Li G, Wang Y, Zhang Y, Zhou L, Wang C, Liu S, Liu S, Wang C. Pyridoxal phosphate synthases PdxS/PdxT are required for Actinobacillus pleuropneumoniae viability, stress tolerance and virulence. PLoS One 2017; 12:e0176374. [PMID: 28448619 PMCID: PMC5407770 DOI: 10.1371/journal.pone.0176374] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 04/10/2017] [Indexed: 11/29/2022] Open
Abstract
Pyridoxal 5’-phosphate (PLP) is an essential cofactor for numerous enzymes involved in a diversity of cellular processes in living organisms. Previous analysis of the Actinobacillus pleuropneumoniae S-8 genome sequence revealed the presence of pdxS and pdxT genes, which are implicated in deoxyxylulose 5-phosphate (DXP)-independent pathway of PLP biosynthesis; however, little is known about their roles in A. pleuropneumoniae pathogenicity. Our data demonstrated that A. pleuropneumoniae could synthesize PLP by PdxS and PdxT enzymes. Disruption of the pdxS and pdxT genes rendered the pathogen auxotrophic for PLP, and the defective growth as a result of these mutants was chemically compensated by the addition of PLP, suggesting the importance of PLP production for A. pleuropneumoniae growth and viability. Additionally, the pdxS and pdxT deletion mutants displayed morphological defects as indicated by irregular and aberrant shapes in the absence of PLP. The reduced growth of the pdxS and pdxT deletion mutants under osmotic and oxidative stress conditions suggests that the PLP synthases PdxS/PdxT are associated with the stress tolerance of A. pleuropneumoniae. Furthermore, disruption of the PLP biosynthesis pathway led to reduced colonization and attenuated virulence of A. pleuropneumoniae in the BALB/c mouse model. The data presented in this study reveal the critical role of PLP synthases PdxS/PdxT in viability, stress tolerance, and virulence of A. pleuropneumoniae.
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Affiliation(s)
- Fang Xie
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Gang Li
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Yalei Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Yanhe Zhang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Long Zhou
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Chengcheng Wang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Shuanghong Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Chunlai Wang
- State Key Laboratory of Veterinary Biotechnology, Division of Bacterial Diseases, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- * E-mail:
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21
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Tramonti A, Milano T, Nardella C, di Salvo ML, Pascarella S, Contestabile R. Salmonella typhimurium PtsJ is a novel MocR-like transcriptional repressor involved in regulating the vitamin B 6 salvage pathway. FEBS J 2017; 284:466-484. [PMID: 27987384 DOI: 10.1111/febs.13994] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/11/2022]
Abstract
The vitamin B6 salvage pathway, involving pyridoxine 5'-phosphate oxidase (PNPOx) and pyridoxal kinase (PLK), recycles B6 vitamers from nutrients and protein turnover to produce pyridoxal 5'-phosphate (PLP), the catalytically active form of the vitamin. Regulation of this pathway, widespread in living organisms including humans and many bacteria, is very important to vitamin B6 homeostasis but poorly understood. Although some information is available on the enzymatic regulation of PNPOx and PLK, little is known on their regulation at the transcriptional level. In the present work, we identified a new MocR-like regulator, PtsJ from Salmonella typhimurium, which controls the expression of the pdxK gene encoding one of the two PLKs expressed in this organism (PLK1). Analysis of pdxK expression in a ptsJ knockout strain demonstrated that PtsJ acts as a transcriptional repressor. This is the first case of a MocR-like regulator acting as repressor of its target gene. Expression and purification of PtsJ allowed a detailed characterisation of its effector and DNA-binding properties. PLP is the only B6 vitamer acting as effector molecule for PtsJ. A DNA-binding region composed of four repeated nucleotide sequences is responsible for binding of PtsJ to its target promoter. Analysis of binding stoichiometry revealed that protein subunits/DNA molar ratio varies from 4 : 1 to 2 : 1, depending on the presence or absence of PLP. Structural characteristics of DNA transcriptional factor-binding sites suggest that PtsJ binds DNA according to a different model with respect to other characterised members of the MocR subgroup.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy.,Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Teresa Milano
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
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22
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Pettersen VK, Mosevoll KA, Lindemann PC, Wiker HG. Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis. Mol Cell Proteomics 2016; 15:2890-907. [PMID: 27364158 PMCID: PMC5013306 DOI: 10.1074/mcp.m116.060582] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 02/06/2023] Open
Abstract
One of the trademarks of extraintestinal pathogenic Escherichia coli is adaptation of metabolism and basic physiology to diverse host sites. However, little is known how this common human pathogen adapts to permit survival and growth in blood. We used label-free quantitative proteomics to characterize five E. coli strains purified from clinical blood cultures associated with sepsis and urinary tract infections. Further comparison of proteome profiles of the clinical strains and a reference uropathogenic E. coli strain 536 cultivated in blood culture and on two different solid media distinguished cellular features altered in response to the pathogenically relevant condition. The analysis covered nearly 60% of the strains predicted proteomes, and included quantitative description based on label-free intensity scores for 90% of the detected proteins. Statistical comparison of anaerobic and aerobic blood cultures revealed 32 differentially expressed proteins (1.5% of the shared proteins), mostly associated with acquisition and utilization of metal ions critical for anaerobic or aerobic respiration. Analysis of variance identified significantly altered amounts of 47 proteins shared by the strains (2.7%), including proteins involved in vitamin B6 metabolism and virulence. Although the proteomes derived from blood cultures were fairly similar for the investigated strains, quantitative proteomic comparison to the growth on solid media identified 200 proteins with substantially changed levels (11% of the shared proteins). Blood culture was characterized by up-regulation of anaerobic fermentative metabolism and multiple virulence traits, including cell motility and iron acquisition. In a response to the growth on solid media there were increased levels of proteins functional in aerobic respiration, catabolism of medium-specific carbon sources and protection against oxidative and osmotic stresses. These results demonstrate on the expressed proteome level that expression of extraintestinal virulence factors and overall cellular metabolism closely reflects specific growth conditions. Data are available via ProteomeXchange with identifier PXD002912.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway;
| | | | - Paul Christoffer Lindemann
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; ¶Department of Microbiology; Haukeland University Hospital, N-5021 Bergen, Norway
| | - Harald G Wiker
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; ¶Department of Microbiology; Haukeland University Hospital, N-5021 Bergen, Norway
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Involvement of Vitamin B6 Biosynthesis Pathways in the Insecticidal Activity of Photorhabdus luminescens. Appl Environ Microbiol 2016; 82:3546-3553. [PMID: 27060119 DOI: 10.1128/aem.00522-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/02/2016] [Indexed: 02/04/2023] Open
Abstract
UNLABELLED Photorhabdus luminescens is a Gram-negative entomopathogenic bacterium which symbiotically associates with the entomopathogenic nematode Heterorhabditis bacteriophora P. luminescens is highly virulent to many insects and nonsymbiotic nematodes, including Caenorhabditis elegans To understand the virulence mechanisms of P. luminescens, we obtained virulence-deficient and -attenuated mutants against C. elegans through a transposon-mutagenized library. From the genetic screening, we identified the pdxB gene, encoding erythronate-4-phosphate dehydrogenase, as required for de novo vitamin B6 biosynthesis. Mutation in pdxB caused growth deficiency of P. luminescens in nutrient-poor medium, which was restored under nutrient-rich conditions or by supplementation with pyridoxal 5'-phosphate (PLP), an active form of vitamin B6 Supplementation with three other B6 vitamers (pyridoxal, pyridoxine, and pyridoxamine) also restored the growth of the pdxB mutant, suggesting the existence of a salvage pathway for vitamin B6 biosynthesis in P. luminescens Moreover, supplementation with PLP restored the virulence-deficient phenotype against C. elegans Combining these results with the fact that pdxB mutation also caused attenuation of insecticidal activity, we concluded that the production of appropriate amounts of vitamin B6 is critical for P. luminescens pathogenicity. IMPORTANCE The Gram-negative entomopathogenic bacterium Photorhabdus luminescens symbiotically associates with the entomopathogenic nematode Heterorhabditis bacteriophora P. luminescens is highly virulent to many insects and nonsymbiotic nematodes, including Caenorhabditis elegans We have obtained several virulence-deficient and -attenuated P. luminescens mutants against C. elegans through genetic screening. From the genetic analysis, we present the vitamin B6 biosynthetic pathways in P. luminescens that are important for its insecticidal activity. Mutation in pdxB, encoding erythronate-4-phosphate dehydrogenase and required for the de novo vitamin B6 biosynthesis pathway, caused virulence deficiency against C. elegans and growth deficiency of P. luminescens in nutrient-poor medium. Because such phenotypes were restored under nutrient-rich conditions or by supplementation with B6 vitamers, we showed the presence of the two vitamin B6 synthetic pathways (de novo and salvage) in P. luminescens and also showed that the ability to produce an appropriate amount of vitamin B6 is critical for P. luminescens pathogenicity.
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24
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Xu M, Yang X, Yang XA, Zhou L, Liu TZ, Fan Z, Jiang T. Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system. Protein Cell 2016; 7:403-16. [PMID: 27113583 PMCID: PMC4887326 DOI: 10.1007/s13238-016-0264-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/10/2016] [Indexed: 11/29/2022] Open
Abstract
YfiBNR is a recently identified bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. It is a key regulator of biofilm formation, which is correlated with prolonged persistence of infection and antibiotic drug resistance. In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. However, the detailed regulatory mechanism remains elusive. Here, we report the crystal structures of YfiB alone and of an active mutant YfiBL43P complexed with YfiR with 2:2 stoichiometry. Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiBL43P adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiBL43P shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiBL43P-induced biofilm formation. Based on the structural and biochemical data, we propose an updated regulatory model of the YfiBNR system.
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Affiliation(s)
- Min Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuan Yang
- Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiu-An Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tie-Zheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zusen Fan
- Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Tao Jiang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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25
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Helicobacter pylori adaptation in vivo in response to a high-salt diet. Infect Immun 2015; 83:4871-83. [PMID: 26438795 DOI: 10.1128/iai.00918-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/30/2015] [Indexed: 12/21/2022] Open
Abstract
Helicobacter pylori exhibits a high level of intraspecies genetic diversity. In this study, we investigated whether the diversification of H. pylori is influenced by the composition of the diet. Specifically, we investigated the effect of a high-salt diet (a known risk factor for gastric adenocarcinoma) on H. pylori diversification within a host. We analyzed H. pylori strains isolated from Mongolian gerbils fed either a high-salt diet or a regular diet for 4 months by proteomic and whole-genome sequencing methods. Compared to the input strain and output strains from animals fed a regular diet, the output strains from animals fed a high-salt diet produced higher levels of proteins involved in iron acquisition and oxidative-stress resistance. Several of these changes were attributable to a nonsynonymous mutation in fur (fur-R88H). Further experiments indicated that this mutation conferred increased resistance to high-salt conditions and oxidative stress. We propose a model in which a high-salt diet leads to high levels of gastric inflammation and associated oxidative stress in H. pylori-infected animals and that these conditions, along with the high intraluminal concentrations of sodium chloride, lead to selection of H. pylori strains that are most fit for growth in this environment.
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26
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Turner L, Praszkier J, Hutton ML, Steer D, Ramm G, Kaparakis-Liaskos M, Ferrero RL. Increased Outer Membrane Vesicle Formation in a Helicobacter pylori tolB Mutant. Helicobacter 2015; 20:269-83. [PMID: 25669590 DOI: 10.1111/hel.12196] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Multiple studies have established the importance of the tol-pal gene cluster in bacterial cell membrane integrity and outer membrane vesicle (OMV) formation in Escherichia coli. In contrast, the functions of Tol-Pal proteins in pathogenic organisms, including those of the Epsilonproteobacteria, remain poorly if at all defined. The aim of this study was to characterize the roles of two key components of the Tol-Pal system, TolB and Pal, in OMV formation in the pathogenic bacterium, Helicobacter pylori. METHODS H. pylori ΔtolB, Δpal and ΔtolBpal mutants, as well as complemented strains, were generated and assessed for changes in morphology and OMV production by scanning electron microscopy and enzyme-linked immunoassay (ELISA), respectively. The protein content and pro-inflammatory properties of OMVs were determined by mass spectroscopy and interleukin-8 (IL-8) ELISA on culture supernatants from OMV-stimulated cells, respectively. RESULTS H. pylori ΔtolB and Δpal bacteria exhibited aberrant cell morphology and/or flagella biosynthesis. Importantly, the disruption of H. pylori tolB but not pal resulted in a significant increase in OMV production. The OMVs from H. pylori ΔtolB and Δpal bacteria harbored many of the major outer membrane and virulence proteins observed in wild-type (WT) OMVs. Interestingly, ΔtolB, Δpal and ΔtolBpal OMVs induced significantly higher levels of IL-8 production by host cells, compared with WT OMVs. CONCLUSIONS This work demonstrates that TolB and Pal are important for membrane integrity in H. pylori. Moreover, it shows how H. pylori tolB-pal genes may be manipulated to develop "hypervesiculating" strains for vaccine purposes.
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Affiliation(s)
- Lorinda Turner
- Centre for Innate Immunity and Infectious Diseases, MIMR-PHI Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, (3168), Victoria, Australia
| | - Judyta Praszkier
- Centre for Innate Immunity and Infectious Diseases, MIMR-PHI Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, (3168), Victoria, Australia
| | - Melanie L Hutton
- Centre for Innate Immunity and Infectious Diseases, MIMR-PHI Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, (3168), Victoria, Australia
| | - David Steer
- Monash Biomedical Proteomics Facility, Monash University, Wellington Road, Clayton, (3800), Victoria, Australia
| | - Georg Ramm
- Monash Micro Imaging, Monash University, Clayton, Victoria, Australia
| | - Maria Kaparakis-Liaskos
- Centre for Innate Immunity and Infectious Diseases, MIMR-PHI Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, (3168), Victoria, Australia
| | - Richard L Ferrero
- Centre for Innate Immunity and Infectious Diseases, MIMR-PHI Institute of Medical Research, Monash University, 27-31 Wright Street, Clayton, (3168), Victoria, Australia
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27
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Belitsky BR. Role of PdxR in the activation of vitamin B6 biosynthesis in Listeria monocytogenes. Mol Microbiol 2014; 92:1113-28. [PMID: 24730374 DOI: 10.1111/mmi.12618] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2014] [Indexed: 11/28/2022]
Abstract
Listeria monocytogenes PdxR is a member of the poorly characterized but widespread group of MocR/GabR-type chimeric bacterial proteins that have DNA-binding and aminotransferase-like domains. Using mutational analysis, real-time RT-PCR, transcriptional fusions, gel-shift assays, DNase I footprinting, and in vitro transcription, it was shown that PdxR is a direct activator of the pdxST operon, transcribed divergently from pdxR and responsible for the de novo synthesis of pyridoxal 5'-phosphate (PLP), the major active form of vitamin B6 . PLP acts as an anti-activator of PdxR and is the only effector required to reduce the activity of PdxR. PdxR is also a negative autoregulator, and its ability to repress is increased by PLP. A dyad-symmetry sequence, which overlaps the -35 region of the pdxS promoter and lies downstream of the pdxR transcription start point, serves as an important element of the PdxR binding site. Unexpectedly, some mutations in this activator binding site, disrupting the dyad-symmetry element, caused constitutive, B6 -independent expression from the pdxS promoter. The data suggest that PdxR-like proteins, for which PLP plays just a signalling role, form a separate functional group among the MocR/GabR-type proteins.
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Affiliation(s)
- Boris R Belitsky
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
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28
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Nodwell MB, Koch MF, Alte F, Schneider S, Sieber SA. A subfamily of bacterial ribokinases utilizes a hemithioacetal for pyridoxal phosphate salvage. J Am Chem Soc 2014; 136:4992-9. [PMID: 24601602 DOI: 10.1021/ja411785r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) is the active vitamer of vitamin B6 and acts as an essential cofactor in many aspects of amino acid and sugar metabolism. The virulence and survival of pathogenic bacteria such as Mycobacterium tuberculosis depend on PLP, and deficiencies in humans have also been associated with neurological disorders and inflammation. While PLP can be synthesized by a de novo pathway in bacteria and plants, most higher organisms rely on a salvage pathway that phosphorylates either pyridoxal (PL) or its related vitamers, pyridoxine (PN) and pyridoxamine (PM). PL kinases (PLKs) are essential for this phosphorylation step and are thus of major importance for cellular viability. We recently identified a pyridoxal kinase (SaPLK) as a target of the natural product antibiotic rugulactone (Ru) in Staphylococcus aureus. Surprisingly, Ru selectively modified SaPLK not at the active site cysteine, but on a remote cysteine residue. Based on structural and biochemical studies, we now provide insight into an unprecedented dual Cys charge relay network that is mandatory for PL phosphorylation. The key component is the reactive Cys 110 residue in the lid region that forms a hemithioactetal intermediate with the 4'-aldehyde of PL. This hemithioacetal, in concert with the catalytic Cys 214, increases the nucleophilicity of the PL 5'-OH group for the inline displacement reaction with the γ-phosphate of ATP. A closer inspection of related enzymes reveals that Cys 110 is conserved and thus serves as a characteristic mechanistic feature for a dual-function ribokinase subfamily herein termed CC-PLKs.
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Affiliation(s)
- Matthew B Nodwell
- Organic Chemistry II, Centre for Integrated Protein Science CIPSM, Institute of Advanced Studies, and ‡Biochemistry, Department of Chemistry, Technische Universität München , Lichtenbergstrasse 4, 85747 Garching, Germany
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29
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Brown MJ, Russo BC, O'Dee DM, Schmitt DM, Nau GJ. The contribution of the glycine cleavage system to the pathogenesis of Francisella tularensis. Microbes Infect 2013; 16:300-9. [PMID: 24374051 DOI: 10.1016/j.micinf.2013.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 12/04/2013] [Accepted: 12/17/2013] [Indexed: 02/07/2023]
Abstract
Biosynthesis and acquisition of nutrients during infection are integral to pathogenesis. Members of a metabolic pathway, the glycine cleavage system, have been identified in virulence screens of the intracellular bacterium Francisella tularensis but their role in pathogenesis remains unknown. This system generates 5,10-methylenetetrahydrofolate, a precursor of amino acid and DNA synthesis, from glycine degradation. To characterize this pathway, deletion of the gcvT homolog, an essential member of this system, was performed in attenuated and virulent F. tularensis strains. Deletion mutants were auxotrophic for serine but behaved similar to wild-type strains with respect to host cell invasion, intracellular replication, and stimulation of TNF-α. Unexpectedly, the glycine cleavage system was required for the pathogenesis of virulent F. tularensis in a murine model. Deletion of the gcvT homolog delayed mortality and lowered bacterial burden, particularly in the liver and bloodstream. To reconcile differences between the cell culture model and animal model, minimal tissue culture media was employed to mimic the nutritionally limiting environment of the host. This reevaluation demonstrated that the glycine cleavage system contributes to the intracellular replication of virulent F. tularensis in serine limiting environments. Thus, the glycine cleavage system is the serine biosynthetic pathway of F. tularensis and contributes to pathogenesis in vivo.
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Affiliation(s)
- Matthew J Brown
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Brian C Russo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Dawn M O'Dee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Deanna M Schmitt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Gerard J Nau
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Department of Medicine - Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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30
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Pich OQ, Merrell DS. The ferric uptake regulator of Helicobacter pylori: a critical player in the battle for iron and colonization of the stomach. Future Microbiol 2013; 8:725-38. [PMID: 23701330 DOI: 10.2217/fmb.13.43] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Helicobacter pylori is arguably one of the most successful pathogens; it colonizes the stomachs of more than half of the human population. Colonization and persistence in such an inhospitable niche requires the presence of exquisite adaptive mechanisms. One of the proteins that contributes significantly to the remarkable adaptability of H. pylori is the ferric uptake regulator (Fur), which functions as a master regulator of gene expression. In addition to genes directly related to iron homeostasis, Fur controls expression of several enzymes that play a central role in metabolism and energy production. The absence of Fur leads to severe H. pylori colonization defects and, accordingly, several Fur-regulated genes have been shown to be essential for colonization. Moreover, proteins encoded by Fur-regulated genes have a strong impact on redox homeostasis in the stomach and are major determinants of inflammation. In this review, we discuss the main roles of Fur in the biology of H. pylori and highlight the importance of this regulatory protein in the infectious process.
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Affiliation(s)
- Oscar Q Pich
- Department of Microbiology & Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
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31
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Mani S, Boelsterli UA, Redinbo MR. Understanding and modulating mammalian-microbial communication for improved human health. Annu Rev Pharmacol Toxicol 2013; 54:559-80. [PMID: 24160697 DOI: 10.1146/annurev-pharmtox-011613-140007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The fact that the bacteria in the human gastrointestinal (GI) tract play a symbiotic role was noted as early as 1885, well before we began to manage microbial infections using antibiotics. However, even with the first antimicrobial compounds used in humans, the sulfa drugs, microbes were recognized to be critically involved in the biotransformation of these therapeutics. Thus, the roles played by the microbiota in physiology and in the management of human health have long been appreciated. Detailed examinations of GI symbiotic bacteria that started in the early 2000s and the first phases of the Human Microbiome Project that were completed in 2012 have ushered in an exciting period of granularity with respect to the ecology, genetics, and chemistry of the mammalian-microbial axes of communication. Here we review aspects of the biochemical pathways at play between commensal GI bacteria and several mammalian systems, including both local-epithelia and nonlocal responses impacting inflammation, immunology, metabolism, and neurobiology. Finally, we discuss how the microbial biotransformation of therapeutic compounds, such as anticancer or nonsteroidal anti-inflammatory drugs, can be modulated to reduce toxicity and potentially improve therapeutic efficacy.
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Affiliation(s)
- Sridhar Mani
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
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32
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Mani S, Boelsterli UA, Redinbo MR. Understanding and modulating mammalian-microbial communication for improved human health. Annu Rev Pharmacol Toxicol 2013; 3. [PMID: 27942535 PMCID: PMC5145265 DOI: 10.11131/2016/101199] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The molecular basis for the regulation of the intestinal barrier is a very fertile research area. A growing body of knowledge supports the targeting of various components of intestinal barrier function as means to treat a variety of diseases, including the inflammatory bowel diseases. Herein, we will summarize the current state of knowledge of key xenobiotic receptor regulators of barrier function, highlighting recent advances, such that the field and its future are succinctly reviewed. We posit that these receptors confer an additional dimension of host-microbe interaction in the gut, by sensing and responding to metabolites released from the symbiotic microbiota, in innate immunity and also in host drug metabolism. The scientific evidence for involvement of the receptors and its molecular basis for the control of barrier function and innate immunity regulation would serve as a rationale towards development of non-toxic probes and ligands as drugs.
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Affiliation(s)
- Sridhar Mani
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
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33
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Asakura H, Hashii N, Uema M, Kawasaki N, Sugita-Konishi Y, Igimi S, Yamamoto S. Campylobacter jejuni pdxA affects flagellum-mediated motility to alter host colonization. PLoS One 2013; 8:e70418. [PMID: 23936426 PMCID: PMC3735588 DOI: 10.1371/journal.pone.0070418] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 06/24/2013] [Indexed: 11/18/2022] Open
Abstract
Vitamin B6 (pyridoxal-5'-phosphate, PLP) is linked to a variety of biological functions in prokaryotes. Here, we report that the pdxA (putative 4-hydroxy-L-threonine phosphate dehydrogenase) gene plays a pivotal role in the PLP-dependent regulation of flagellar motility, thereby altering host colonization in a leading foodborne pathogen, Campylobacter jejuni. A C. jejuni pdxA mutant failed to produce PLP and exhibited a coincident loss of flagellar motility. Mass spectrometric analyses showed a 3-fold reduction in the main flagellar glycan pseudaminic acid (Pse) associated with the disruption of pdxA. The pdxA mutant also exhibited reduced growth rates compared with the WT strain. Comparative metabolomic analyses revealed differences in respiratory/energy metabolism between WT C. jejuni and the pdxA mutant, providing a possible explanation for the differential growth fitness between the two strains. Consistent with the lack of flagellar motility, the pdxA mutant showed impaired motility-mediated responses (bacterial adhesion, ERK1/2 activation, and IL-8 production) in INT407 cells and reduced colonization of chickens compared with the WT strain. Overall, this study demonstrated that the pdxA gene affects the PLP-mediated flagellar motility function, mainly through alteration of Pse modification, and the disruption of this gene also alters the respiratory/energy metabolisms to potentially affect host colonization. Our data therefore present novel implications regarding the utility of PLP and its dependent enzymes as potent target(s) for the control of this pathogen in the poultry host.
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Affiliation(s)
- Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, Setagaya-ku, Tokyo, Japan.
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The vitamin B₆ biosynthesis pathway in Streptococcus pneumoniae is controlled by pyridoxal 5'-phosphate and the transcription factor PdxR and has an impact on ear infection. J Bacteriol 2013; 195:2187-96. [PMID: 23475965 DOI: 10.1128/jb.00041-13] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vitamin B₆ is an essential cofactor for a large number of enzymes in both prokaryotes and eukaryotes. In this study, we characterized the pyridoxal 5'-phosphate (PLP) biosynthesis pathway in Streptococcus pneumoniae. Our results revealed that S. pneumoniae possesses a de novo vitamin B₆ biosynthesis pathway encoded by the pdxST genes. Purified PdxS functionally displayed as PLP synthase, whereas PdxT exhibited glutaminase activity in vitro. Deletion of pdxS, but not pdxT, resulted in a vitamin B₆ auxotrophic mutant. The defective growth of the ΔpdxS mutant in a vitamin B₆-depleted medium could be chemically restored in the presence of the B₆ vitamers at optimal concentrations. By analyzing PdxS expression levels, we demonstrated that the expression of pdxS was repressed by PLP and activated by a transcription factor, PdxR. A pneumococcal ΔpdxR mutant also exhibited as a vitamin B₆ auxotroph. In addition, we found that disruption of the vitamin B₆ biosynthesis pathway in S. pneumoniae caused a significant attenuation in a chinchilla middle ear infection model and a minor attenuation in a mouse pneumonia model, indicating that the impact of vitamin B₆ synthesis on virulence depends upon the bacterial infection niche.
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Pich OQ, Carpenter BM, Gilbreath JJ, Merrell DS. Detailed analysis of Helicobacter pylori Fur-regulated promoters reveals a Fur box core sequence and novel Fur-regulated genes. Mol Microbiol 2012; 84:921-41. [PMID: 22507395 DOI: 10.1111/j.1365-2958.2012.08066.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In Helicobacter pylori, iron balance is controlled by the Ferric uptake regulator (Fur), an iron-sensing repressor protein that typically regulates expression of genes implicated in iron transport and storage. Herein, we carried out extensive analysis of Fur-regulated promoters and identified a 7-1-7 motif with dyad symmetry (5'-TAATAATnATTATTA-3'), which functions as the Fur box core sequence of H. pylori. Addition of this sequence to the promoter region of a typically non-Fur regulated gene was sufficient to impose Fur-dependent regulation in vivo. Moreover, mutation of this sequence within Fur-controlled promoters negated regulation. Analysis of the H. pylori chromosome for the occurrence of the Fur box established the existence of well-conserved Fur boxes in the promoters of numerous known Fur-regulated genes, and revealed novel putative Fur targets. Transcriptional analysis of the new candidate genes demonstrated Fur-dependent repression of HPG27_51, HPG27_52, HPG27_199, HPG27_445, HPG27_825 and HPG27_1063, as well as Fur-mediated activation of the cytotoxin associated gene A, cagA (HPG27_507). Furthermore, electrophoretic mobility shift assays confirmed specific binding of Fur to the promoters of each of these genes. Future experiments will determine whether loss of Fur regulation of any of these particular genes contributes to the defects in colonization exhibited by the H. pylori fur mutant.
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Affiliation(s)
- Oscar Q Pich
- Department of Microbiology and Immunology, Uniformed Services University of the Heath Sciences, Bethesda, MD 20814, USA
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Vitamin B6 hits H. pylori sweet spot. Nat Rev Microbiol 2010. [DOI: 10.1038/nrmicro2444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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