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Tsai CY, Oo M, Peh JH, Yeo BCM, Aptekmann A, Lee B, Liu JJJ, Tsao WS, Dick T, Fink K, Gengenbacher M. Splenic marginal zone B cells restrict Mycobacterium tuberculosis infection by shaping the cytokine pattern and cell-mediated immunity. Cell Rep 2024; 43:114426. [PMID: 38959109 DOI: 10.1016/j.celrep.2024.114426] [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: 12/14/2023] [Revised: 04/29/2024] [Accepted: 06/17/2024] [Indexed: 07/05/2024] Open
Abstract
Understanding the role of B cells in tuberculosis (TB) is crucial for developing new TB vaccines. However, the changes in B cell immune landscapes during TB and their functional implications remain incompletely explored. Using high-dimensional flow cytometry to map the immune landscape in response to Mycobacterium tuberculosis (Mtb) infection, our results show an accumulation of marginal zone B (MZB) cells and other unconventional B cell subsets in the lungs and spleen, shaping an unconventional B cell landscape. These MZB cells exhibit activated and memory-like phenotypes, distinguishing their functional profiles from those of conventional B cells. Notably, functional studies show that MZB cells produce multiple cytokines and contribute to systemic protection against TB by shaping cytokine patterns and cell-mediated immunity. These changes in the immune landscape are reversible upon successful TB chemotherapy. Our study suggests that, beyond antibody production, targeting the regulatory function of B cells may be a valuable strategy for TB vaccine development.
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Affiliation(s)
- Chen-Yu Tsai
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Myo Oo
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Jih Hou Peh
- Biosafety Level 3 Core, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Level 15, Centre for Translational Medicine (MD6), NUS, 14 Medical Drive, Singapore 117599, Singapore
| | - Benjamin C M Yeo
- Infectious Diseases Translational Research Programme and Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Level 2, Blk MD4, 5 Science Drive 2, Singapore 117545, Singapore
| | - Ariel Aptekmann
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Bernett Lee
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research, Biopolis, 8A Biomedical Grove, Level 3 & 4, Immunos Building, Singapore 138648, Singapore; Centre for Biomedical Informatics, Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; A(∗)STAR Infectious Diseases Labs, Agency for Science, Technology and Research, 8A Biomedical Grove #05-13, Immunos, Singapore 138648, Singapore
| | - Joe J J Liu
- Biosafety Level 3 Core, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Level 15, Centre for Translational Medicine (MD6), NUS, 14 Medical Drive, Singapore 117599, Singapore
| | - Wen-Shan Tsao
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Thomas Dick
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA; Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
| | - Katja Fink
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research, Biopolis, 8A Biomedical Grove, Level 3 & 4, Immunos Building, Singapore 138648, Singapore
| | - Martin Gengenbacher
- Center for Discovery and Innovation (CDI), Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA; Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA.
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2
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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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3
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Barra ALC, Ullah N, Brognaro H, Gutierrez RF, Wrenger C, Betzel C, Nascimento AS. Structure and dynamics of the staphylococcal pyridoxal 5-phosphate synthase complex reveal transient interactions at the enzyme interface. J Biol Chem 2024; 300:107404. [PMID: 38782204 PMCID: PMC11237949 DOI: 10.1016/j.jbc.2024.107404] [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: 10/31/2023] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Infectious diseases are a significant cause of death, and recent studies estimate that common bacterial infectious diseases were responsible for 13.6% of all global deaths in 2019. Among the most significant bacterial pathogens is Staphylococcus aureus, accounting for more than 1.1 million deaths worldwide in 2019. Vitamin biosynthesis has been proposed as a promising target for antibacterial therapy. Here, we investigated the biochemical, structural, and dynamic properties of the enzyme complex responsible for vitamin B6 (pyridoxal 5-phosphate, PLP) biosynthesis in S. aureus, which comprises enzymes SaPdx1 and SaPdx2. The crystal structure of the 24-mer complex of SaPdx1-SaPdx2 enzymes indicated that the S. aureus PLP synthase complex forms a highly dynamic assembly with transient interaction between the enzymes. Solution scattering data indicated that SaPdx2 typically binds to SaPdx1 at a substoichiometric ratio. We propose a structure-based view of the PLP synthesis mechanism initiated with the assembly of SaPLP synthase complex that proceeds in a highly dynamic interaction between Pdx1 and Pdx2. This interface interaction can be further explored as a potentially druggable site for the design of new antibiotics.
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Affiliation(s)
- Angélica Luana C Barra
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil; Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Najeeb Ullah
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany; Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Raissa F Gutierrez
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany; Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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4
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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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5
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Farkas C, Retamal-Fredes E, Ávila A, Fehlings MG, Vidal PM. Degenerative Cervical Myelopathy induces sex-specific dysbiosis in mice. Front Microbiol 2023; 14:1229783. [PMID: 37928672 PMCID: PMC10623434 DOI: 10.3389/fmicb.2023.1229783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023] Open
Abstract
Degenerative Cervical Myelopathy (DCM) is the most common cause of spinal cord impairment in elderly populations. It describes a spectrum of disorders that cause progressive spinal cord compression, neurological impairment, loss of bladder and bowel functions, and gastrointestinal dysfunction. The gut microbiota has been recognized as an environmental factor that can modulate both the function of the central nervous system and the immune response through the microbiota-gut-brain axis. Changes in gut microbiota composition or microbiota-producing factors have been linked to the progression and development of several pathologies. However, little is known about the potential role of the gut microbiota in the pathobiology of DCM. Here, DCM was induced in C57BL/6 mice by implanting an aromatic polyether material underneath the C5-6 laminae. The extent of DCM-induced changes in microbiota composition was assessed by 16S rRNA sequencing of the fecal samples. The immune cell composition was assessed using flow cytometry. To date, several bacterial members have been identified using BLAST against the largest collection of metagenome-derived genomes from the mouse gut. In both, female and males DCM caused gut dysbiosis compared to the sham group. However, dysbiosis was more pronounced in males than in females, and several bacterial members of the families Lachnospiraceae and Muribaculaceae were significantly altered in the DCM group. These changes were also associated with altered microbe-derived metabolic changes in propionate-, butyrate-, and lactate-producing bacterial members. Our results demonstrate that DCM causes dynamic changes over time in the gut microbiota, reducing the abundance of butyrate-producing bacteria, and lactate-producing bacteria to a lesser extent. Genome-scale metabolic modeling using gapseq successfully identified pyruvate-to-butanoate and pyruvate-to-propionate reactions involving genes such as Buk and ACH1, respectively. These results provide a better understanding of the sex-specific molecular effects of changes in the gut microbiota on DCM pathobiology.
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Affiliation(s)
- Carlos Farkas
- Biomedical Science Research Laboratory, Department of Basic Sciences, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Eduardo Retamal-Fredes
- Biomedical Science Research Laboratory, Developmental Neurobiology Unit, Department of Basic Sciences, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Ariel Ávila
- Biomedical Science Research Laboratory, Developmental Neurobiology Unit, Department of Basic Sciences, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Michael G Fehlings
- Department of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Spinal Program, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Pia M Vidal
- Biomedical Science Research Laboratory, Neuroimmunology and Regeneration of the Central Nervous System Unit, Department of Basic Sciences, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción, Chile
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6
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Lu P, Dong X, Ji X. Cronobacter sakazakii Pyridoxal Kinase PdxY Mediated by TreR and pESA3 Is Essential for Vitamin B 6 (PLP) Maintenance and Virulence. Appl Environ Microbiol 2023; 89:e0092423. [PMID: 37458600 PMCID: PMC10467337 DOI: 10.1128/aem.00924-23] [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: 06/01/2023] [Accepted: 06/27/2023] [Indexed: 08/31/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen capable of causing severe infections, particularly in neonates. Despite the bacterium's strong pathogenicity, the pathogenicity of C. sakazakii is not yet well understood. Using a comparative proteomic profiling approach, we successfully identified pdxY, encoding a pyridoxal kinase involved in the recycling of pyridoxal 5'-phosphate (PLP), as a gene essential for the successful pathogenesis of C. sakazakii. Knocking out the pdxY gene resulted in slower growth and reduced virulence. Our study sheds light on the fundamental importance of pyridoxal kinase for the survival and virulence of C. sakazakii. The identification of pdxY as gene essential for successful pathogenesis provides a potential target for the development of new antibiotic treatments. IMPORTANCE The opportunistic pathogen Cronobacter sakazakii is known to cause severe infections, particularly in neonates, and can result in high mortality rates. In this study, we used a comparative proteomic profiling approach to identify genes essential for the successful pathogenesis of C. sakazakii. We successfully identified pdxY, encoding a pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP), as a gene essential for the successful pathogenesis of C. sakazakii. Knocking out the pdxY gene resulted in impaired growth and reduced virulence. This study sheds light on the fundamental importance of pyridoxal kinase for the survival and virulence of C. sakazakii, which can be a potential target for the development of new antibiotic treatments. This study highlights the importance of comparative proteomic profiling in identifying virulence factors that can be targeted for the development of new antibiotics.
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Affiliation(s)
- Ping Lu
- Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye Hospital, Tianjin, China
- Nankai University Affiliated Eye Hospital, Nankai University, Tianjin, China
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Xiaoli Dong
- Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin Eye Hospital, Tianjin, China
- Nankai University Affiliated Eye Hospital, Nankai University, Tianjin, China
- Clinical College of Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Xuemeng Ji
- School of Medicine, Nankai University, Tianjin, China
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Nimma R, Kumar A, Gani Z, Gahlawat A, Dilawari R, Rohilla RK, Kumbhar H, Garg P, Chopra S, Raje M, Iyengar Raje C. Characterization of the enzymatic and multifunctional properties of Acinetobacter baumannii erythrose-4-phosphate dehydrogenase (E4PDH). Microb Pathog 2023; 175:105992. [PMID: 36649779 DOI: 10.1016/j.micpath.2023.105992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
Infections due to Acinetobacter baumannii (A. baumannii) are rapidly increasing worldwide and consequently therapeutic options for treatment are limited. The emergence of multi drug resistant (MDR) strains has rendered available antibiotics ineffective, necessitating the urgent discovery of new drugs and drug targets. The vitamin B6 biosynthetic pathway has been considered as a potential antibacterial drug target but it is as yet uncharacterized for A. baumannii. In the current work, we have carried out in silico and biochemical characterization of Erythrose-4-phosphate dehydrogenase (E4PDH) (EC 1.2.1.72). This enzyme catalyzes the first step in the deoxyxylulose-5-phosphate (DXP) dependent Vitamin B6 biosynthetic pathway i.e. the conversion of d-erythrose-4-phosphate (E4P) to 4-Phosphoerythronate. E4PDH also possesses an additional activity whereby it can catalyze the conversion of Glyceraldehyde-3-phosphate (G3P) to 1,3 bisphosphoglycerate (1,3BPG). Our studies have revealed that this enzyme exhibits an alternate moonlighting function as a cell surface receptor for the human iron transport proteins transferrin (Tf) and lactoferrin (Lf). The present work reports the internalization of Tf and consequent iron acquisition as an alternate strategy for iron acquisition. Given its essential role in two crucial pathways i.e. metabolism and iron acquisition, A. baumannii E4PDH may play a vital role in bacterial pathogenesis.
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Affiliation(s)
- Ramesh Nimma
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Ajay Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Zahid Gani
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Anuj Gahlawat
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Rahul Dilawari
- Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Sector 39A, Chandigarh, 160036, India
| | - Rajesh Kumar Rohilla
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Hemangi Kumbhar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India
| | - Sidharth Chopra
- Council of Scientific and Industrial Research-CSIR (CSIR-CDRI), Sector10, Janakipuram Extension, Sitapur Road, Lucknow, 226031, UP, India
| | - Manoj Raje
- Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Sector 39A, Chandigarh, 160036, India
| | - Chaaya Iyengar Raje
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, Punjab, 160062, India.
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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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9
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Carfrae LA, Brown ED. Nutrient stress is a target for new antibiotics. Trends Microbiol 2023; 31:571-585. [PMID: 36709096 DOI: 10.1016/j.tim.2023.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/28/2023]
Abstract
Novel approaches are required to address the looming threat of pan-resistant Gram-negative pathogens and forestall the rise of untreatable infections. Unconventional targets that are uniquely important during infection and tractable to high-throughput drug discovery methods hold high potential for innovation in antibiotic discovery programs. In this context, inhibitors of bacterial nutrient stress are particularly exciting candidates for future antibiotic development. Amino acid, nucleotide, and vitamin biosynthesis pathways are critical for bacterial growth in nutrient-limiting conditions in the laboratory and the host. Although historically dismissed as dispensable for pathogens, a wealth of transposon mutagenesis and single-mutant studies have emerged which demonstrate that several such pathways are critical for infection. Indeed, high-throughput screens of diverse synthetic compounds and natural products have uncovered inhibitors of nutrient biosynthesis. Herein, we review bacterial nutrient biosynthesis and its role during host infection. Further, we explore screening platforms developed to search for inhibitors of these targets and highlight successes among these. Finally, we feature important and sometimes surprising connections between bacterial nutrient biosynthesis, antibiotic activity, and antibiotic resistance.
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Affiliation(s)
- Lindsey A Carfrae
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Eric D Brown
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Present address: Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada.
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10
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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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11
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Auxotrophic Mycobacterium bovis BCG: Updates and Perspectives. Vaccines (Basel) 2022; 10:vaccines10050802. [PMID: 35632558 PMCID: PMC9146772 DOI: 10.3390/vaccines10050802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 12/05/2022] Open
Abstract
Mycobacterium bovis BCG has been used for a century as the only licensed vaccine against tuberculosis. Owing to its strong adjuvant properties, BCG has also been employed as an oncological immunotherapeutic as well as a live vaccine vector against other pathogens. However, BCG vaccination has limited efficacy in protecting against adult forms of tuberculosis (TB), raises concerns about its safety in immunocompromised populations, compromises the diagnosis of TB through the tuberculin test and lacks predictability for successful antigen expression and immune responses to heterologous antigens. Together, these factors propelled the construction and evaluation of auxotrophic BCG strains. Auxotrophs of BCG have been developed from mutations in the genes required for their growth using different approaches and have shown the potential to provide a model to study M. tuberculosis, a more stable, safe, and effective alternative to BCG and a vector for the development of recombinant live vaccines, especially against HIV infection. In this review, we provide an overview of the strategies for developing and using the auxotrophic BCG strains in different scenarios.
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12
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Li ZB, Shi LY, Han YS, Chen J, Zhang SQ, Chen JX, Liu J, Tu HH, Lu QQ, Yu Y, Jiang TT, Li JC. Pyridoxal phosphate, pyridoxamine phosphate, and folic acid based on ceRNA regulatory network as potential biomarkers for the diagnosis of pulmonary tuberculosis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105240. [PMID: 35150890 DOI: 10.1016/j.meegid.2022.105240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 10/27/2021] [Accepted: 02/06/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pulmonary tuberculosis (TB) is a serious disease burden worldwide, and its effective early diagnosis is still facing challenges. Knowledge, acquired from multi-omics integration analysis about the association between different types of differentially expressed molecules in the plasma of TB patients and the disease traits, is anticipated to improve the accuracy of TB diagnosis through the "integrative pattern". METHODS In this study, the lncRNA-miRNA-mRNA interaction network was constructed based on the competing endogenous RNA (ceRNA) hypothesis by integrating our previous data sets of lncRNA, mRNA, miRNA, and metabolites. Moreover, the key regulatory axis was established by co-expression analysis and verified at the level of metabolites. RESULTS A ceRNA regulatory network consisting of 23 lncRNAs, 10 miRNAs, and 113 mRNAs was constructed. The analysis results suggested that lncRNA (OSBPL10-AS1), miRNA (has-miR-485-5p), and mRNA (SLC23A2) might be involved in the regulation of vitamin metabolism in patients with TB. Metabolite analysis showed that compared with the normal control group, TB patients had abnormal vitamin metabolism, and the expression levels of pyridoxal phosphate, pyridoxamine phosphate, and folic acid were significantly different between the two groups (p < 0.05). CONCLUSION Integrated multi-omics analysis showed that vitamin metabolism disorder may be one of the pathological characteristic of TB. OSBPL10-AS1, hsa-miR-485-5p, SLC23A2, pyridoxal phosphate, pyridoxamine phosphate, and folic acid may collectively constitute the "integrative pattern" of multiple biomarkers, which may provide an accurate diagnosis of TB.
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Affiliation(s)
- Zhi-Bin Li
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310058, China
| | - Yu-Shuai Han
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jing Chen
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shan-Qiang Zhang
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Jia-Xi Chen
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jun Liu
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Hui-Hui Tu
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qi-Qi Lu
- Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Yi Yu
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ting-Ting Jiang
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China
| | - Ji-Cheng Li
- The Central Laboratory, Yangjiang People's Hospital, Yangjiang 529500, China; Medical Research Center, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan 512025, China; Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China.
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13
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Smith CM, Baker RE, Proulx MK, Mishra BB, Long JE, Park SW, Lee HN, Kiritsy MC, Bellerose MM, Olive AJ, Murphy KC, Papavinasasundaram K, Boehm FJ, Reames CJ, Meade RK, Hampton BK, Linnertz CL, Shaw GD, Hock P, Bell TA, Ehrt S, Schnappinger D, Pardo-Manuel de Villena F, Ferris MT, Ioerger TR, Sassetti CM. Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. eLife 2022; 11:74419. [PMID: 35112666 PMCID: PMC8846590 DOI: 10.7554/elife.74419] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/27/2022] [Indexed: 11/21/2022] Open
Abstract
The outcome of an encounter with Mycobacterium tuberculosis (Mtb) depends on the pathogen’s ability to adapt to the variable immune pressures exerted by the host. Understanding this interplay has proven difficult, largely because experimentally tractable animal models do not recapitulate the heterogeneity of tuberculosis disease. We leveraged the genetically diverse Collaborative Cross (CC) mouse panel in conjunction with a library of Mtb mutants to create a resource for associating bacterial genetic requirements with host genetics and immunity. We report that CC strains vary dramatically in their susceptibility to infection and produce qualitatively distinct immune states. Global analysis of Mtb transposon mutant fitness (TnSeq) across the CC panel revealed that many virulence pathways are only required in specific host microenvironments, identifying a large fraction of the pathogen’s genome that has been maintained to ensure fitness in a diverse population. Both immunological and bacterial traits can be associated with genetic variants distributed across the mouse genome, making the CC a unique population for identifying specific host-pathogen genetic interactions that influence pathogenesis.
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Affiliation(s)
- Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Megan K Proulx
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Bibhuti B Mishra
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Jarukit E Long
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Michael C Kiritsy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Michelle M Bellerose
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Andrew J Olive
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Frederick J Boehm
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Charlotte J Reames
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Morrisville, United States
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Timothy A Bell
- Department of Genetics,, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | | | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, United States
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
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14
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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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15
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Pina AF, Sousa SF, Cerqueira NMFSA. The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys-His-Glu Triad: A Computational Study. Chembiochem 2021; 23:e202100555. [PMID: 34762772 DOI: 10.1002/cbic.202100555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/10/2021] [Indexed: 11/08/2022]
Abstract
The catalytic mechanism of Pdx2 was studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia - the source of the nitrogen of pyridoxal 5'-phosphate (PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens that rely on this mechanism to obtain PLP. For this reason, Pdx2 is considered a novel and promising drug target to treat these diseases. The results obtained show that the catalytic mechanism of Pdx2 occurs in six steps that can be divided into four stages: (i) activation of Cys87 , (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover. The kinetic data available in the literature (19.1-19.5 kcal mol-1 ) agree very well with the calculated free energy barrier of the hydrolytic step (18.2 kcal.mol-11 ), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site. This catalytic mechanism differs from other known amidases in three main points: i) it requires the activation of the nucleophile Cys87 to a thiolate; ii) the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii) Glu198 does not have a direct role in the catalytic process. Together, these results can be used for the synthesis of new transition state analogue inhibitors capable of inhibiting Pdx2 and impair diseases like Malaria and Tuberculosis.
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Affiliation(s)
- André F Pina
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Sérgio F Sousa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Nuno M F S A Cerqueira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
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16
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Patti G, Pellegrino C, Ricciardi A, Novara R, Cotugno S, Papagni R, Guido G, Totaro V, De Iaco G, Romanelli F, Stolfa S, Minardi ML, Ronga L, Fato I, Lattanzio R, Bavaro DF, Gualano G, Sarmati L, Saracino A, Palmieri F, Di Gennaro F. Potential Role of Vitamins A, B, C, D and E in TB Treatment and Prevention: A Narrative Review. Antibiotics (Basel) 2021; 10:1354. [PMID: 34827292 PMCID: PMC8614960 DOI: 10.3390/antibiotics10111354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 10/31/2021] [Accepted: 11/04/2021] [Indexed: 12/26/2022] Open
Abstract
(1) Background: Tuberculosis (TB) is one of the world's top infectious killers, in fact every year 10 million people fall ill with TB and 1.5 million people die from TB. Vitamins have an important role in vital functions, due to their anti-oxidant, pro-oxidant, anti-inflammatory effects and to metabolic functions. The aim of this review is to discuss and summarize the evidence and still open questions regarding vitamin supplementation as a prophylactic measure in those who are at high risk of Mycobacterium tuberculosis (MTB) infection and active TB; (2) Methods: We conducted a search on PubMed, Scopus, Google Scholar, EMBASE, Cochrane Library and WHO websites starting from March 1950 to September 2021, in order to identify articles discussing the role of Vitamins A, B, C, D and E and Tuberculosis; (3) Results: Supplementation with multiple micronutrients (including zinc) rather than vitamin A alone may be more beneficial in TB. The WHO recommend Pyridoxine (vitamin B6) when high-dose isoniazid is administered. High concentrations of vitamin C sterilize drug-susceptible, MDR and extensively drug-resistant MTB cultures and prevent the emergence of drug persisters; Vitamin D suppresses the replication of mycobacterium in vitro while VE showed a promising role in TB management as a result of its connection with oxidative balance; (4) Conclusions: Our review suggests and encourages the use of vitamins in TB patients. In fact, their use may improve outcomes by helping both nutritionally and by interacting directly and/or indirectly with MTB. Several and more comprehensive trials are needed to reinforce these suggestions.
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Affiliation(s)
- Giulia Patti
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Carmen Pellegrino
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Aurelia Ricciardi
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Roberta Novara
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Sergio Cotugno
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Roberta Papagni
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Giacomo Guido
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Valentina Totaro
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Giuseppina De Iaco
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Federica Romanelli
- Microbiology and Virology Unit, University of Bari, University Hospital Policlinico, 70124 Bari, Italy; (F.R.); (S.S.); (L.R.)
| | - Stefania Stolfa
- Microbiology and Virology Unit, University of Bari, University Hospital Policlinico, 70124 Bari, Italy; (F.R.); (S.S.); (L.R.)
| | - Maria Letizia Minardi
- Infectious Diseases Clinic, University Hospital “Tor Vergata”, Department of Systems Medicine, University of Rome Tor Vergata, 00173 Rome, Italy; (M.L.M.); (I.F.); (L.S.)
| | - Luigi Ronga
- Microbiology and Virology Unit, University of Bari, University Hospital Policlinico, 70124 Bari, Italy; (F.R.); (S.S.); (L.R.)
| | - Ilenia Fato
- Infectious Diseases Clinic, University Hospital “Tor Vergata”, Department of Systems Medicine, University of Rome Tor Vergata, 00173 Rome, Italy; (M.L.M.); (I.F.); (L.S.)
| | - Rossana Lattanzio
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Davide Fiore Bavaro
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Gina Gualano
- National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00161 Rome, Italy;
| | - Loredana Sarmati
- Infectious Diseases Clinic, University Hospital “Tor Vergata”, Department of Systems Medicine, University of Rome Tor Vergata, 00173 Rome, Italy; (M.L.M.); (I.F.); (L.S.)
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Fabrizio Palmieri
- National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00161 Rome, Italy;
| | - Francesco Di Gennaro
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
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Lozano C, Lee C, Wattiez R, Lebaron P, Matallana-Surget S. Unraveling the molecular effects of oxybenzone on the proteome of an environmentally relevant marine bacterium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148431. [PMID: 34182435 DOI: 10.1016/j.scitotenv.2021.148431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
The use of Benzophenone-3 (BP3), also known as oxybenzone, a common UV filter, is a growing environmental concern in regard to its toxicity on aquatic organisms. Our previous work stressed that BP3 is toxic to Epibacterium mobile, an environmentally relevant marine α-proteobacterium. In this study, we implemented a label-free quantitative proteomics workflow to decipher the effects of BP3 on the E. mobile proteome. Furthermore, the effect of DMSO, one of the most common solvents used to vehicle low concentrations of lipophilic chemicals, was assessed to emphasize the importance of limiting solvent concentration in ecotoxicological studies. Data-independent analysis proteomics highlighted that BP3 induced changes in the regulation of 56 proteins involved in xenobiotic export, detoxification, oxidative stress response, motility, and fatty acid, iron and amino acid metabolisms. Our results also outlined that the use of DMSO at 0.046% caused regulation changes in proteins related to transport, iron uptake and metabolism, and housekeeping functions, underlining the need to reduce the concentration of solvents in ecotoxicological studies.
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Affiliation(s)
- Clément Lozano
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650 Banyuls-sur-mer, France; Division of Biological and Environmental Sciences, Faculty of Natural Sciences, Stirling University, United Kingdom
| | - Charlotte Lee
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, Stirling University, United Kingdom
| | - Ruddy Wattiez
- Department of Proteomic and Microbiology, University of Mons, Mons, Belgium
| | - Philippe Lebaron
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR3579, Observatoire Océanologique, 66650 Banyuls-sur-mer, France
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, Stirling University, United Kingdom.
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18
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Sinthusiri A, Champasri C, Trongpanich Y. Recombinant Expression, Purification and Characterization of Pyridoxal 5'-phosphate Synthase from Geobacillus sp. H6a, Thermophilic Bacterium Producing Extracellular Vitamin B6. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2575. [PMID: 35350642 PMCID: PMC8926315 DOI: 10.30498/ijb.2021.201202.2575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background Pyridoxal 5' -phosphate synthase (PLPS) is present in deoxyxylose 5'-phosphate-independent of the de novo vitamin B6 biosynthesis pathway. This enzyme complex consists of PdxS and PdxT, which function as synthase and glutamine amidotranferase respectively to produce PLP. Objectives This study aimed to clone, express, and purify PLPS of Geobacillus sp. H6a, followed by its characterization. Material and Methods The PdxS and PdxT genes were amplified from Geobacillus (Gh) sp. H6a. Recombinant vectors pET28a-GhpdxS and pET28a-GhpdxT were constructed and the resulting His-tagged proteins were expressed in E. coli BL21(DE3). The soluble rGhpdxS and rGhpdxT were purified via nickel-affinity chromatography and cation-exchange chromatography. The mixture of rGhpdxS and rGhpdxT was further characterized. Results The molecular weights of rGhpdxS and rGhpdxT were estimated to be 35 and 23 kDa by SDS-PAGE, respectively. The native form of rGhpdxS showed hexamer and dodecamer, whereas those of rGhpdxT were a monomer upon detection with non-denaturing gel electrophoresis and gel filtration. A molar ratio of 1:1 of rGhpdxS:rGhpdxT showed the highest PLP synthesis activity (4.16 U.mg-1) and was used for analyzing the biochemical properties. The kinetic values were obtained by using glyceraldehyde 3-phosphate, ribose 5-phosphate, and glutamine as the substrates. The rGhPLPS showed pentose phosphate isomerization without triose phosphate isomerase activity. The metal ions affected PLP synthesis activity. The optimum pH and optimum temperature of rGhPLPS were 9 and 70 °C, respectively. The rGhPLPS was active over a broad range of temperatures and pH values. Conclusions These results support the potential of rGhPLPS as a candidate for industrial application.
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Affiliation(s)
| | | | - Yanee Trongpanich
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
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19
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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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20
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Barra ALC, Ullah N, Morão LG, Wrenger C, Betzel C, Nascimento AS. Structural Dynamics and Perspectives of Vitamin B6 Biosynthesis Enzymes in Plasmodium: Advances and Open Questions. Front Cell Infect Microbiol 2021; 11:688380. [PMID: 34327152 PMCID: PMC8313854 DOI: 10.3389/fcimb.2021.688380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022] Open
Abstract
Malaria is still today one of the most concerning diseases, with 219 million infections in 2019, most of them in Sub-Saharan Africa and Latin America, causing approx. 409,000 deaths per year. Despite the tremendous advances in malaria treatment and prevention, there is still no vaccine for this disease yet available and the increasing parasite resistance to already existing drugs is becoming an alarming issue globally. In this context, several potential targets for the development of new drug candidates have been proposed and, among those, the de novo biosynthesis pathway for the B6 vitamin was identified to be a promising candidate. The reason behind its significance is the absence of the pathway in humans and its essential presence in the metabolism of major pathogenic organisms. The pathway consists of two enzymes i.e. Pdx1 (PLP synthase domain) and Pdx2 (glutaminase domain), the last constituting a transient and dynamic complex with Pdx1 as the prime player and harboring the catalytic center. In this review, we discuss the structural biology of Pdx1 and Pdx2, together with and the understanding of the PLP biosynthesis provided by the crystallographic data. We also highlight the existing evidence of the effect of PLP synthesis inhibition on parasite proliferation. The existing data provide a flourishing environment for the structure-based design and optimization of new substrate analogs that could serve as inhibitors or even suicide inhibitors.
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Affiliation(s)
- Angélica Luana C Barra
- Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil.,Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Najeeb Ullah
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Luana G Morão
- Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
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21
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Sanoussi CN, Coscolla M, Ofori-Anyinam B, Otchere ID, Antonio M, Niemann S, Parkhill J, Harris S, Yeboah-Manu D, Gagneux S, Rigouts L, Affolabi D, de Jong BC, Meehan CJ. Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv. Microb Genom 2021; 7:000437. [PMID: 34241588 PMCID: PMC8477398 DOI: 10.1099/mgen.0.000437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/22/2021] [Indexed: 12/27/2022] Open
Abstract
Pathogens of the Mycobacterium tuberculosis complex (MTBC) are considered to be monomorphic, with little gene content variation between strains. Nevertheless, several genotypic and phenotypic factors separate strains of the different MTBC lineages (L), especially L5 and L6 (traditionally termed Mycobacterium africanum) strains, from each other. However, this genome variability and gene content, especially of L5 strains, has not been fully explored and may be important for pathobiology and current approaches for genomic analysis of MTBC strains, including transmission studies. By comparing the genomes of 355 L5 clinical strains (including 3 complete genomes and 352 Illumina whole-genome sequenced isolates) to each other and to H37Rv, we identified multiple genes that were differentially present or absent between H37Rv and L5 strains. Additionally, considerable gene content variability was found across L5 strains, including a split in the L5.3 sub-lineage into L5.3.1 and L5.3.2. These gene content differences had a small knock-on effect on transmission cluster estimation, with clustering rates influenced by the selected reference genome, and with potential overestimation of recent transmission when using H37Rv as the reference genome. We conclude that full capture of the gene diversity, especially high-resolution outbreak analysis, requires a variation of the single H37Rv-centric reference genome mapping approach currently used in most whole-genome sequencing data analysis pipelines. Moreover, the high within-lineage gene content variability suggests that the pan-genome of M. tuberculosis is at least several kilobases larger than previously thought, implying that a concatenated or reference-free genome assembly (de novo) approach may be needed for particular questions.
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Affiliation(s)
- C. N'Dira Sanoussi
- Laboratoire de Référence des Mycobactéries, Cotonou, Benin
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mireia Coscolla
- I2SysBio, University of Valencia-FISABIO Joint Unit, Valencia, Spain
| | - Boatema Ofori-Anyinam
- Food and Drugs Authority, Accra, Ghana
- Rutgers New Jersey Medical School, Rutgers University, New Jersey, USA
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Martin Antonio
- Medical Research Council Unit in The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Stefan Niemann
- German Center for Infection Research, partner site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Research Center Borstel, Molecular and Experimental Mycobacteriology, Borstel, Germany
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Bouke C. de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
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22
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Navarrete-Euan H, Rodríguez-Escamilla Z, Pérez-Rueda E, Escalante-Herrera K, Martínez-Núñez MA. Comparing Sediment Microbiomes in Contaminated and Pristine Wetlands along the Coast of Yucatan. Microorganisms 2021; 9:microorganisms9040877. [PMID: 33923859 PMCID: PMC8073884 DOI: 10.3390/microorganisms9040877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 12/27/2022] Open
Abstract
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.
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Affiliation(s)
- Herón Navarrete-Euan
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Zuemy Rodríguez-Escamilla
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Unidad Académica Yucatán, Mérida, Yucatán 97302, Mexico;
| | - Karla Escalante-Herrera
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
| | - Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; (H.N.-E.); (Z.R.-E.); (K.E.-H.)
- Correspondence: ; Tel.: +52-999-3410860 (ext. 7631)
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23
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Yelamanchi SD, Surolia A. Targeting amino acid metabolism of Mycobacterium tuberculosis for developing inhibitors to curtail its survival. IUBMB Life 2021; 73:643-658. [PMID: 33624925 DOI: 10.1002/iub.2455] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 12/29/2022]
Abstract
Tuberculosis caused by the bacterium, Mycobacterium tuberculosis (Mtb), continues to remain one of the most devastating infectious diseases afflicting humans. Although there are several drugs for treating tuberculosis available currently, the emergence of the drug resistant forms of this pathogen has made its treatment and eradication a challenging task. While the replication machinery, protein synthesis and cell wall biogenesis of Mtb have been targeted often for anti-tubercular drug development a number of essential metabolic pathways crucial to its survival have received relatively less attention. In this context a number of amino acid biosynthesis pathways have recently been shown to be essential for the survival and pathogenesis of Mtb. Many of these pathways and or their key enzymes homologs are absent in humans hence they could be harnessed for anti-tubercular drug development. In this review, we describe comprehensively the amino acid metabolic pathways essential in Mtb and the key enzymes involved therein that are being investigated for developing inhibitors that compromise the survival and pathogenesis caused by this pathogen.
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Affiliation(s)
| | - Avadhesha Surolia
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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24
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Isonicotinoyl hydrazones of pyridoxine derivatives: synthesis and antimycobacterial activity. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02705-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Zheng W, Chen K, Fang S, Cheng X, Xu G, Yang L, Wu J. Construction and Application of PLP Self-sufficient Biocatalysis System for Threonine Aldolase. Enzyme Microb Technol 2020; 141:109667. [PMID: 33051017 DOI: 10.1016/j.enzmictec.2020.109667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 01/09/2023]
Abstract
A number of organic synthesis involve threonine aldolase (TA), a pyridoxal phosphate (PLP)-dependent enzyme. Although the addition of exogenous PLP is necessary for the reactions, it increases the cost and complicates the purification of the product. This work constructed a PLP self-sufficient biocatalysis system for TA, which included an improvement of the intracellular PLP level and co-immobilization of TA with PLP. Engineered strain BL-ST was constructed by introducing PLP synthase PdxS/T to Escherichia coli BL21(ED3). The intracellular PLP concentration of the strain increased approximately fivefold to 48.5 μmol/gDCW. l-TA, from Bacillus nealsonii (BnLTA), was co-expressed in the strain BL-ST with PdxS/T, resulting in the engineered strain BL-BnLTA-ST. Compared with the control strain BL-BnLTA (254.1 U/L), the enzyme activity of the strain BL-BnLTA-ST reached 1518.4 U/L without the addition of exogenous PLP. An efficient co-immobilization system was then designed. The epoxy resin LX-1000HFA wrapped by polyethyleneimine (PEI) acted as a carrier to immobilize the crude enzyme solution of the strain BL-BnLTA-ST mixed with an extra 100 μM of exogenous PLP, resulting in the catalyst HFAPEI-BnLTA-STPLP 100. HFAPEI-BnLTA-STPLP 100 exhibited a half-life of approximately 450 h, and the application of the catalyst in the continuous biosynthesis of 3-[4-(methylsulfonyl) phenyl] serine had more than 180 batch reactions (>60%conv) without the extra addition of exogenous PLP. The excellent compatibility and stability of the system were further confirmed by other TAs. This work introduced a PLP self-sufficient biocatalysis system that can reduce the cost of PLP and contribute to the industrial application of TA. In addition, the system may also be applied in other PLP-dependent enzymes.
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Affiliation(s)
- Wenlong Zheng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Kaitong Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Sai Fang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Xiuli Cheng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Gang Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, China.
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26
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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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27
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Pradal I, Esteban J, Mediero A, García-Coca M, Aguilera-Correa JJ. Contact Effect of a Methylobacterium sp. Extract on Biofilm of a Mycobacterium chimaera Strain Isolated from a 3T Heater-Cooler System. Antibiotics (Basel) 2020; 9:E474. [PMID: 32756304 PMCID: PMC7460266 DOI: 10.3390/antibiotics9080474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 11/17/2022] Open
Abstract
Mycobacterium chimaera is an opportunistic slowly growing non-tuberculous mycobacteriumof increasing importance due to the outbreak of cases associated with contaminated 3T heater-cooler device (HCD) extracorporeal membrane oxygenator (ECMO). The aim of this study was to evaluate the effect of pre-treating a surface with a Methylobacterium sp. CECT 7180 extract to inhibit the M. chimaera ECMO biofilm as well as of the treatment after different dehydration times. Surface adherence, biofilm formation and treatment effect were evaluated by estimating colony-forming units (CFU) per square centimeter and characterizing the amount of covered surface area, thickness, cell viability, and presence of intrinsic autofluorescence at different times using confocal laser scanning microscopy and image analysis. We found that exposing a surface to the Methylobacterium sp. CECT 7180 extract inhibited M. chimaera ECMO biofilm development. This effect could be result of the effect of Methylobacterium proteins, such as DNaK, trigger factor, and xanthine oxidase. In conclusion, exposing a surface to the Methylobacteriumsp. extract inhibits M. chimaera ECMO biofilm development. Furthermore, this extract could be used as a pre-treatment prior to disinfection protocols for equipment contaminated with mycobacteria after dehydration for at least 96 h.
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Affiliation(s)
- Inés Pradal
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, UAM, 28040 Madrid, Spain
| | - Jaime Esteban
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, UAM, 28040 Madrid, Spain
| | - Arancha Mediero
- Bone and Joint Unit, IIS-Fundación Jiménez Díaz, UAM, 28040 Madrid, Spain
| | - Marta García-Coca
- Clinical Microbiology Department, Quironsalud-Madrid University Hospital, 28223 Pozuelo de Alarcón, Spain
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28
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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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29
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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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30
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Krishnan A, Kloehn J, Lunghi M, Chiappino-Pepe A, Waldman BS, Nicolas D, Varesio E, Hehl A, Lourido S, Hatzimanikatis V, Soldati-Favre D. Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism. Cell Host Microbe 2020; 27:290-306.e11. [PMID: 31991093 DOI: 10.1016/j.chom.2020.01.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/02/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022]
Abstract
To survive and proliferate in diverse host environments with varying nutrient availability, the obligate intracellular parasite Toxoplasma gondii reprograms its metabolism. We have generated and curated a genome-scale metabolic model (iTgo) for the fast-replicating tachyzoite stage, harmonized with experimentally observed phenotypes. To validate the importance of four metabolic pathways predicted by the model, we have performed in-depth in vitro and in vivo phenotyping of mutant parasites including targeted metabolomics and CRISPR-Cas9 fitness screening of all known metabolic genes. This led to unexpected insights into the remarkable flexibility of the parasite, addressing the dependency on biosynthesis or salvage of fatty acids (FAs), purine nucleotides (AMP and GMP), a vitamin (pyridoxal-5P), and a cofactor (heme) in both the acute and latent stages of infection. Taken together, our experimentally validated metabolic network leads to a deeper understanding of the parasite's biology, opening avenues for the development of therapeutic intervention against apicomplexans.
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Affiliation(s)
- Aarti Krishnan
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Joachim Kloehn
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Matteo Lunghi
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | | | - Damien Nicolas
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Emmanuel Varesio
- School of Pharmaceutical Sciences Geneva-Lausanne (EPGL), Geneva 1211, Switzerland; Mass Spectrometry Core Facility (MZ 2.0), University of Geneva, Geneva 1211, Switzerland
| | - Adrian Hehl
- Institute of Parasitology, University of Zürich, Zürich 8057, Switzerland
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland.
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31
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Jun YW, Hebenbrock M, Kool ET. A fluorescent hydrazone exchange probe of pyridoxal phosphate for the assessment of vitamin B6 status. Chem Commun (Camb) 2019; 56:317-320. [PMID: 31808778 PMCID: PMC7061904 DOI: 10.1039/c9cc08458d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abnormal vitamin B6 status, marked by deficient intracellular concentrations of pyridoxal phosphate (PLP), is classified as a direct biomarker based on its biomedical significance. However, there exist no direct methods for measuring vitamin B6 status in intact cells. Here we describe the development of a fluorogenic probe, RAB6, which shows remarkable selectivity for PLP among the B6 vitamers and other cellular aldehydes.
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Affiliation(s)
- Yong Woong Jun
- Department of Chemistry and ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
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32
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Galán-Vásquez E, Perez-Rueda E. Identification of Modules With Similar Gene Regulation and Metabolic Functions Based on Co-expression Data. Front Mol Biosci 2019; 6:139. [PMID: 31921888 PMCID: PMC6929668 DOI: 10.3389/fmolb.2019.00139] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022] Open
Abstract
Biological systems respond to environmental perturbations and to a large diversity of compounds through gene interactions, and these genetic factors comprise complex networks. In particular, a wide variety of gene co-expression networks have been constructed in recent years thanks to the dramatic increase of experimental information obtained with techniques, such as microarrays and RNA sequencing. These networks allow the identification of groups of co-expressed genes that can function in the same process and, in turn, these networks may be related to biological functions of industrial, medical and academic interest. In this study, gene co-expression networks for 17 bacterial organisms from the COLOMBOS database were analyzed via weighted gene co-expression network analysis and clustered into modules of genes with similar expression patterns for each species. These networks were analyzed to determine relevant modules through a hypergeometric approach based on a set of transcription factors and enzymes for each genome. The richest modules were characterized using PFAM families and KEGG metabolic maps. Additionally, we conducted a Gene Ontology analysis for enrichment of biological functions. Finally, we identified modules that shared similarity through all the studied organisms by using comparative genomics.
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Affiliation(s)
- Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Ciudad Universitaria, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Mexico.,Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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33
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Plasma metabolites Xanthine, 4-Pyridoxate, and d-glutamic acid as novel potential biomarkers for pulmonary tuberculosis. Clin Chim Acta 2019; 498:135-142. [DOI: 10.1016/j.cca.2019.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/18/2019] [Accepted: 08/19/2019] [Indexed: 12/14/2022]
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34
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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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35
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Metabolic principles of persistence and pathogenicity in Mycobacterium tuberculosis. Nat Rev Microbiol 2019; 16:496-507. [PMID: 29691481 DOI: 10.1038/s41579-018-0013-4] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metabolism was once relegated to the supply of energy and biosynthetic precursors, but it has now become clear that it is a specific mediator of nearly all physiological processes. In the context of microbial pathogenesis, metabolism has expanded outside its canonical role in bacterial replication. Among human pathogens, this expansion has emerged perhaps nowhere more visibly than for Mycobacterium tuberculosis, the causative agent of tuberculosis. Unlike most pathogens, M. tuberculosis has evolved within humans, which are both host and reservoir. This makes unrestrained replication and perpetual quiescence equally incompatible strategies for survival as a species. In this Review, we summarize recent work that illustrates the diversity of metabolic functions that not only enable M. tuberculosis to establish and maintain a state of chronic infection within the host but also facilitate its survival in the face of drug pressure and, ultimately, completion of its life cycle.
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36
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Kumar V, Sharma M, Rakesh BR, Malik CK, Neelagiri S, Neerupudi KB, Garg P, Singh S. Pyridoxal kinase: A vitamin B6 salvage pathway enzyme from Leishmania donovani. Int J Biol Macromol 2018; 119:320-334. [DOI: 10.1016/j.ijbiomac.2018.07.095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/21/2022]
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37
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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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38
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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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39
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Chai Q, Zhang Y, Liu CH. Mycobacterium tuberculosis: An Adaptable Pathogen Associated With Multiple Human Diseases. Front Cell Infect Microbiol 2018; 8:158. [PMID: 29868514 PMCID: PMC5962710 DOI: 10.3389/fcimb.2018.00158] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/25/2018] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), is an extremely successful pathogen that adapts to survive within the host. During the latency phase of infection, M. tuberculosis employs a range of effector proteins to be cloud the host immune system and shapes its lifestyle to reside in granulomas, sophisticated, and organized structures of immune cells that are established by the host in response to persistent infection. While normally being restrained in immunocompetent hosts, M. tuberculosis within granulomas can cause the recrudescence of TB when host immunity is compromised. Aside from causing TB, accumulating evidence suggests that M. tuberculosis is also associated with multiple other human diseases, such as pulmonary complications, autoimmune diseases, and metabolic syndromes. Furthermore, it has been recently appreciated that M. tuberculosis infection can also reciprocally interact with the human microbiome, which has a strong link to immune balance and health. In this review, we highlight the adaptive survival of M. tuberculosis within the host and provide an overview for regulatory mechanisms underlying interactions between M. tuberculosis infection and multiple important human diseases. A better understanding of how M. tuberculosis regulates the host immune system to cause TB and reciprocally regulates other human diseases is critical for developing rational treatments to better control TB and help alleviate its associated comorbidities.
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Affiliation(s)
- Qiyao Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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40
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Dietl AM, Meir Z, Shadkchan Y, Osherov N, Haas H. Riboflavin and pantothenic acid biosynthesis are crucial for iron homeostasis and virulence in the pathogenic mold Aspergillus fumigatus. Virulence 2018; 9:1036-1049. [PMID: 30052132 PMCID: PMC6068542 DOI: 10.1080/21505594.2018.1482181] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Aspergillus fumigatus is the most prevalent airborne fungal pathogen, causing invasive fungal infections mainly in immunosuppressed individuals. Death rates from invasive aspergillosis remain high because of limited treatment options and increasing antifungal resistance. The aim of this study was to identify key fungal-specific genes participating in vitamin B biosynthesis in A. fumigatus. Because these genes are absent in humans they can serve as possible novel targets for antifungal drug development. METHODS By sequence homology we identified, deleted and analysed four key A. fumigatus genes (riboB, panA, pyroA, thiB) involved respectively in the biosynthesis of riboflavin (vitamin B2), pantothenic acid (vitamin B5), pyridoxine (vitamin B6) and thiamine (vitamin B1). RESULTS Deletion of riboB, panA, pyroA or thiB resulted in respective vitamin auxotrophy. Lack of riboflavin and pantothenic acid biosynthesis perturbed many cellular processes including iron homeostasis. Virulence in murine pulmonary and systemic models of infection was severely attenuated following deletion of riboB and panA, strongly reduced after pyroA deletion and weakly attenuated after thiB deletion. CONCLUSIONS This study reveals the biosynthetic pathways of the vitamins riboflavin and pantothenic acid as attractive targets for novel antifungal therapy. Moreover, the virulence studies with auxotrophic mutants serve to identify the availability of nutrients to pathogens in host niches. ABBREVIATIONS BPS: bathophenanthrolinedisulfonate; BSA: bovine serum albumin; CFU: colony forming unit; -Fe: iron starvation; +Fe: iron sufficiency; hFe: high iron; NRPSs: nonribosomal peptide synthetases; PKSs: polyketide synthaseses; wt: wild type.
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Affiliation(s)
- Anna-Maria Dietl
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Zohar Meir
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Yona Shadkchan
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine Ramat-Aviv, Tel-Aviv, Israel
| | - Hubertus Haas
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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41
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Abstract
Coevolution of pathogens and host has led to many metabolic strategies employed by intracellular pathogens to deal with the immune response and the scarcity of food during infection. Simply put, bacterial pathogens are just looking for food. As a consequence, the host has developed strategies to limit nutrients for the bacterium by containment of the intruder in a pathogen-containing vacuole and/or by actively depleting nutrients from the intracellular space, a process called nutritional immunity. Since metabolism is a prerequisite for virulence, such pathways could potentially be good targets for antimicrobial therapies. In this chapter, we review the current knowledge about the in vivo diet of Mycobacterium tuberculosis, with a focus on amino acid and cofactors, discuss evidence for the bacilli's nutritionally independent lifestyle in the host, and evaluate strategies for new chemotherapeutic interventions.
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42
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Gehrke SS, Kumar G, Yokubynas NA, Côté JP, Wang W, French S, MacNair CR, Wright GD, Brown ED. Exploiting the Sensitivity of Nutrient Transporter Deletion Strains in Discovery of Natural Product Antimetabolites. ACS Infect Dis 2017; 3:955-965. [PMID: 29069544 DOI: 10.1021/acsinfecdis.7b00149] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Actinomycete secondary metabolites are a renowned source of antibacterial chemical scaffolds. Herein, we present a target-specific approach that increases the detection of antimetabolites from natural sources by screening actinomycete-derived extracts against nutrient transporter deletion strains. On the basis of the growth rescue patterns of a collection of 22 Escherichia coli (E. coli) auxotrophic deletion strains representative of the major nutrient biosynthetic pathways, we demonstrate that antimetabolite detection from actinomycete-derived extracts prepared using traditional extraction platforms is masked by nutrient supplementation. In particular, we find poor sensitivity for the detection of antimetabolites targeting vitamin biosynthesis. To circumvent this and as a proof of principle, we exploit the differential activity of actinomycete extracts against E. coli ΔyigM, a biotin transporter deletion strain versus wildtype E. coli. We achieve more than a 100-fold increase in antimetabolite sensitivity using this method and demonstrate a successful bioassay-guided purification of the known biotin antimetabolite, amiclenomycin. Our findings provide a unique solution to uncover the full potential of naturally derived antibiotics.
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Affiliation(s)
- Sebastian S. Gehrke
- Michael G. DeGroote
Institute of Infectious Disease Research, Department of Biochemistry
and Biomedical Science, McMaster University, 1200 Main Street West, Hamilton Ontario L8N 3ZS, Canada
| | - Garima Kumar
- Michael G. DeGroote
Institute of Infectious Disease Research, Department of Biochemistry
and Biomedical Science, McMaster University, 1200 Main Street West, Hamilton Ontario L8N 3ZS, Canada
| | - Nicole A. Yokubynas
- Michael G. DeGroote
Institute of Infectious Disease Research, Department of Biochemistry
and Biomedical Science, McMaster University, 1200 Main Street West, Hamilton Ontario L8N 3ZS, Canada
| | - Jean-Philippe Côté
- Michael G. DeGroote
Institute of Infectious Disease Research, Department of Biochemistry
and Biomedical Science, McMaster University, 1200 Main Street West, Hamilton Ontario L8N 3ZS, Canada
| | - Wenliang Wang
- Michael G. DeGroote
Institute of Infectious Disease Research, Department of Biochemistry
and Biomedical Science, McMaster University, 1200 Main Street West, Hamilton Ontario L8N 3ZS, Canada
| | - Shawn French
- Michael G. DeGroote
Institute of Infectious Disease Research, Department of Biochemistry
and Biomedical Science, McMaster University, 1200 Main Street West, Hamilton Ontario L8N 3ZS, Canada
| | - Craig R. MacNair
- Michael G. DeGroote
Institute of Infectious Disease Research, Department of Biochemistry
and Biomedical Science, McMaster University, 1200 Main Street West, Hamilton Ontario L8N 3ZS, Canada
| | - Gerard D. Wright
- Michael G. DeGroote
Institute of Infectious Disease Research, Department of Biochemistry
and Biomedical Science, McMaster University, 1200 Main Street West, Hamilton Ontario L8N 3ZS, Canada
| | - Eric D. Brown
- Michael G. DeGroote
Institute of Infectious Disease Research, Department of Biochemistry
and Biomedical Science, McMaster University, 1200 Main Street West, Hamilton Ontario L8N 3ZS, Canada
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43
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Tan JL, Ng KP, Ong CS, Ngeow YF. Genomic Comparisons Reveal Microevolutionary Differences in Mycobacterium abscessus Subspecies. Front Microbiol 2017; 8:2042. [PMID: 29109707 PMCID: PMC5660101 DOI: 10.3389/fmicb.2017.02042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/06/2017] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear. We compared genome data from 243 M. abscessus strains downloaded from the NCBI ftp Refseq database to understand how the microevolutionary processes of homologous recombination and positive selection influenced the diversification of the M. abscessus complex at the subspecies level. The three subspecies are clearly separated in the Minimum Spanning Tree. Their MUMi-based genomic distances support the separation of M. massiliense and M. bolletii into two subspecies. Maximum Likelihood analysis through dN/dS (the ratio of number of non-synonymous substitutions per non-synonymous site, to the number of synonymous substitutions per synonymous site) identified distinct genes in each subspecies that could have been affected by positive selection during evolution. The results of genome-wide alignment based on concatenated locally-collinear blocks suggest that (a) recombination has affected the M. abscessus complex more than mutation and positive selection; (b) recombination occurred more frequently in M. massiliense than in the other two subspecies; and (c) the recombined segments in the three subspecies have come from different intra-species and inter-species origins. The results lead to the identification of possible gene sets that could have been responsible for the subspecies-specific features and suggest independent evolution among the three subspecies, with recombination playing a more significant role than positive selection in the diversification among members in this complex.
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Affiliation(s)
- Joon L Tan
- Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysia
| | - Kee P Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chia S Ong
- Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysia
| | - Yun F Ngeow
- Department of Pre-clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Petaling Jaya, Malaysia
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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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Xavier JC, Patil KR, Rocha I. Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes. Metab Eng 2016; 39:200-208. [PMID: 27939572 PMCID: PMC5249239 DOI: 10.1016/j.ymben.2016.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 10/28/2016] [Accepted: 12/05/2016] [Indexed: 12/26/2022]
Abstract
The composition of a cell in terms of macromolecular building blocks and other organic molecules underlies the metabolic needs and capabilities of a species. Although some core biomass components such as nucleic acids and proteins are evident for most species, the essentiality of the pool of other organic molecules, especially cofactors and prosthetic groups, is yet unclear. Here we integrate biomass compositions from 71 manually curated genome-scale models, 33 large-scale gene essentiality datasets, enzyme-cofactor association data and a vast array of publications, revealing universally essential cofactors for prokaryotic metabolism and also others that are specific for phylogenetic branches or metabolic modes. Our results revise predictions of essential genes in Klebsiella pneumoniae and identify missing biosynthetic pathways in models of Mycobacterium tuberculosis. This work provides fundamental insights into the essentiality of organic cofactors and has implications for minimal cell studies as well as for modeling genotype-phenotype relations in prokaryotic metabolic networks. Seventy one biomass equations of manually curated genome-scale metabolic models are compared. Eight classes of universally essential prokaryotic organic cofactors are proposed. Conditionally essential organic cofactors are presented and discussed. Gene essentiality predictions for Klebsiella pneumoniae are revised. A missing essential pathway in models of Mycobacterium tuberculosis is predicted.
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Affiliation(s)
- Joana C Xavier
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Kiran Raosaheb Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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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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48
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Ankisettypalli K, Cheng JJY, Baker EN, Bashiri G. PdxH proteins of mycobacteria are typical members of the classical pyridoxine/pyridoxamine 5'-phosphate oxidase family. FEBS Lett 2016; 590:453-60. [PMID: 26823273 DOI: 10.1002/1873-3468.12080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 11/08/2022]
Abstract
Pyridoxal 5'-phosphate (PLP) biosynthesis is essential for the survival and virulence of Mycobacterium tuberculosis (Mtb). PLP functions as a cofactor for 58 putative PLP-binding proteins encoded by the Mtb genome and could also act as a potential antioxidant. De novo biosynthesis of PLP in Mtb takes place through the 'deoxyxylulose 5'-phosphate (DXP)-independent' pathway, whereas PdxH enzymes, possessing pyridoxine/pyridoxamine 5'-phosphate oxidase (PNPOx) activity, are involved in the PLP salvage pathway. In this study, we demonstrate that the annotated PdxH enzymes from various mycobacterial species are bona fide members of the classical PNPOx enzyme family, capable of producing PLP using both pyridoxine 5'-phosphate (PNP) and pyridoxamine 5'-phosphate (PMP) substrates.
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Affiliation(s)
- Karthik Ankisettypalli
- Structural Biology Laboratory and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, New Zealand
| | - Jasmin Jo-Yu Cheng
- Structural Biology Laboratory and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, New Zealand
| | - Edward N Baker
- Structural Biology Laboratory and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, New Zealand
| | - Ghader Bashiri
- Structural Biology Laboratory and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, New Zealand
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49
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Essential roles of methionine and S-adenosylmethionine in the autarkic lifestyle of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2015. [PMID: 26221021 DOI: 10.1073/pnas.1513033112] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Multidrug resistance, strong side effects, and compliance problems in TB chemotherapy mandate new ways to kill Mycobacterium tuberculosis (Mtb). Here we show that deletion of the gene encoding homoserine transacetylase (metA) inactivates methionine and S-adenosylmethionine (SAM) biosynthesis in Mtb and renders this pathogen exquisitely sensitive to killing in immunocompetent or immunocompromised mice, leading to rapid clearance from host tissues. Mtb ΔmetA is unable to proliferate in primary human macrophages, and in vitro starvation leads to extraordinarily rapid killing with no appearance of suppressor mutants. Cell death of Mtb ΔmetA is faster than that of other auxotrophic mutants (i.e., tryptophan, pantothenate, leucine, biotin), suggesting a particularly potent mechanism of killing. Time-course metabolomics showed complete depletion of intracellular methionine and SAM. SAM depletion was consistent with a significant decrease in methylation at the DNA level (measured by single-molecule real-time sequencing) and with the induction of several essential methyltransferases involved in biotin and menaquinone biosynthesis, both of which are vital biological processes and validated targets of antimycobacterial drugs. Mtb ΔmetA could be partially rescued by biotin supplementation, confirming a multitarget cell death mechanism. The work presented here uncovers a previously unidentified vulnerability of Mtb-the incapacity to scavenge intermediates of SAM and methionine biosynthesis from the host. This vulnerability unveils an entirely new drug target space with the promise of rapid killing of the tubercle bacillus by a new mechanism of action.
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50
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Targeting bacterial central metabolism for drug development. ACTA ACUST UNITED AC 2014; 21:1423-32. [PMID: 25442374 DOI: 10.1016/j.chembiol.2014.08.020] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/25/2014] [Accepted: 08/08/2014] [Indexed: 11/23/2022]
Abstract
Current antibiotics, derived mainly from natural sources, inhibit a narrow spectrum of cellular processes, namely DNA replication, protein synthesis, and cell wall biosynthesis. With the worldwide explosion of drug resistance, there is renewed interest in the investigation of alternate essential cellular processes, including bacterial central metabolic pathways, as a drug target space for the next generation of antibiotics. However, the validation of targets in central metabolism is more complex, as essentiality of such targets can be conditional and/or contextual. Bearing in mind our enhanced understanding of prokaryotic central metabolism, a key question arises: can central metabolism be bacteria's Achilles' heel and a therapeutic target for the development of new classes of antibiotics? In this review, we draw lessons from oncology and attempt to address some of the open questions related to feasibility of targeting bacterial central metabolism as a strategy for developing new antibacterial drugs.
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