1
|
Martins D, McKay GA, English AM, Nguyen D. Sublethal Paraquat Confers Multidrug Tolerance in Pseudomonas aeruginosa by Inducing Superoxide Dismutase Activity and Lowering Envelope Permeability. Front Microbiol 2020; 11:576708. [PMID: 33101252 PMCID: PMC7546422 DOI: 10.3389/fmicb.2020.576708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Stressors and environmental cues shape the physiological state of bacteria, and thus how they subsequently respond to antibiotic toxicity. To understand how superoxide stress can modulate survival to bactericidal antibiotics, we examined the effect of intracellular superoxide generators, paraquat and menadione, on stationary-phase antibiotic tolerance of the opportunistic pathogen, Pseudomonas aeruginosa. We tested how pre-challenge with sublethal paraquat and menadione alters the tolerance to ofloxacin and meropenem in wild-type P. aeruginosa and mutants lacking superoxide dismutase (SOD) activity (sodAB), the paraquat responsive regulator soxR, (p)ppGpp signaling (relA spoT mutant), or the alternative sigma factor rpoS. We confirmed that loss of SOD activity impairs ofloxacin and meropenem tolerance in stationary phase cells, and found that sublethal superoxide generators induce drug tolerance by stimulating SOD activity. This response is rapid, requires de novo protein synthesis, and is RpoS-dependent but does not require (p)ppGpp signaling nor SoxR. We further showed that pre-challenge with sublethal paraquat induces a SOD-dependent reduction in cell-envelope permeability and ofloxacin penetration. Our results highlight a novel mechanism of hormetic protection by superoxide generators, which may have important implications for stress-induced antibiotic tolerance in P. aeruginosa cells.
Collapse
Affiliation(s)
- Dorival Martins
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Geoffrey A McKay
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Ann M English
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC, Canada
| | - Dao Nguyen
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| |
Collapse
|
2
|
Danchin A, Sekowska A, You C. One-carbon metabolism, folate, zinc and translation. Microb Biotechnol 2020; 13:899-925. [PMID: 32153134 PMCID: PMC7264889 DOI: 10.1111/1751-7915.13550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells. Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.
Collapse
Affiliation(s)
- Antoine Danchin
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
- School of Biomedical SciencesLi Ka Shing Faculty of MedicineThe University of Hong KongS.A.R. Hong KongChina
| | - Agnieszka Sekowska
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen University1066 Xueyuan Rd518055ShenzhenChina
| |
Collapse
|
3
|
Structural properties of [2Fe-2S] ISCA2-IBA57: a complex of the mitochondrial iron-sulfur cluster assembly machinery. Sci Rep 2019; 9:18986. [PMID: 31831856 PMCID: PMC6908724 DOI: 10.1038/s41598-019-55313-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/11/2019] [Indexed: 01/22/2023] Open
Abstract
In mitochondria, a complex protein machinery is devoted to the maturation of iron-sulfur cluster proteins. Structural information on the last steps of the machinery, which involve ISCA1, ISCA2 and IBA57 proteins, needs to be acquired in order to define how these proteins cooperate each other. We report here the use of an integrative approach, utilizing information from small-angle X-ray scattering (SAXS) and bioinformatics-driven docking prediction, to determine a low-resolution structural model of the human mitochondrial [2Fe-2S]2+ ISCA2-IBA57 complex. In the applied experimental conditions, all the data converge to a structural organization of dimer of dimers for the [2Fe-2S]2+ ISCA2-IBA57 complex with ISCA2 providing the homodimerization core interface. The [2Fe-2S] cluster is out of the ISCA2 core while being shared with IBA57 in the dimer. The specific interaction pattern identified from the dimeric [2Fe-2S]2+ ISCA2-IBA57 structural model allowed us to define the molecular grounds of the pathogenic Arg146Trp mutation of IBA57. This finding suggests that the dimeric [2Fe-2S] ISCA2-IBA57 hetero-complex is a physiologically relevant species playing a role in mitochondrial [4Fe-4S] protein biogenesis.
Collapse
|
4
|
Gourdoupis S, Nasta V, Calderone V, Ciofi-Baffoni S, Banci L. IBA57 Recruits ISCA2 to Form a [2Fe-2S] Cluster-Mediated Complex. J Am Chem Soc 2018; 140:14401-14412. [DOI: 10.1021/jacs.8b09061] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Spyridon Gourdoupis
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Veronica Nasta
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Vito Calderone
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| |
Collapse
|
5
|
Reddy PJ, Ray S, Sathe GJ, Prasad TSK, Rapole S, Panda D, Srivastava S. Proteomics analyses of Bacillus subtilis after treatment with plumbagin, a plant-derived naphthoquinone. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:12-23. [PMID: 25562197 DOI: 10.1089/omi.2014.0099] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Infectious diseases and increasing antibiotic resistance among diverse classes of microbes are global health concerns and a prime focus of omics systems science applications in novel drug discovery. Plumbagin is a plant-derived naphthoquinone, a natural product that exhibits antibacterial activity against gram-positive bacteria. In the present study, we investigated the antimicrobial effects of plumbagin against Bacillus subtilis using two complementary proteomics techniques: two-dimensional electrophoresis (2-DE) and isobaric tag for relative and absolute quantification (iTRAQ). Comparative quantitative proteomics analysis of plumbagin treated and untreated control samples identified differential expression of 230 proteins (1% FDR, 1.5 fold-change and ≥2 peptides) in B. subtilis after plumbagin treatment. Pathway analysis involving the differentially expressed proteins suggested that plumbagin effectively increases heme and protein biosynthesis, whereas fatty acid synthesis was significantly reduced. Gene expression and metabolic activity assays further corroborated the proteomics findings. We anticipate that plumbagin blocks the cell division by altering the membrane permeability required for energy generation. This is the first report, to the best of our knowledge, offering new insights, at proteome level, for the putative mode(s) of action of plumbagin and attendant cellular targets in B. subtilis. The findings also suggest new ways forward for the modern omics-guided drug target discovery, building on traditional plant medicine.
Collapse
Affiliation(s)
- Panga Jaipal Reddy
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Powai, Mumbai, India
| | | | | | | | | | | | | |
Collapse
|
6
|
Wong FC, Tan ST, Chai TT. Phytochemical-mediated Protein Expression Profiling and the Potential Applications in Therapeutic Drug Target Identifications. Crit Rev Food Sci Nutr 2015; 56 Suppl 1:S162-70. [DOI: 10.1080/10408398.2015.1045967] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
7
|
Khaw AK, Sameni S, Venkatesan S, Kalthur G, Hande MP. Plumbagin alters telomere dynamics, induces DNA damage and cell death in human brain tumour cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 793:86-95. [PMID: 26520377 DOI: 10.1016/j.mrgentox.2015.06.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 02/08/2023]
Abstract
Natural plant products may possess much potential in palliative therapy and supportive strategies of current cancer treatments with lesser cytotoxicity to normal cells compared to conventional chemotherapy. In the current study, anti-cancer properties of plumbagin, a plant-derived naphthoquinone, on brain cancer cells were determined. Plumbagin treatment resulted in the induction of DNA damage, cell cycle arrest and apoptosis, followed by suppression of the colony forming ability of the brain tumour cells. These effects were substantiated by upregulation of PTEN, TNFRSF1A and downregulation of E2F1 genes, along with a drop in MDM2, cyclin B1, survivin and BCL2 protein expression. Plumbagin induced elevated levels of caspase-3/7 activity as well. For the first time, we show here that plumbagin inhibits telomerase in brain tumour cells and results in telomere shortening following chronic long-term treatment. This observation implies considerable cytotoxicity of plumbagin towards cancer cells with higher telomerase activity. Collectively, our findings suggest plumbagin as a potential chemotherapeutic phytochemical in brain tumour treatment modalities.
Collapse
Affiliation(s)
- Aik Kia Khaw
- Genome Stability Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Safoura Sameni
- Genome Stability Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Shriram Venkatesan
- Genome Stability Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Guruprasad Kalthur
- Genome Stability Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Division of Clinical Embryology, Department of Obstetrics and Gynaecology, Kasturba Medical College, Manipal University, Manipal, 576104, India
| | - M Prakash Hande
- Genome Stability Laboratory, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore; Tembusu College, National University of Singapore, Singapore 138597, Singapore.
| |
Collapse
|
8
|
Sun WSW, Syu WJ, Ho WL, Lin CN, Tsai SF, Wang SH. SitA contributes to the virulence of Klebsiella pneumoniae in a mouse infection model. Microbes Infect 2014; 16:161-70. [DOI: 10.1016/j.micinf.2013.10.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 01/08/2023]
|
9
|
Superoxide-mediated protection of Escherichia coli from antimicrobials. Antimicrob Agents Chemother 2013; 57:5755-9. [PMID: 23979754 DOI: 10.1128/aac.00754-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial lethality is promoted by reactive oxygen species (ROS), such as superoxide, peroxide, and hydroxyl radical. Pretreatment with subinhibitory concentrations of plumbagin or paraquat, metabolic generators of superoxide, paradoxically reduced killing for oxolinic acid, kanamycin, and ampicillin. These pretreatments also reduced an oxolinic acid-mediated ROS surge. Defects in SoxS MarA or AcrB eliminated plumbagin- and paraquat-mediated MIC increases but maintained protection from killing. Thus, superoxide has both protective and detrimental roles in response to antimicrobial stress.
Collapse
|
10
|
Bhattacharya A, Jindal B, Singh P, Datta A, Panda D. Plumbagin inhibits cytokinesis inBacillus subtilisby inhibiting FtsZ assembly - a mechanistic study of its antibacterial activity. FEBS J 2013; 280:4585-99. [DOI: 10.1111/febs.12429] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/24/2013] [Accepted: 07/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Anusri Bhattacharya
- Department of Chemistry; Indian Institute of Technology Bombay; Mumbai India
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| | - Bhavya Jindal
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| | - Parminder Singh
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| | - Anindya Datta
- Department of Chemistry; Indian Institute of Technology Bombay; Mumbai India
| | - Dulal Panda
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| |
Collapse
|
11
|
Antimutagenic and antioxidant properties of plumbagin and other naphthoquinones. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 755:30-41. [DOI: 10.1016/j.mrgentox.2013.05.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 04/23/2013] [Accepted: 05/02/2013] [Indexed: 11/19/2022]
|
12
|
Dorsey-Oresto A, Lu T, Mosel M, Wang X, Salz T, Drlica K, Zhao X. YihE kinase is a central regulator of programmed cell death in bacteria. Cell Rep 2013; 3:528-37. [PMID: 23416055 DOI: 10.1016/j.celrep.2013.01.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/15/2013] [Accepted: 01/22/2013] [Indexed: 02/01/2023] Open
Abstract
Stress-mediated programmed cell death (PCD) in bacteria has recently attracted attention, largely because it raises novel possibilities for controlling pathogens. How PCD in bacteria is regulated to avoid population extinction due to transient, moderate stress remains a central question. Here, we report that the YihE protein kinase is a key regulator that protects Escherichia coli from antimicrobial and environmental stressors by antagonizing the MazEF toxin-antitoxin module. YihE was linked to a reactive oxygen species (ROS) cascade, and a deficiency of yihE stimulated stress-induced PCD even after stress dissipated. YihE was partially regulated by the Cpx envelope stress-response system, which, along with MazF toxin and superoxide, has both protective and destructive roles that help bacteria make a live-or-die decision in response to stress. YihE probably acts early in the stress response to limit self-sustaining ROS production and PCD. Inhibition of YihE may provide a way of enhancing antimicrobial lethality and attenuating virulence.
Collapse
Affiliation(s)
- Angella Dorsey-Oresto
- Public Health Research Institute Center, New Jersey Medical School, UMDNJ, Newark, NJ 07103, USA
| | | | | | | | | | | | | |
Collapse
|
13
|
Yu H, Kim KS. YgfZ contributes to secretion of cytotoxic necrotizing factor 1 into outer-membrane vesicles in Escherichia coli. MICROBIOLOGY-SGM 2011; 158:612-621. [PMID: 22174383 DOI: 10.1099/mic.0.054122-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cytotoxic necrotizing factor 1 (CNF1), a Rho GTPase-activating bacterial toxin, has been shown to contribute to invasion by meningitis-causing Escherichia coli K1 of human brain microvascular endothelial cells (HBMEC), which constitute the blood-brain barrier. However, CNF1 is a cytosolic protein and it remains unclear how its secretion occurs, contributing to E. coli invasion of HBMEC. To investigate the genetic requirement for CNF1 secretion in E. coli K1 strain RS218, we performed mini-Tn5 in vitro mutagenesis and constructed a transposon mutant library of strain NBC, in which β-lactamase was fused to the C-terminus of CNF1 in the chromosome of strain RS218. We identified a transposon mutant (NBC-1E6) that exhibited reduced β-lactamase activity in its culture supernatant and had the transposon inserted into the ygfZ gene. When ygfZ was deleted from the genome of strain RS218 (ΔygfZ), the translocation of CNF1 into HBMEC was impaired. Subcellular localization analysis of CNF1 demonstrated that YgfZ, a periplasmic protein, contributes to secretion of CNF1 into outer-membrane vesicles (OMVs). The ΔygfZ mutant was significantly defective in invasion of HBMEC compared to the parent E. coli K1 strain. The defects of the ΔygfZ mutant in CNF1 secretion into OMVs and translocation into HBMEC as well as invasion of HBMEC were abrogated by complementation with ygfZ. Taken together, our findings demonstrate that YgfZ contributes to CNF1 secretion into OMVs in meningitis-causing E. coli K1.
Collapse
Affiliation(s)
- Hao Yu
- Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, 200 North Wolfe Street, Room 3157, Baltimore, MD 21287, USA
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, Johns Hopkins University School of Medicine, 200 North Wolfe Street, Room 3157, Baltimore, MD 21287, USA
| |
Collapse
|
14
|
Evidence that the folate-dependent proteins YgfZ and MnmEG have opposing effects on growth and on activity of the iron-sulfur enzyme MiaB. J Bacteriol 2011; 194:362-7. [PMID: 22081392 DOI: 10.1128/jb.06226-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The folate-dependent protein YgfZ of Escherichia coli participates in the synthesis and repair of iron-sulfur (Fe-S) clusters; it belongs to a family of enzymes that use folate to capture formaldehyde units. Ablation of ygfZ is known to reduce growth, to increase sensitivity to oxidative stress, and to lower the activities of MiaB and other Fe-S enzymes. It has been reported that the growth phenotype can be suppressed by disrupting the tRNA modification gene mnmE. We first confirmed the latter observation using deletions in a simpler, more defined genetic background. We then showed that deleting mnmE substantially restores MiaB activity in ygfZ deletant cells and that overexpressing MnmE with its partner MnmG exacerbates the growth and MiaB activity phenotypes of the ygfZ deletant. MnmE, with MnmG, normally mediates a folate-dependent transfer of a formaldehyde unit to tRNA, and the MnmEG-mediated effects on the phenotypes of the ΔygfZ mutant apparently require folate, as evidenced by the effect of eliminating all folates by deleting folE. The expression of YgfZ was unaffected by deleting mnmE or overexpressing MnmEG or by folate status. Since formaldehyde transfer is a potential link between MnmEG and YgfZ, we inactivated formaldehyde detoxification by deleting frmA. This deletion had little effect on growth or MiaB activity in the ΔygfZ strain in the presence of formaldehyde, making it unlikely that formaldehyde alone connects the actions of MnmEG and YgfZ. A more plausible explanation is that MnmEG erroneously transfers a folate-bound formaldehyde unit to MiaB and that YgfZ reverses this.
Collapse
|
15
|
Gerdes S, El Yacoubi B, Bailly M, Blaby IK, Blaby-Haas CE, Jeanguenin L, Lara-Núñez A, Pribat A, Waller JC, Wilke A, Overbeek R, Hanson AD, de Crécy-Lagard V. Synergistic use of plant-prokaryote comparative genomics for functional annotations. BMC Genomics 2011; 12 Suppl 1:S2. [PMID: 21810204 PMCID: PMC3223725 DOI: 10.1186/1471-2164-12-s1-s2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown or vaguely known function, and a large number are wrongly annotated. Many of these 'unknown' proteins are common to prokaryotes and plants. We set out to predict and experimentally test the functions of such proteins. Our approach to functional prediction integrates comparative genomics based mainly on microbial genomes with functional genomic data from model microorganisms and post-genomic data from plants. This approach bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is more powerful than purely computational approaches to identifying gene-function associations. RESULTS Among Arabidopsis genes, we focused on those (2,325 in total) that (i) are unique or belong to families with no more than three members, (ii) occur in prokaryotes, and (iii) have unknown or poorly known functions. Computer-assisted selection of promising targets for deeper analysis was based on homology-independent characteristics associated in the SEED database with the prokaryotic members of each family. In-depth comparative genomic analysis was performed for 360 top candidate families. From this pool, 78 families were connected to general areas of metabolism and, of these families, specific functional predictions were made for 41. Twenty-one predicted functions have been experimentally tested or are currently under investigation by our group in at least one prokaryotic organism (nine of them have been validated, four invalidated, and eight are in progress). Ten additional predictions have been independently validated by other groups. Discovering the function of very widespread but hitherto enigmatic proteins such as the YrdC or YgfZ families illustrates the power of our approach. CONCLUSIONS Our approach correctly predicted functions for 19 uncharacterized protein families from plants and prokaryotes; none of these functions had previously been correctly predicted by computational methods. The resulting annotations could be propagated with confidence to over six thousand homologous proteins encoded in over 900 bacterial, archaeal, and eukaryotic genomes currently available in public databases.
Collapse
Affiliation(s)
- Svetlana Gerdes
- Fellowship for Interpretation of Genomes, Burr Ridge, IL, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Padhye S, Dandawate P, Yusufi M, Ahmad A, Sarkar FH. Perspectives on medicinal properties of plumbagin and its analogs. Med Res Rev 2010; 32:1131-58. [PMID: 23059762 DOI: 10.1002/med.20235] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plumbagin is one of the simplest plant secondary metabolite of three major phylogenic families viz. Plumbaginaceae, Droseraceae, and Ebenceae, and exhibits highly potent biological activities, including antioxidant, antiinflammatory, anticancer, antibacterial, and antifungal activities. Recent investigations indicate that these activities arise mainly out of its ability to undergo redox cycling, generating reactive oxygen species and chelating trace metals in biological system. The compound is endowed with a property to inhibit the drug efflux mechanism in drug-resistant bacteria, thereby allowing intracellular accumulation of the potent drug molecules. An interesting bioactivity exhibited by this compound is the elimination of stringent, conjugative, multidrug-resistant plasmids from several bacterial strains including opportunistic bacteria, such as Acinetobacter baumannii. Moreover, plumbagin effectively induces apoptosis and causes cell cycle arrest, which is, in part, due to the inactivation of NF-κB in cancer cells. Therefore, it has been suggested that designing "hybrid drug molecules" of plumbagin by combining it with other appropriate anticancer agents may lead to the generation of novel and potent anticancer drugs with pleiotropic action against human cancers. This comprehensive review is an attempt to understand the chemistry of plumbagin and catalog its biological activities reported to date.
Collapse
Affiliation(s)
- Subhash Padhye
- Department of Pathology, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Hudson Webber Cancer Research Center, Detroit, Michigan 48201, USA
| | | | | | | | | |
Collapse
|
17
|
Lin CN, Syu WJ, Sun WSW, Chen JW, Chen TH, Don MJ, Wang SH. A role of ygfZ in the Escherichia coli response to plumbagin challenge. J Biomed Sci 2010; 17:84. [PMID: 21059273 PMCID: PMC2989944 DOI: 10.1186/1423-0127-17-84] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 11/09/2010] [Indexed: 11/28/2022] Open
Abstract
Plumbagin is found in many herbal plants and inhibits the growth of various bacteria. Escherichia coli strains are relatively resistant to this drug. The mechanism of resistance is not clear. Previous findings showed that plumbagin treatment triggered up-regulation of many genes in E. coli including ahpC, mdaB, nfnB, nfo, sodA, yggX and ygfZ. By analyzing minimal inhibition concentration and inhibition zones of plumbagin in various gene-disruption mutants, ygfZ and sodA were found critical for the bacteria to resist plumbagin toxicity. We also found that the roles of YgfZ and SodA in detoxifying plumbagin are independent of each other. This is because of the fact that ectopically expressed SodA reduced the superoxide stress but not restore the resistance of bacteria when encountering plumbagin at the absence of ygfZ. On the other hand, an ectopically expressed YgfZ was unable to complement and failed to rescue the plumbagin resistance when sodA was perturbed. Furthermore, mutagenesis analysis showed that residue Cys228 within YgfZ fingerprint region was critical for the resistance of E. coli to plumbagin. By solvent extraction and HPLC analysis to follow the fate of the chemical, it was found that plumbagin vanished apparently from the culture of YgfZ-expressing E. coli. A less toxic form, methylated plumbagin, which may represent one of the YgfZ-dependent metabolites, was found in the culture supernatant of the wild type E. coli but not in the ΔygfZ mutant. Our results showed that the presence of ygfZ is not only critical for the E coli resistance to plumbagin but also facilitates the plumbagin degradation.
Collapse
Affiliation(s)
- Ching-Nan Lin
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, 112 Taiwan
| | | | | | | | | | | | | |
Collapse
|
18
|
Damle MS, Newton LAA, Villalba MM, Leslie R, Davis J. Plumbagin: A New Route to the Electroanalytical Determination of Cystine. ELECTROANAL 2010. [DOI: 10.1002/elan.201000198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
19
|
Waller JC, Alvarez S, Naponelli V, Lara-Nuñez A, Blaby IK, Da Silva V, Ziemak MJ, Vickers TJ, Beverley SM, Edison AS, Rocca JR, Gregory JF, de Crécy-Lagard V, Hanson AD. A role for tetrahydrofolates in the metabolism of iron-sulfur clusters in all domains of life. Proc Natl Acad Sci U S A 2010; 107:10412-7. [PMID: 20489182 PMCID: PMC2890791 DOI: 10.1073/pnas.0911586107] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Iron-sulfur (Fe/S) cluster enzymes are crucial to life. Their assembly requires a suite of proteins, some of which are specific for particular subsets of Fe/S enzymes. One such protein is yeast Iba57p, which aconitase and certain radical S-adenosylmethionine enzymes require for activity. Iba57p homologs occur in all domains of life; they belong to the COG0354 protein family and are structurally similar to various folate-dependent enzymes. We therefore investigated the possible relationship between folates and Fe/S cluster enzymes using the Escherichia coli Iba57p homolog, YgfZ. NMR analysis confirmed that purified YgfZ showed stereoselective folate binding. Inactivating ygfZ reduced the activities of the Fe/S tRNA modification enzyme MiaB and certain other Fe/S enzymes, although not aconitase. When successive steps in folate biosynthesis were ablated, folE (lacking pterins and folates) and folP (lacking folates) mutants mimicked the ygfZ mutant in having low MiaB activities, whereas folE thyA mutants supplemented with 5-formyltetrahydrofolate (lacking pterins and depleted in dihydrofolate) and gcvP glyA mutants (lacking one-carbon tetrahydrofolates) had intermediate MiaB activities. These data indicate that YgfZ requires a folate, most probably tetrahydrofolate. Importantly, the ygfZ mutant was hypersensitive to oxidative stress and grew poorly on minimal media. COG0354 genes of bacterial, archaeal, fungal, protistan, animal, or plant origin complemented one or both of these growth phenotypes as well as the MiaB activity phenotype. Comparative genomic analysis indicated widespread functional associations between COG0354 proteins and Fe/S cluster metabolism. Thus COG0354 proteins have an ancient, conserved, folate-dependent function in the activity of certain Fe/S cluster enzymes.
Collapse
Affiliation(s)
| | - Sophie Alvarez
- Donald Danforth Plant Science Center, Saint Louis, MO 63132; and
| | | | | | | | | | | | - Tim J. Vickers
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110
| | - Stephen M. Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110
| | - Arthur S. Edison
- Department of Biochemistry and Molecular Biology and National High Magnetic Field Laboratory, and
| | - James R. Rocca
- McKnight Brain Institute, University of Florida, Gainesville, FL 32611
| | | | | | | |
Collapse
|
20
|
Newton LAA, Cowham E, Sharp D, Leslie R, Davis J. Plumbagin: a natural product for smart materials? NEW J CHEM 2010. [DOI: 10.1039/b9nj00534j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|