1
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Chaudhari NM, Pérez-Carrascal OM, Overholt WA, Totsche KU, Küsel K. Genome streamlining in Parcubacteria transitioning from soil to groundwater. ENVIRONMENTAL MICROBIOME 2024; 19:41. [PMID: 38902796 PMCID: PMC11188291 DOI: 10.1186/s40793-024-00581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics. RESULTS Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer. CONCLUSIONS Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.
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Affiliation(s)
- Narendrakumar M Chaudhari
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany
| | - Olga M Pérez-Carrascal
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Will A Overholt
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geowissenschaften, Friedrich-Schiller-Universität Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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2
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Carabias A, Camara-Wilpert S, Mestre MR, Lopéz-Méndez B, Hendriks IA, Zhao R, Pape T, Fuglsang A, Luk SHC, Nielsen ML, Pinilla-Redondo R, Montoya G. Retron-Eco1 assembles NAD +-hydrolyzing filaments that provide immunity against bacteriophages. Mol Cell 2024; 84:2185-2202.e12. [PMID: 38788717 DOI: 10.1016/j.molcel.2024.05.001] [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: 09/26/2023] [Revised: 03/15/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024]
Abstract
Retrons are toxin-antitoxin systems protecting bacteria against bacteriophages via abortive infection. The Retron-Eco1 antitoxin is formed by a reverse transcriptase (RT) and a non-coding RNA (ncRNA)/multi-copy single-stranded DNA (msDNA) hybrid that neutralizes an uncharacterized toxic effector. Yet, the molecular mechanisms underlying phage defense remain unknown. Here, we show that the N-glycosidase effector, which belongs to the STIR superfamily, hydrolyzes NAD+ during infection. Cryoelectron microscopy (cryo-EM) analysis shows that the msDNA stabilizes a filament that cages the effector in a low-activity state in which ADPr, a NAD+ hydrolysis product, is covalently linked to the catalytic E106 residue. Mutations shortening the msDNA induce filament disassembly and the effector's toxicity, underscoring the msDNA role in immunity. Furthermore, we discovered a phage-encoded Retron-Eco1 inhibitor (U56) that binds ADPr, highlighting the intricate interplay between retron systems and phage evolution. Our work outlines the structural basis of Retron-Eco1 defense, uncovering ADPr's pivotal role in immunity.
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Affiliation(s)
- Arturo Carabias
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Sarah Camara-Wilpert
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mario Rodríguez Mestre
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Blanca Lopéz-Méndez
- Protein Purification and Characterization Facility, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Department, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ruiliang Zhao
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Tillmann Pape
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Core Facility for Integrated Microscopy (CFIM), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders Fuglsang
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Sean Hoi-Ching Luk
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics Department, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rafael Pinilla-Redondo
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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3
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Cihlova B, Lu Y, Mikoč A, Schuller M, Ahel I. Specificity of DNA ADP-Ribosylation Reversal by NADARs. Toxins (Basel) 2024; 16:208. [PMID: 38787060 PMCID: PMC11125620 DOI: 10.3390/toxins16050208] [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: 03/18/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
Recent discoveries establish DNA and RNA as bona fide substrates for ADP-ribosylation. NADAR ("NAD- and ADP-ribose"-associated) enzymes reverse guanine ADP-ribosylation and serve as antitoxins in the DarT-NADAR operon. Although NADARs are widespread across prokaryotes, eukaryotes, and viruses, their specificity and broader physiological roles remain poorly understood. Using phylogenetic and biochemical analyses, we further explore de-ADP-ribosylation activity and antitoxin functions of NADAR domains. We demonstrate that different subfamilies of NADAR proteins from representative E. coli strains and an E. coli-infecting phage retain biochemical activity while displaying specificity in providing protection from toxic guanine ADP-ribosylation in cells. Furthermore, we identify a myxobacterial enzyme within the YbiA subfamily that functions as an antitoxin for its associated DarT-unrelated ART toxin, which we termed YarT, thus presenting a hitherto uncharacterised ART-YbiA toxin-antitoxin pair. Our studies contribute to the burgeoning field of DNA ADP-ribosylation, supporting its physiological relevance within and beyond bacterial toxin-antitoxin systems. Notably, the specificity and confinement of NADARs to non-mammals infer their potential as highly specific targets for antimicrobial drugs with minimal off-target effects.
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Affiliation(s)
- Bara Cihlova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (B.C.); (Y.L.)
| | - Yang Lu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (B.C.); (Y.L.)
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (B.C.); (Y.L.)
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; (B.C.); (Y.L.)
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4
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Schuller M, Raggiaschi R, Mikolcevic P, Rack JGM, Ariza A, Zhang Y, Ledermann R, Tang C, Mikoc A, Ahel I. Molecular basis for the reversible ADP-ribosylation of guanosine bases. Mol Cell 2023:S1097-2765(23)00457-4. [PMID: 37390817 DOI: 10.1016/j.molcel.2023.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/13/2023] [Accepted: 06/08/2023] [Indexed: 07/02/2023]
Abstract
Modification of nucleic acids by ADP-ribosylation is catalyzed by various ADP-ribosyltransferases, including the DarT enzyme. The latter is part of the bacterial toxin-antitoxin (TA) system DarTG, which was shown to provide control of DNA replication and bacterial growth as well as protection against bacteriophages. Two subfamilies have been identified, DarTG1 and DarTG2, which are distinguished by their associated antitoxins. While DarTG2 catalyzes reversible ADP-ribosylation of thymidine bases employing a macrodomain as antitoxin, the DNA ADP-ribosylation activity of DarTG1 and the biochemical function of its antitoxin, a NADAR domain, are as yet unknown. Using structural and biochemical approaches, we show that DarT1-NADAR is a TA system for reversible ADP-ribosylation of guanosine bases. DarT1 evolved the ability to link ADP-ribose to the guanine amino group, which is specifically hydrolyzed by NADAR. We show that guanine de-ADP-ribosylation is also conserved among eukaryotic and non-DarT-associated NADAR members, indicating a wide distribution of reversible guanine modifications beyond DarTG systems.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Petra Mikolcevic
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Johannes G M Rack
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Antonio Ariza
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - YuGeng Zhang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Christoph Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Andreja Mikoc
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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5
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Apprehending the NAD+–ADPr-Dependent Systems in the Virus World. Viruses 2022; 14:v14091977. [PMID: 36146784 PMCID: PMC9503650 DOI: 10.3390/v14091977] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022] Open
Abstract
NAD+ and ADP-ribose (ADPr)-containing molecules are at the interface of virus–host conflicts across life encompassing RNA processing, restriction, lysogeny/dormancy and functional hijacking. We objectively defined the central components of the NAD+–ADPr networks involved in these conflicts and systematically surveyed 21,191 completely sequenced viral proteomes representative of all publicly available branches of the viral world to reconstruct a comprehensive picture of the viral NAD+–ADPr systems. These systems have been widely and repeatedly exploited by positive-strand RNA and DNA viruses, especially those with larger genomes and more intricate life-history strategies. We present evidence that ADP-ribosyltransferases (ARTs), ADPr-targeting Macro, NADAR and Nudix proteins are frequently packaged into virions, particularly in phages with contractile tails (Myoviruses), and deployed during infection to modify host macromolecules and counter NAD+-derived signals involved in viral restriction. Genes encoding NAD+–ADPr-utilizing domains were repeatedly exchanged between distantly related viruses, hosts and endo-parasites/symbionts, suggesting selection for them across the virus world. Contextual analysis indicates that the bacteriophage versions of ADPr-targeting domains are more likely to counter soluble ADPr derivatives, while the eukaryotic RNA viral versions might prefer macromolecular ADPr adducts. Finally, we also use comparative genomics to predict host systems involved in countering viral ADP ribosylation of host molecules.
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6
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Thomas JN, Johnston TL, Litvak IM, Ramaswamy V, Merritt ME, Rocca JR, Edison AS, Brey WW. Implementing High Q-Factor HTS Resonators to Enhance Probe Sensitivity in 13C NMR Spectroscopy. JOURNAL OF PHYSICS. CONFERENCE SERIES 2022; 2323:012030. [PMID: 36187328 PMCID: PMC9524303 DOI: 10.1088/1742-6596/2323/1/012030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nuclear magnetic resonance spectroscopy (NMR) probes using thin-film high temperature superconducting (HTS) resonators provide exceptional mass sensitivity in small-sample NMR experiments for natural products chemistry and metabolomics. We report improvements in sensitivity to our 1.5 mm 13C-optimized NMR probe based on HTS resonators. The probe has a sample volume of 35 microliters and operates in a 14.1 T magnet. The probe also features HTS resonators for 1H transmission and detection and the 2H lock. The probe utilizes a 13C resonator design that provides greater efficiency than our previous design. The quality factor of the new resonator in the 14.1 T background field was measured to be 4,300, which is over 3x the value of the previous design. To effectively implement the improved quality factor, we demonstrate the effect of adding a shorted transmission line stub to increase the bandwidth and reduce the rise/fall time of 13C irradiation pulses. Initial NMR measurements verify 13C NMR sensitivity is significantly improved while preserving detection bandwidth. The probe will be used for applications in metabolomics.
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Affiliation(s)
- J N Thomas
- National High Magnetic Field Laboratory, Tallahassee FL, USA
| | - T L Johnston
- National High Magnetic Field Laboratory, Tallahassee FL, USA
| | - I M Litvak
- National High Magnetic Field Laboratory, Tallahassee FL, USA
| | | | | | - J R Rocca
- University of Florida, Gainesville FL, USA
| | | | - W W Brey
- National High Magnetic Field Laboratory, Tallahassee FL, USA
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7
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Yurgel SN, Johnson SA, Rice J, Sa N, Bailes C, Baumgartner J, Pitzer JE, Roop RM, Roje S. A novel formamidase is required for riboflavin biosynthesis in invasive bacteria. J Biol Chem 2022; 298:102377. [PMID: 35970388 PMCID: PMC9478397 DOI: 10.1016/j.jbc.2022.102377] [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: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/03/2022] Open
Abstract
Biosynthesis of riboflavin, the precursor of the redox cofactors FMN and FAD, was thought to be well understood in bacteria, with all the pathway enzymes presumed to be known and essential. Our previous research has challenged this view by showing that, in the bacterium Sinorhizobium meliloti, deletion of the ribBA gene encoding the enzyme that catalyzes the initial steps on the riboflavin biosynthesis pathway only causes a reduction in flavin secretion rather than riboflavin auxotrophy. This finding led us to hypothesize that RibBA participates in the biosynthesis of flavins destined for secretion, while S. meliloti has another enzyme that performs this function for internal cellular metabolism. Here, we identify and biochemically characterize a novel formamidase (SMc02977) involved in the production of riboflavin for intracellular functions in S. meliloti. This catalyst, which we named Sm-BrbF, releases formate from the early riboflavin precursor 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (AFRPP) to yield 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARoPP). We show that homologs of this enzyme are present in many bacteria, are highly abundant in the Rhizobiales order, and that sequence homologs from Brucella abortus and Liberobacter solanacearum complement the riboflavin auxotrophy of the Sm1021ΔSMc02977 mutant. Furthermore, we show that the B. abortus enzyme (Bab2_0247, Ba-BrbF) is also an AFRPP formamidase, and that the bab2_0247 mutant is a riboflavin auxotroph exhibiting a lower level of intracellular infection than the wild-type strain. Finally, we show that Sm-BrbF and Ba-BrbF directly interact with other riboflavin biosynthesis pathway enzymes. Together, our results provide novel insight into the intricacies of riboflavin biosynthesis in bacteria.
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Affiliation(s)
- Svetlana N Yurgel
- Grain Legume Genetics and Physiology Research Unit, USDA, ARS, Prosser, WA, USA.
| | - Skylar A Johnson
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Jennifer Rice
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Na Sa
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Clayton Bailes
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - John Baumgartner
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Josh E Pitzer
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - R Martin Roop
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
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8
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Fasimoye RY, Spencer R, Soto-Martin E, Eijlers P, Elmassoudi H, Brivio S, Mangana C, Sabele V, Rechtorikova R, Wenzel M, Connolly B, Pettitt J, Müller B. A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex. Nucleic Acids Res 2022; 50:7591-7607. [PMID: 35736244 PMCID: PMC9303266 DOI: 10.1093/nar/gkac534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022] Open
Abstract
Spliced leader trans-splicing is essential for gene expression in many eukaryotes. To elucidate the molecular mechanism of this process, we characterise the molecules associated with the Caenorhabditis elegans major spliced leader snRNP (SL1 snRNP), which donates the spliced leader that replaces the 5' untranslated region of most pre-mRNAs. Using a GFP-tagged version of the SL1 snRNP protein SNA-1 created by CRISPR-mediated genome engineering, we immunoprecipitate and identify RNAs and protein components by RIP-Seq and mass spectrometry. This reveals the composition of the SL1 snRNP and identifies associations with spliceosome components PRP-8 and PRP-19. Significantly, we identify a novel, nematode-specific protein required for SL1 trans-splicing, which we designate SNA-3. SNA-3 is an essential, nuclear protein with three NADAR domains whose function is unknown. Mutation of key residues in NADAR domains inactivates the protein, indicating that domain function is required for activity. SNA-3 interacts with the CBC-ARS2 complex and other factors involved in RNA metabolism, including SUT-1 protein, through RNA or protein-mediated contacts revealed by yeast two-hybrid assays, localisation studies and immunoprecipitations. Our data are compatible with a role for SNA-3 in coordinating trans-splicing with target pre-mRNA transcription or in the processing of the Y-branch product of the trans-splicing reaction.
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Affiliation(s)
- Rotimi Yemi Fasimoye
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Rosie Elizabeth Barker Spencer
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Eva Soto-Martin
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Peter Eijlers
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Haitem Elmassoudi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Sarah Brivio
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Carolina Mangana
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Viktorija Sabele
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Radoslava Rechtorikova
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Marius Wenzel
- Centre of Genome-Enabled Biology and Medicine, University of Aberdeen, 23 St Machar Drive, Aberdeen AB24 3RY, Scotland, UK
| | - Bernadette Connolly
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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9
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Characterization of Stenotrophomonas maltophilia phage AXL1 as a member of the genus Pamexvirus encoding resistance to trimethoprim-sulfamethoxazole. Sci Rep 2022; 12:10299. [PMID: 35717537 PMCID: PMC9206674 DOI: 10.1038/s41598-022-14025-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Stenotrophomonas maltophilia is a ubiquitous environmental bacterium capable of causing disease in humans. Antibiotics are largely ineffective against this pathogen due to numerous chromosomally encoded antibiotic resistance mechanisms. An alternative treatment option is phage therapy, the use of bacteriophages to selectively kill target bacteria that are causing infection. To this aim, we isolated the Siphoviridae bacteriophage AXL1 (vB_SmaS-AXL_1) from soil and herein describe its characterization. Host range analysis on a panel of 30 clinical S. maltophilia strains reveals a moderate tropism that includes cross-species infection of Xanthomonas, with AXL1 using the type IV pilus as its host surface receptor for infection. Complete genome sequencing and analysis revealed a 63,962 bp genome encoding 83 putative proteins. Comparative genomics place AXL1 in the genus Pamexvirus, along with seven other phages that infect one of Stenotrophomonas, Pseudomonas or Xanthomonas species. Functional genomic analyses identified an AXL1-encoded dihydrofolate reductase enzyme that provides additional resistance to the antibiotic combination trimethoprim-sulfamethoxazole, the current recommended treatment option for S. maltophilia infections. This research characterizes the sixth type IV pilus-binding phage of S. maltophilia and is an example of phage-encoded antibiotic resistance.
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10
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Johnston TL, Edison AS, Ramaswamy V, Freytag N, Merritt ME, Thomas JN, Hooker JW, Litvak IM, Brey WW. Application of Counter-wound Multi-arm Spirals in HTS Resonator Design. IEEE TRANSACTIONS ON APPLIED SUPERCONDUCTIVITY : A PUBLICATION OF THE IEEE SUPERCONDUCTIVITY COMMITTEE 2022; 32:1500304. [PMID: 35449718 PMCID: PMC9017787 DOI: 10.1109/tasc.2022.3146109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Significant sensitivity improvements have been achieved by utilizing high temperature superconducting (HTS) resonators in nuclear magnetic resonance (NMR) probes. Many nuclei such as 13C benefit from strong excitation fields which cannot be produced by traditional HTS resonator designs. We investigate the use of double-sided, counter-wound multi-arm spiral HTS resonators with the aim of increasing the excitation field at the required nuclear Larmor frequency for 13C. When compared to double-sided, counter-wound spiral resonators with similar geometry, simulations indicate that the multi-arm spiral version develops a more uniform current distribution. Preliminary tests of a two-arm resonator indicate that it may produce a stronger excitation field.
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Affiliation(s)
- Taylor L Johnston
- National High Magnetic Laboratory, Tallahassee, FL 32310, USA and also with the Department of Chemistry and Biochemistry, Florida State University
| | | | | | | | - Matthew E Merritt
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32601, USA
| | - Jeremy N Thomas
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA and also with the Department of Physics, Florida State University
| | - Jerris W Hooker
- Department of Electrical and Computer Engineering, FAMU-FSU College of Engineering, Tallahassee, FL 32310, USA
| | - Ilya M Litvak
- National High Magnetic Laboratory, Tallahassee, FL 32310, USA and also with Florida State University
| | - William W Brey
- National High Magnetic Laboratory, Tallahassee, FL 32310, USA and also with Florida State University
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11
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Jeffryes JG, Lerma-Ortiz C, Liu F, Golubev A, Niehaus TD, Elbadawi-Sidhu M, Fiehn O, Hanson AD, Tyo KE, Henry CS. Chemical-damage MINE: A database of curated and predicted spontaneous metabolic reactions. Metab Eng 2021; 69:302-312. [PMID: 34958914 DOI: 10.1016/j.ymben.2021.11.009] [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: 10/19/2020] [Revised: 10/05/2021] [Accepted: 11/23/2021] [Indexed: 01/27/2023]
Abstract
Spontaneous reactions between metabolites are often neglected in favor of emphasizing enzyme-catalyzed chemistry because spontaneous reaction rates are assumed to be insignificant under physiological conditions. However, synthetic biology and engineering efforts can raise natural metabolites' levels or introduce unnatural ones, so that previously innocuous or nonexistent spontaneous reactions become an issue. Problems arise when spontaneous reaction rates exceed the capacity of a platform organism to dispose of toxic or chemically active reaction products. While various reliable sources list competing or toxic enzymatic pathways' side-reactions, no corresponding compilation of spontaneous side-reactions exists, nor is it possible to predict their occurrence. We addressed this deficiency by creating the Chemical Damage (CD)-MINE resource. First, we used literature data to construct a comprehensive database of metabolite reactions that occur spontaneously in physiological conditions. We then leveraged this data to construct 148 reaction rules describing the known spontaneous chemistry in a substrate-generic way. We applied these rules to all compounds in the ModelSEED database, predicting 180,891 spontaneous reactions. The resulting (CD)-MINE is available at https://minedatabase.mcs.anl.gov/cdmine/#/home and through developer tools. We also demonstrate how damage-prone intermediates and end products are widely distributed among metabolic pathways, and how predicting spontaneous chemical damage helps rationalize toxicity and carbon loss using examples from published pathways to commercial products. We explain how analyzing damage-prone areas in metabolism helps design effective engineering strategies. Finally, we use the CD-MINE toolset to predict the formation of the novel damage product N-carbamoyl proline, and present mass spectrometric evidence for its presence in Escherichia coli.
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Affiliation(s)
- James G Jeffryes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Claudia Lerma-Ortiz
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60637, USA; Department of Data Science and Learning, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Filipe Liu
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Alexey Golubev
- Department of Carcinogenesis and Oncogerontology, N.N. Petrov National Medical Research Center of Oncology, Saint Petersburg, 197758, Russia
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA; Plant and Microbial Biology Department, University of Minnesota, Saint Paul, MN, 55108, USA
| | | | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, CA, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Keith Ej Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA; Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60637, USA.
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12
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Thomas JN, Ramaswamy V, Litvak IM, Johnston TL, Edison AS, Brey WW. Progress Towards a Higher Sensitivity 13C-Optimized 1.5 mm HTS NMR Probe. IEEE TRANSACTIONS ON APPLIED SUPERCONDUCTIVITY : A PUBLICATION OF THE IEEE SUPERCONDUCTIVITY COMMITTEE 2021; 31:1500504. [PMID: 33867781 PMCID: PMC8045891 DOI: 10.1109/tasc.2021.3061042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nuclear magnetic resonance (NMR) probes using thin-film high temperature superconducting (HTS) resonators offer high sensitivity and are particularly suitable for small-sample applications. We are developing an improved 1.5 mm HTS NMR probe designed for operation at 14.1 T and optimized for 13C detection. The total sample volume is about 35 μL and the active sample volume is 20 μL. The probe employs HTS resonators for 13C and 1H transmission and detection and the 2H lock. We examine the interactions of multiple superconducting resonators and normal metal tuning loops on coil resonance frequency and probe sensitivity. We test a recently introduced 13C resonator design, engineered to significantly increase 13C detection sensitivity over previous all-HTS probes. At zero field, we observe a 13C quality factor of 6000 which is several times higher than previous resonators. In this work the coil design considerations and probe build-out procedure are discussed.
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Affiliation(s)
- Jeremy N Thomas
- National High Magnetic Laboratory and the Department of Physics, Florida State University, Tallahassee, FL 32310 USA
| | | | - Ilya M Litvak
- National High Magnetic Laboratory, Florida State University, Tallahassee, FL 32310 USA
| | - Taylor L Johnston
- National High Magnetic Laboratory and the Department of Chemistry, Florida State University, Tallahassee, FL 32310 USA
| | | | - William W Brey
- National High Magnetic Laboratory, Florida State University, Tallahassee, FL 32310 USA
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13
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Eljounaidi K, Lichman BR. Dreaming of clean bean protein. NATURE PLANTS 2021; 7:860-861. [PMID: 34226691 DOI: 10.1038/s41477-021-00949-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Kaouthar Eljounaidi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK.
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14
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Björnsdotter E, Nadzieja M, Chang W, Escobar-Herrera L, Mancinotti D, Angra D, Xia X, Tacke R, Khazaei H, Crocoll C, Vandenberg A, Link W, Stoddard FL, O'Sullivan DM, Stougaard J, Schulman AH, Andersen SU, Geu-Flores F. VC1 catalyses a key step in the biosynthesis of vicine in faba bean. NATURE PLANTS 2021; 7:923-931. [PMID: 34226693 DOI: 10.1101/2020.02.26.966523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/24/2021] [Indexed: 05/20/2023]
Abstract
Faba bean (Vicia faba L.) is a widely adapted and high-yielding legume cultivated for its protein-rich seeds1. However, the seeds accumulate the pyrimidine glucosides vicine and convicine, which can cause haemolytic anaemia (favism) in 400 million genetically predisposed individuals2. Here, we use gene-to-metabolite correlations, gene mapping and genetic complementation to identify VC1 as a key enzyme in vicine and convicine biosynthesis. We demonstrate that VC1 has GTP cyclohydrolase II activity and that the purine GTP is a precursor of both vicine and convicine. Finally, we show that cultivars with low vicine and convicine levels carry an inactivating insertion in the coding sequence of VC1. Our results reveal an unexpected, purine rather than pyrimidine, biosynthetic origin for vicine and convicine and pave the way for the development of faba bean cultivars that are free of these anti-nutrients.
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Affiliation(s)
- Emilie Björnsdotter
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Wei Chang
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | | | - Davide Mancinotti
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Xinxing Xia
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Rebecca Tacke
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Hamid Khazaei
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Christoph Crocoll
- DynaMo Center, Section for Molecular Plant Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Wolfgang Link
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Frederick L Stoddard
- Department of Agricultural Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alan H Schulman
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
- Natural Resources Institute Finland (Luke), Helsinki, Finland.
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Fernando Geu-Flores
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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15
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Björnsdotter E, Nadzieja M, Chang W, Escobar-Herrera L, Mancinotti D, Angra D, Xia X, Tacke R, Khazaei H, Crocoll C, Vandenberg A, Link W, Stoddard FL, O'Sullivan DM, Stougaard J, Schulman AH, Andersen SU, Geu-Flores F. VC1 catalyses a key step in the biosynthesis of vicine in faba bean. NATURE PLANTS 2021; 7:923-931. [PMID: 34226693 PMCID: PMC7611347 DOI: 10.1038/s41477-021-00950-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/24/2021] [Indexed: 05/05/2023]
Abstract
Faba bean (Vicia faba L.) is a widely adapted and high-yielding legume cultivated for its protein-rich seeds1. However, the seeds accumulate the pyrimidine glucosides vicine and convicine, which can cause haemolytic anaemia (favism) in 400 million genetically predisposed individuals2. Here, we use gene-to-metabolite correlations, gene mapping and genetic complementation to identify VC1 as a key enzyme in vicine and convicine biosynthesis. We demonstrate that VC1 has GTP cyclohydrolase II activity and that the purine GTP is a precursor of both vicine and convicine. Finally, we show that cultivars with low vicine and convicine levels carry an inactivating insertion in the coding sequence of VC1. Our results reveal an unexpected, purine rather than pyrimidine, biosynthetic origin for vicine and convicine and pave the way for the development of faba bean cultivars that are free of these anti-nutrients.
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Affiliation(s)
- Emilie Björnsdotter
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Wei Chang
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | | | - Davide Mancinotti
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Xinxing Xia
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Rebecca Tacke
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Hamid Khazaei
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Christoph Crocoll
- DynaMo Center, Section for Molecular Plant Biology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Wolfgang Link
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Frederick L Stoddard
- Department of Agricultural Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alan H Schulman
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
- Natural Resources Institute Finland (Luke), Helsinki, Finland.
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Fernando Geu-Flores
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
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16
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Using D- and L-Amino Acid Oxidases to Generate the Imino Acid Substrate to Measure the Activity of the Novel Rid (Enamine/Imine Deaminase) Class of Enzymes. Methods Mol Biol 2021. [PMID: 33751437 DOI: 10.1007/978-1-0716-1286-6_13] [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: 07/30/2023]
Abstract
This chapter describes a method to assay the activity of reactive intermediate deaminases (Rid), a large family of conserved soluble enzymes, which have been proposed to prevent damages from metabolic intermediates such as the highly reactive and unstable compounds enamines/imines. In this method, the flavin adenine dinucleotide-dependent L- or D-amino acid oxidases generate an imino acid starting from a L- or D- amino acid, respectively. This reaction is coupled to the hydrolysis of the imino acid to the corresponding α-keto acid and ammonium ion catalyzed by a Rid enzyme. The spectrophotometric assay consists of measuring the decrease of the initial rate of formation of the semicarbazone, derived from the spontaneous reaction of the imino acid and semicarbazide, caused by the presence of the Rid enzyme. The set-up and testing of this method imply a preliminary characterization of the ability of the amino acid oxidase to release the imino acid required for the subsequent reactions. To this purpose, the activity of the L- or D-amino acid oxidases with different amino acids can be measured as production of hydrogen peroxide or formation of semicarbazone in parallel assays. The advantages and limitations of this assay of Rid activity are discussed.
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17
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Zhao G, Guo YY, Yao S, Shi X, Lv L, Du YL. Nitric oxide as a source for bacterial triazole biosynthesis. Nat Commun 2020; 11:1614. [PMID: 32235841 PMCID: PMC7109123 DOI: 10.1038/s41467-020-15420-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/02/2020] [Indexed: 11/09/2022] Open
Abstract
The heterocycle 1,2,3-triazole is among the most versatile chemical scaffolds and has been widely used in diverse fields. However, how nature creates this nitrogen-rich ring system remains unknown. Here, we report the biosynthetic route to the triazole-bearing antimetabolite 8-azaguanine. We reveal that its triazole moiety can be assembled through an enzymatic and non-enzymatic cascade, in which nitric oxide is used as a building block. These results expand our knowledge of the physiological role of nitric oxide synthase in building natural products with a nitrogen-nitrogen bond, and should also inspire the development of synthetic biology approaches for triazole production.
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Affiliation(s)
- Guiyun Zhao
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yuan-Yang Guo
- School of Chemistry and Chemical Engineering, Henan Normal University, 453007, Xinxiang, China
| | - Shunyu Yao
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Xinjie Shi
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology and The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China. .,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, 310003, Hangzhou, China.
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18
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Dai D, Tong H, Cheng L, Peng F, Zhang T, Qi W, Song R. Maize Dek33 encodes a pyrimidine reductase in riboflavin biosynthesis that is essential for oil-body formation and ABA biosynthesis during seed development. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5173-5187. [PMID: 31173102 PMCID: PMC6793443 DOI: 10.1093/jxb/erz268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/28/2019] [Indexed: 05/05/2023]
Abstract
The maize (Zea mays) defective kernel 33 (dek33) mutant produces defective and occasionally viviparous kernel phenotypes. In this study, we cloned Dek33 by positional cloning and found that it encodes a pyrimidine reductase in riboflavin biosynthesis. In dek33, a single-base mutation (G to A) in the C-terminal COG3236 domain caused a premature stop codon (TGA), producing a weak mutant allele with only a truncated form of the DEK33 protein that occurred at much lower levels that the completed WT form, and with a reduced riboflavin content. The dek33 mutation significantly affected oil-body formation and suppressed endoreduplication. It also disrupted ABA biosynthesis, resulting in lower ABA content that might be responsible for the viviparous embryo. In addition, our results indicated that the COG3236 domain is important for the protein stability of DEK33. Yeast two-hybrid experiments identified several proteins that interacted with DEK33, including RGLG2 and SnRK1, suggesting possible post-translational regulation of DEK33 stability. The interaction between DEK33 and these proteins was further confirmed by luciferase complementation image assays. This study provides a weak mutant allele that can be utilized to explore cellular responses to impaired riboflavin biosynthesis during seed development. Our findings indicate that the COG3236 domain might be an essential regulatory structure for DEK33 stability in maize.
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Affiliation(s)
- Dawei Dai
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Hongyang Tong
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Lijun Cheng
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Fei Peng
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Tingting Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Rentao Song
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Correspondence:
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19
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Wang D, Zhang L, Xu Y, Qi X, Wang X, Wang X, Zhang Q, Li P. Optimization of an Ultrasound-Assisted Extraction for Simultaneous Determination of Antioxidants in Sesame with Response Surface Methodology. Antioxidants (Basel) 2019; 8:antiox8080321. [PMID: 31430991 PMCID: PMC6720519 DOI: 10.3390/antiox8080321] [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: 08/02/2019] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 12/17/2022] Open
Abstract
Sesame is a nutritional agricultural product with medicinal properties. Accurate determination of micronutrients is important for the improvement of sesame quality and nutrition assessments. Our previous study showed that 10 antioxidants—d-homoproline, vitamin B2, coniferyl aldehyde, hesperidin, phloretin, N-acetyl-l-leucine, l-hyoscyamine, ferulic acid, 5-methoxypsoralen, and 8-methoxypsoralen—in sesame were potential characteristic nutrients in sesame. Herein, simultaneous detection of 10 different types of antioxidants was developed by using ultrasound-assisted extraction coupled with liquid chromatography-tandem mass spectrometry (UAE-LC-MS/MS) with the help of response surface methodology. The significant variables and levels were screened and optimized by combining the single factor experiment, Plackett–Burman test, and Box–Behnken design. The optimal conditions for extraction of target antioxidants in sesame were methanol solution of 75.0%, liquid-to-material ratio of 20:1 (mL/g), extraction temperature of 50 °C, extraction power of 410.0 W, extraction time of 65 min. The total yield of targets was 21.74 μg/g under the optimized conditions. The mobile phase used was 0.1% formic acid in acetonitrile and 0.1% formic acid in water, and the column was a Thermo Syncronis C18 reverse phase column (100 mm × 2.1 mm, 3 μm). All targets required only one injection and could be quickly separated and assayed within 7 min. The limits of detection and limits of quantification for these 10 nutritional compounds ranged from 0.01 to 0.11 µg/kg and from 0.04 to 0.34 µg/kg, respectively. The validation results indicated that the method had reasonable linearity (R2 ≥ 0.9990), good recoveries (71.1%–118.3%), satisfactory intra-day precision (≤9.6%) and inter-day precision (≤12.9%), and negligible matrix effects (≤13.8%). This simultaneous quantification method was accurate, fast, and robust for the assessment of sesame nutrition.
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Affiliation(s)
- Dandan Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062 China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Liangxiao Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062 China
- Laboratory of Quality and Safety Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Yueqing Xu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062 China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xin Qi
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062 China
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xuefang Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062 China
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiupin Wang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062 China
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Qi Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062 China
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Peiwu Li
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062 China.
- Laboratory of Quality and Safety Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs, Wuhan 430062, China.
- Quality Inspection and Test Center for Oilseed Products, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China.
- Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China.
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20
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Peters DL, McCutcheon JG, Stothard P, Dennis JJ. Novel Stenotrophomonas maltophilia temperate phage DLP4 is capable of lysogenic conversion. BMC Genomics 2019; 20:300. [PMID: 30991961 PMCID: PMC6469090 DOI: 10.1186/s12864-019-5674-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Temperate bacteriophages are capable of lysogenic conversion of new bacterial hosts. This phenomenon is often ascribed to "moron" elements that are acquired horizontally and transcribed independently from the rest of the phage genes. Whereas some bacterial species exhibit relatively little prophage-dependent phenotypic changes, other bacterial species such as Stenotrophomonas maltophilia appear to commonly adopt prophage genetic contributions. RESULTS The novel S. maltophilia bacteriophage DLP4 was isolated from soil using the highly antibiotic-resistant S. maltophilia strain D1585. Genome sequence analysis and functionality testing showed that DLP4 is a temperate phage capable of lysogenizing D1585. Two moron genes of interest, folA (BIT20_024) and ybiA (BIT20_065), were identified and investigated for their putative activities using complementation testing and phenotypic and transcriptomic changes between wild-type D1585 and the D1585::DLP4 lysogen. The gp24 / folA gene encodes dihydrofolate reductase (DHFR: FolA), an enzyme responsible for resistance to the antibiotic trimethoprim. I-TASSER analysis of DLP4 FolA predicted structural similarity to Bacillus anthracis DHFR and minimum inhibitory concentration experiments demonstrated that lysogenic conversion of D1585 by DLP4 provided the host cell with an increase in trimethoprim resistance. The gp65 / ybiA gene encodes N-glycosidase YbiA, which in E. coli BW25113 is required for its swarming motility phenotype. Expressing DLP4 ybiA in strain ybiA770(del)::kan restored its swarming motility activity to wildtype levels. Reverse transcription-PCR confirmed the expression of both of these genes during DLP4 lysogeny. CONCLUSIONS S. maltophilia temperate phage DLP4 contributes to the antibiotic resistance exhibited by its lysogenized host strain. Genomic analyses can greatly assist in the identification of phage moron genes potentially involved in lysogenic conversion. Further research is required to fully understand the specific contributions temperate phage moron genes provide with respect to the antibiotic resistance and virulence of S. maltophilia host cells.
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Affiliation(s)
- Danielle L. Peters
- Department of Biological Sciences, 6-065 Centennial Centre for Interdisciplinery Science, University of Alberta, Edmonton, Alberta T6G 2E9 Canada
| | - Jaclyn G. McCutcheon
- Department of Biological Sciences, 6-065 Centennial Centre for Interdisciplinery Science, University of Alberta, Edmonton, Alberta T6G 2E9 Canada
| | - Paul Stothard
- Department of Biological Sciences, 6-065 Centennial Centre for Interdisciplinery Science, University of Alberta, Edmonton, Alberta T6G 2E9 Canada
| | - Jonathan J. Dennis
- Department of Biological Sciences, 6-065 Centennial Centre for Interdisciplinery Science, University of Alberta, Edmonton, Alberta T6G 2E9 Canada
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21
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Zhang Y, Dong D, Li D, Lu L, Li J, Zhang Y, Chen L. Computational Method for the Identification of Molecular Metabolites Involved in Cereal Hull Color Variations. Comb Chem High Throughput Screen 2019; 21:760-770. [DOI: 10.2174/1386207322666190129105441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 08/02/2018] [Accepted: 08/16/2018] [Indexed: 11/22/2022]
Abstract
Background:
Cereal hull color is an important quality specification characteristic. Many
studies were conducted to identify genetic changes underlying cereal hull color diversity. However,
these studies mainly focused on the gene level. Recent studies have suggested that metabolomics can
accurately reflect the integrated and real-time cell processes that contribute to the formation of
different cereal colors.
Methods:
In this study, we exploited published metabolomics databases and applied several
advanced computational methods, such as minimum redundancy maximum relevance (mRMR),
incremental forward search (IFS), random forest (RF) to investigate cereal hull color at the metabolic
level. First, the mRMR was applied to analyze cereal hull samples represented by metabolite
features, yielding a feature list. Then, the IFS and RF were used to test several feature sets,
constructed according to the aforementioned feature list. Finally, the optimal feature sets and RF
classifier were accessed based on the testing results.
Results and Conclusion:
A total of 158 key metabolites were found to be useful in distinguishing
white cereal hulls from colorful cereal hulls. A prediction model constructed with these metabolites
and a random forest algorithm generated a high Matthews coefficient correlation value of 0.701.
Furthermore, 24 of these metabolites were previously found to be relevant to cereal color. Our study
can provide new insights into the molecular basis of cereal hull color formation.
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Affiliation(s)
- Yunhua Zhang
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Dong Dong
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Dai Li
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Lin Lu
- Department of Radiology, Columbia University Medical Center, New York, United States
| | - JiaRui Li
- School of Life Sciences, Shanghai University, Shanghai, China
| | - YuHang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lijuan Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
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22
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de Crécy-Lagard V, Haas D, Hanson AD. Newly-discovered enzymes that function in metabolite damage-control. Curr Opin Chem Biol 2018; 47:101-108. [PMID: 30268903 DOI: 10.1016/j.cbpa.2018.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/19/2018] [Accepted: 09/11/2018] [Indexed: 01/26/2023]
Abstract
Enzymes of unknown function are estimated to make up around 25% of the sequenced proteome. In the past decade, over 20 conserved families have been shown to function in the metabolism of 'damaged' or abnormal metabolites that are wasteful and often toxic. These newly discovered damage-control enzymes either repair or inactivate the offending metabolites, or pre-empt their formation in the first place. Comparative genomics has been of prime importance in predicting the functions of damage-control enzymes and in guiding the biochemical and genetic tests required to validate these functions.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA; Genetics Institute, University of Florida, Gainesville, FL, USA.
| | - Drago Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
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23
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Hüdig M, Schmitz J, Engqvist MKM, Maurino VG. Biochemical control systems for small molecule damage in plants. PLANT SIGNALING & BEHAVIOR 2018; 13:e1477906. [PMID: 29944438 PMCID: PMC6103286 DOI: 10.1080/15592324.2018.1477906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 05/11/2018] [Indexed: 05/29/2023]
Abstract
As a system, plant metabolism is far from perfect: small molecules (metabolites, cofactors, coenzymes, and inorganic molecules) are frequently damaged by unwanted enzymatic or spontaneous reactions. Here, we discuss the emerging principles in small molecule damage biology. We propose that plants evolved at least three distinct systems to control small molecule damage: (i) repair, which returns a damaged molecule to its original state; (ii) scavenging, which converts reactive molecules to harmless products; and (iii) steering, in which the possible formation of a damaged molecule is suppressed. We illustrate the concept of small molecule damage control in plants by describing specific examples for each of these three categories. We highlight interesting insights that we expect future research will provide on those systems, and we discuss promising strategies to discover new small molecule damage-control systems in plants.
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Affiliation(s)
- M. Hüdig
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - J. Schmitz
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - M. K. M. Engqvist
- Department of Biology and Biological engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - V. G. Maurino
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University, and Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
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24
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Sepúlveda-Cisternas I, Lozano Aguirre L, Fuentes Flores A, Vásquez Solis de Ovando I, García-Angulo VA. Transcriptomics reveals a cross-modulatory effect between riboflavin and iron and outlines responses to riboflavin biosynthesis and uptake in Vibrio cholerae. Sci Rep 2018; 8:3149. [PMID: 29453341 PMCID: PMC5816637 DOI: 10.1038/s41598-018-21302-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/31/2018] [Indexed: 12/19/2022] Open
Abstract
Vibrio cholerae, a pandemic diarrheagenic bacterium, is able to synthesize the essential vitamin riboflavin through the riboflavin biosynthetic pathway (RBP) and also to internalize it through the RibN importer. In bacteria, the way riboflavin biosynthesis and uptake functions correlate is unclear. To gain insights into the role of the riboflavin provision pathways in the physiology of V. cholerae, we analyzed the transcriptomics response to extracellular riboflavin and to deletions of ribD (RBP-deficient strain) or ribN. Many riboflavin-responsive genes were previously reported to belong to the iron regulon, including various iron uptake genes. Real time PCR analysis confirmed this effect and further documented that reciprocally, iron regulates RBP and ribN genes in a riboflavin-dependent way. A subset of genes were responding to both ribD and ribN deletions. However, in the subset of genes specifically affected in the ∆ribD strain, the functional terms protein folding and oxidation reduction process were enriched, as determined by a Gene Ontology analysis. In the gene subset specifically affected in the ∆ribN strain, the cytochrome complex assembly functional term was enriched. Results suggest that iron and riboflavin interrelate to regulate its respective provision genes and that both common and specific effects of biosynthesized and internalized riboflavin exist.
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Affiliation(s)
- Ignacio Sepúlveda-Cisternas
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile.,Escuela de Biotecnología, Universidad Mayor, Campus Huechuraba, Santiago, Chile
| | - Luis Lozano Aguirre
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, campus Chamilpa Cuernavaca, Morelos, Mexico
| | - Andrés Fuentes Flores
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
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25
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Fuentes Flores A, Sepúlveda Cisternas I, Vásquez Solis de Ovando JI, Torres A, García-Angulo VA. Contribution of riboflavin supply pathways to Vibrio cholerae in different environments. Gut Pathog 2017; 9:64. [PMID: 29163672 PMCID: PMC5686954 DOI: 10.1186/s13099-017-0214-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/06/2017] [Indexed: 12/15/2022] Open
Abstract
Background The waterborne diarrheagenic bacterium Vibrio cholerae, cause of the pandemic cholera disease, thrives in a variety of environments ranging from estuarine waters to the human intestinal tract. This species has two ways to obtain the essential micronutrient riboflavin, de novo biosynthesis and environmental uptake through the RibN importer. The way these functions interrelate to fulfill riboflavin needs in different conditions in this species is unknown. Results This study analyzed the contributions of riboflavin biosynthesis and transport to the culturability of Vibrio cholerae in river and seawater in vitro and in the Caenorhabditis elegans nematode host model. Elimination of the ribD riboflavin biosynthetic gene renders the bacteria riboflavin-auxotrophic, while a ribN mutant strain has no growth defect in minimal media. When growing in river water, deletion of ribD causes an impairment in culturability. In this condition, the ∆ribN strain has a defect to compete against a wild type strain but outcompetes the ∆ribD strain. The latter effect is inverted by the addition of riboflavin to the water. In contrast, growth in seawater causes a loss in culturability independent of riboflavin biosynthesis or transport. In the C. elegans model, only the ∆ribD strain is attenuated. Conclusion Results indicate that while riboflavin biosynthesis seems to outweigh riboflavin uptake, the latter may still provide a selective advantage to V. cholerae in some environments. Electronic supplementary material The online version of this article (10.1186/s13099-017-0214-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrés Fuentes Flores
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Ignacio Sepúlveda Cisternas
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile.,Escuela de Biotecnología, Universidad Mayor, Campus Huechuraba, Santiago, Chile
| | | | - Alexia Torres
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Víctor Antonio García-Angulo
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile.,Facultad de Medicina Norte, Pabellón L. Santiago de Chile, ZIP 8380453 Santiago, Chile
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26
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Golubev A, Hanson AD, Gladyshev VN. Non-enzymatic molecular damage as a prototypic driver of aging. J Biol Chem 2017; 292:6029-6038. [PMID: 28264930 PMCID: PMC5391736 DOI: 10.1074/jbc.r116.751164] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The chemical potentialities of metabolites far exceed metabolic requirements. The required potentialities are realized mostly through enzymatic catalysis. The rest are realized spontaneously through organic reactions that (i) occur wherever appropriate reactants come together, (ii) are so typical that many have proper names (e.g. Michael addition, Amadori rearrangement, and Pictet-Spengler reaction), and (iii) often have damaging consequences. There are many more causes of non-enzymatic damage to metabolites than reactive oxygen species and free radical processes (the "usual suspects"). Endogenous damage accumulation in non-renewable macromolecules and spontaneously polymerized material is sufficient to account for aging and differentiates aging from wear-and-tear of inanimate objects by deriving it from metabolism, the essential attribute of life.
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Affiliation(s)
- Alexey Golubev
- From the Department of Biochemistry, Saint-Petersburg State University, Saint Petersburg 199034, Russia,
| | - Andrew D Hanson
- the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, and
| | - Vadim N Gladyshev
- the Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
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27
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Cisternas IS, Torres A, Flores AF, Angulo VAG. Differential regulation of riboflavin supply genes in Vibrio cholerae. Gut Pathog 2017; 9:10. [PMID: 28239422 PMCID: PMC5312566 DOI: 10.1186/s13099-017-0159-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/09/2017] [Indexed: 12/01/2022] Open
Abstract
Background Riboflavin is the precursor of important redox cofactors such as flavin mononucleotide (FMN) and flavin adenine dinucleotide, required for several biological processes. Vibrio cholerae, a pathogenic bacterium responsible for the cholera disease, possesses the ability to biosynthesize de novo as well as to uptake riboflavin through the riboflavin biosynthetic pathway (RBP) and the RibN importer, respectively. The intra-organism relationship between riboflavin biosynthesis and uptake functions has not been studied. Results This work determined the transcriptional organization of RBP genes and ribN in V. cholerae through reverse transcription polymerase chain reaction and analyzed their expression when growing with or without extracellular riboflavin using real time PCR. The RBP is organized in three transcriptional units, the major one containing ribD, ribE, ribA and ribH together with genes involved in functions not directly related to riboflavin biosynthesis such as nrdR and nusB. In addition, two independent monocistronic units contain ribA2 and ribB, the later conserving a putative FMN riboswitch. The ribN gene is encoded in operon with a gene coding for a predicted outer membrane protein and a gene encoding a protein with a glutaredoxin domain. Regulation analysis showed that among these transcriptional units, only ribB is negatively regulated by riboflavin and that its repression depends on the RibN riboflavin importer. Moreover, external riboflavin highly induced ribB transcription in a ΔribN strain. Also, a genomic database search found a negative correlation between the presence of nrdR and nusB and the FMN riboswitch in bacterial RBP operons. Conclusions Growing in the presence of riboflavin downregulates only a single element among the transcriptional units of riboflavin supply pathways. Thus, endogenous riboflavin biosynthesis seems to be negatively regulated by extracellular riboflavin through its specific effect on transcription of ribB in V. cholerae. Electronic supplementary material The online version of this article (doi:10.1186/s13099-017-0159-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ignacio Sepúlveda Cisternas
- Escuela de Biotecnología, Universidad Mayor, Campus Huechuraba, Santiago, Chile.,Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Norte, Universidad de Chile, Pabellón L. Independencia, 1027, 8380453 Santiago, Chile
| | - Alexia Torres
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Norte, Universidad de Chile, Pabellón L. Independencia, 1027, 8380453 Santiago, Chile
| | - Andrés Fuentes Flores
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Norte, Universidad de Chile, Pabellón L. Independencia, 1027, 8380453 Santiago, Chile
| | - Víctor Antonio García Angulo
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina Norte, Universidad de Chile, Pabellón L. Independencia, 1027, 8380453 Santiago, Chile
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28
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Sa N, Rawat R, Thornburg C, Walker KD, Roje S. Identification and characterization of the missing phosphatase on the riboflavin biosynthesis pathway in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:705-716. [PMID: 27490826 DOI: 10.1111/tpj.13291] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Despite the importance of riboflavin as the direct precursor of the cofactors flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), the physiologically relevant catalyst dephosphorylating the riboflavin biosynthesis pathway intermediate 5-amino-6-ribitylamino-2,4(1H,3H) pyrimidinedione 5'-phosphate (ARPP) has not been characterized from any organism. By using as the query sequence a previously identified plastidial FMN hydrolase AtcpFHy1 (At1g79790), belonging to the haloacid dehalogenase (HAD) superfamily, seven candidates for the missing ARPP phosphatase were found, cloned, recombinantly expressed, and purified. Activity screening showed that the enzymes encoded by AtcpFHy1, At4g11570, and At4g25840 catalyze dephosphorylation of ARPP. AtcpFHy1 was renamed AtcpFHy/PyrP1, At4g11570 and At4g25840 were named AtPyrP2 and AtGpp1/PyrP3, respectively. Subcellular localization in planta indicated that AtPyrP2 was localized in plastids and AtGpp1/PyrP3 in mitochondria. Biochemical characterization of AtcpFHy/PyrP1 and AtPyrP2 showed that they have similar Km values for the substrate ARPP, with AtcpFHy/PyrP1 having higher catalytic efficiency. Screening of 21 phosphorylated substrates showed that AtPyrP2 is specific for ARPP. Molecular weights of AtcpFHy/PyrP1 and AtPyrP2 were estimated at 46 and 72 kDa, suggesting dimers. pH and temperature optima for AtcpFHy/PyrP1 and AtPyrP2 were ~7.0-8.5 and 40-50°C. T-DNA knockout of AtcpFHy/PyrP1 did not affect the flavin profile of the transgenic plants, whereas silencing of AtPyrP2 decreased accumulation of riboflavin, FMN, and FAD. Our results strongly support AtPyrP2 as the missing phosphatase on the riboflavin biosynthesis pathway in Arabidopsis thaliana. The identification of this enzyme closes a long-standing gap in understanding of the riboflavin biosynthesis in plants.
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Affiliation(s)
- Na Sa
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Renu Rawat
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Chelsea Thornburg
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kevin D Walker
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Sanja Roje
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
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29
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Hanson AD, Beaudoin GA, McCarty DR, Gregory JF. Does Abiotic Stress Cause Functional B Vitamin Deficiency in Plants? PLANT PHYSIOLOGY 2016; 172:2082-2097. [PMID: 27807106 PMCID: PMC5129723 DOI: 10.1104/pp.16.01371] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/19/2016] [Indexed: 05/20/2023]
Abstract
B vitamins are the precursors of essential metabolic cofactors but are prone to destruction under stress conditions. It is therefore a priori reasonable that stressed plants suffer B vitamin deficiencies and that certain stress symptoms are metabolic knock-on effects of these deficiencies. Given the logic of these arguments, and the existence of data to support them, it is a shock to realize that the roles of B vitamins in plant abiotic stress have had minimal attention in the literature (100-fold less than hormones) and continue to be overlooked. In this article, we therefore aim to explain the connections among B vitamins, enzyme cofactors, and stress conditions in plants. We first outline the chemistry and biochemistry of B vitamins and explore the concept of vitamin deficiency with the help of information from mammals. We then summarize classical and recent evidence for stress-induced vitamin deficiencies and for plant responses that counter these deficiencies. Lastly, we consider potential implications for agriculture.
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Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Guillaume A Beaudoin
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Donald R McCarty
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Jesse F Gregory
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
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30
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Abstract
Riboflavin derivatives are essential cofactors for a myriad of flavoproteins. In bacteria, flavins importance extends beyond their role as intracellular protein cofactors, as secreted flavins are a key metabolite in a variety of physiological processes. Bacteria obtain riboflavin through the endogenous riboflavin biosynthetic pathway (RBP) or by the use of importer proteins. Bacteria frequently encode multiple paralogs of the RBP enzymes and as for other micronutrient supply pathways, biosynthesis and uptake functions largely coexist. It is proposed that bacteria shut down biosynthesis and would rather uptake riboflavin when the vitamin is environmentally available. Recently, the overlap of riboflavin provisioning elements has gained attention and the functions of duplicated paralogs of RBP enzymes started to be addressed. Results point towards the existence of a modular structure in the bacterial riboflavin supply pathways. Such structure uses subsets of RBP genes to supply riboflavin for specific functions. Given the importance of riboflavin in intra and extracellular bacterial physiology, this complex array of riboflavin provision pathways may have developed to contend with the various riboflavin requirements. In riboflavin-prototrophic bacteria, riboflavin transporters could represent a module for riboflavin provision for particular, yet unidentified processes, rather than substituting for the RBP as usually assumed.
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Affiliation(s)
- Víctor Antonio García-Angulo
- a Microbiology and Mycology Program, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile , Santiago , Chile
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31
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Stavrinides A, Tatsis EC, Caputi L, Foureau E, Stevenson CEM, Lawson DM, Courdavault V, O'Connor SE. Structural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity. Nat Commun 2016; 7:12116. [PMID: 27418042 PMCID: PMC4947188 DOI: 10.1038/ncomms12116] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 05/31/2016] [Indexed: 02/07/2023] Open
Abstract
Plants produce an enormous array of biologically active metabolites, often with stereochemical variations on the same molecular scaffold. These changes in stereochemistry dramatically impact biological activity. Notably, the stereoisomers of the heteroyohimbine alkaloids show diverse pharmacological activities. We reported a medium chain dehydrogenase/reductase (MDR) from Catharanthus roseus that catalyses formation of a heteroyohimbine isomer. Here we report the discovery of additional heteroyohimbine synthases (HYSs), one of which produces a mixture of diastereomers. The crystal structures for three HYSs have been solved, providing insight into the mechanism of reactivity and stereoselectivity, with mutation of one loop transforming product specificity. Localization and gene silencing experiments provide a basis for understanding the function of these enzymes in vivo. This work sets the stage to explore how MDRs evolved to generate structural and biological diversity in specialized plant metabolism and opens the possibility for metabolic engineering of new compounds based on this scaffold. The stereochemistry of the plant heteroyohimbine alkaloids is a key factor determining their diverse biological activities. Here, the authors carry out structural, localization and genetic experiments to understand the mechanism of stereoselectivity for three heteroyohimbine synthases and to identify their function in vivo.
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Affiliation(s)
- Anna Stavrinides
- The John Innes Centre, Department of Biological Chemistry, Norwich NR4 7UH, UK
| | - Evangelos C Tatsis
- The John Innes Centre, Department of Biological Chemistry, Norwich NR4 7UH, UK
| | - Lorenzo Caputi
- The John Innes Centre, Department of Biological Chemistry, Norwich NR4 7UH, UK
| | - Emilien Foureau
- Université François-Rabelais de Tours, EA2106 'Biomolécules et Biotechnologies Végétales', Tours 37200, France
| | - Clare E M Stevenson
- The John Innes Centre, Department of Biological Chemistry, Norwich NR4 7UH, UK
| | - David M Lawson
- The John Innes Centre, Department of Biological Chemistry, Norwich NR4 7UH, UK
| | - Vincent Courdavault
- Université François-Rabelais de Tours, EA2106 'Biomolécules et Biotechnologies Végétales', Tours 37200, France
| | - Sarah E O'Connor
- The John Innes Centre, Department of Biological Chemistry, Norwich NR4 7UH, UK
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32
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Henry CS, Lerma-Ortiz C, Gerdes SY, Mullen JD, Colasanti R, Zhukov A, Frelin O, Thiaville JJ, Zallot R, Niehaus TD, Hasnain G, Conrad N, Hanson AD, de Crécy-Lagard V. Systematic identification and analysis of frequent gene fusion events in metabolic pathways. BMC Genomics 2016; 17:473. [PMID: 27342196 PMCID: PMC4921024 DOI: 10.1186/s12864-016-2782-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/26/2016] [Indexed: 11/19/2022] Open
Abstract
Background Gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. Results Here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These sets were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database at http://modelseed.org/projects/fusions/. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. Conclusions Customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2782-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. .,Computation Institute, The University of Chicago, Chicago, IL, 60637, USA.
| | - Claudia Lerma-Ortiz
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Svetlana Y Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.,Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jeffrey D Mullen
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Ric Colasanti
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Aleksey Zhukov
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Océane Frelin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jennifer J Thiaville
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Rémi Zallot
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ghulam Hasnain
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Neal Conrad
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Valérie de Crécy-Lagard
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA.
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A family of metal-dependent phosphatases implicated in metabolite damage-control. Nat Chem Biol 2016; 12:621-7. [PMID: 27322068 DOI: 10.1038/nchembio.2108] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 03/30/2016] [Indexed: 12/31/2022]
Abstract
DUF89 family proteins occur widely in both prokaryotes and eukaryotes, but their functions are unknown. Here we define three DUF89 subfamilies (I, II, and III), with subfamily II being split into stand-alone proteins and proteins fused to pantothenate kinase (PanK). We demonstrated that DUF89 proteins have metal-dependent phosphatase activity against reactive phosphoesters or their damaged forms, notably sugar phosphates (subfamilies II and III), phosphopantetheine and its S-sulfonate or sulfonate (subfamily II-PanK fusions), and nucleotides (subfamily I). Genetic and comparative genomic data strongly associated DUF89 genes with phosphoester metabolism. The crystal structure of the yeast (Saccharomyces cerevisiae) subfamily III protein YMR027W revealed a novel phosphatase active site with fructose 6-phosphate and Mg(2+) bound near conserved signature residues Asp254 and Asn255 that are critical for activity. These findings indicate that DUF89 proteins are previously unrecognized hydrolases whose characteristic in vivo function is to limit potentially harmful buildups of normal or damaged phosphometabolites.
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‘Nothing of chemistry disappears in biology’: the Top 30 damage-prone endogenous metabolites. Biochem Soc Trans 2016; 44:961-71. [DOI: 10.1042/bst20160073] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Indexed: 11/17/2022]
Abstract
Many common metabolites are intrinsically unstable and reactive, and hence prone to chemical (i.e. non-enzymatic) damage in vivo. Although this fact is widely recognized, the purely chemical side-reactions of metabolic intermediates can be surprisingly hard to track down in the literature and are often treated in an unprioritized case-by-case way. Moreover, spontaneous chemical side-reactions tend to be overshadowed today by side-reactions mediated by promiscuous (‘sloppy’) enzymes even though chemical damage to metabolites may be even more prevalent than damage from enzyme sloppiness, has similar outcomes, and is held in check by similar biochemical repair or pre-emption mechanisms. To address these limitations and imbalances, here we draw together and systematically integrate information from the (bio)chemical literature, from cheminformatics, and from genome-scale metabolic models to objectively define a ‘Top 30’ list of damage-prone metabolites. A foundational part of this process was to derive general reaction rules for the damage chemistries involved. The criteria for a ‘Top 30’ metabolite included predicted chemical reactivity, essentiality, and occurrence in diverse organisms. We also explain how the damage chemistry reaction rules (‘operators’) are implemented in the Chemical-Damage-MINE (CD-MINE) database (minedatabase.mcs.anl.gov/#/top30) to provide a predictive tool for many additional potential metabolite damage products. Lastly, we illustrate how defining a ‘Top 30’ list can drive genomics-enabled discovery of the enzymes of previously unrecognized damage-control systems, and how applying chemical damage reaction rules can help identify previously unknown peaks in metabolomics profiles.
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Hanson AD, Henry CS, Fiehn O, de Crécy-Lagard V. Metabolite Damage and Metabolite Damage Control in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:131-52. [PMID: 26667673 DOI: 10.1146/annurev-arplant-043015-111648] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
It is increasingly clear that (a) many metabolites undergo spontaneous or enzyme-catalyzed side reactions in vivo, (b) the damaged metabolites formed by these reactions can be harmful, and (c) organisms have biochemical systems that limit the buildup of damaged metabolites. These damage-control systems either return a damaged molecule to its pristine state (metabolite repair) or convert harmful molecules to harmless ones (damage preemption). Because all organisms share a core set of metabolites that suffer the same chemical and enzymatic damage reactions, certain damage-control systems are widely conserved across the kingdoms of life. Relatively few damage reactions and damage-control systems are well known. Uncovering new damage reactions and identifying the corresponding damaged metabolites, damage-control genes, and enzymes demands a coordinated mix of chemistry, metabolomics, cheminformatics, biochemistry, and comparative genomics. This review illustrates the above points using examples from plants, which are at least as prone to metabolite damage as other organisms.
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Affiliation(s)
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439;
- Computation Institute, University of Chicago, Chicago, Illinois 60637
| | - Oliver Fiehn
- Genome Center, University of California, Davis, California 95616;
| | - Valérie de Crécy-Lagard
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611; ,
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Niehaus TD, Thamm AMK, de Crécy-Lagard V, Hanson AD. Proteins of Unknown Biochemical Function: A Persistent Problem and a Roadmap to Help Overcome It. PLANT PHYSIOLOGY 2015; 169:1436-42. [PMID: 26269542 PMCID: PMC4634069 DOI: 10.1104/pp.15.00959] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/11/2015] [Indexed: 05/03/2023]
Abstract
The number of sequenced genomes is rapidly increasing, but functional annotation of the genes in these genomes lags far behind. Even in Arabidopsis (Arabidopsis thaliana), only approximately 40% of enzyme- and transporter-encoding genes have credible functional annotations, and this number is even lower in nonmodel plants. Functional characterization of unknown genes is a challenge, but various databases (e.g. for protein localization and coexpression) can be mined to provide clues. If homologous microbial genes exist-and about one-half the genes encoding unknown enzymes and transporters in Arabidopsis have microbial homologs-cross-kingdom comparative genomics can powerfully complement plant-based data. Multiple lines of evidence can strengthen predictions and warrant experimental characterization. In some cases, relatively quick tests in genetically tractable microbes can determine whether a prediction merits biochemical validation, which is costly and demands specialized skills.
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Affiliation(s)
- Thomas D Niehaus
- Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611
| | - Antje M K Thamm
- Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611
| | - Valérie de Crécy-Lagard
- Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611
| | - Andrew D Hanson
- Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611
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Joo M, Yoo HG, Kim HJ, Kwon HJ. ToxB encodes a canonical GTP cyclohydrolase II in toxoflavin biosynthesis and ribA expression restored toxoflavin production in a ΔtoxB mutant. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13765-015-0116-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Jeffryes JG, Colastani RL, Elbadawi-Sidhu M, Kind T, Niehaus TD, Broadbelt LJ, Hanson AD, Fiehn O, Tyo KEJ, Henry CS. MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. J Cheminform 2015; 7:44. [PMID: 26322134 PMCID: PMC4550642 DOI: 10.1186/s13321-015-0087-1] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography-mass spectrometry (LC-MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases. DESCRIPTION Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not present in the PubChem database. However, these MINE compounds have on average higher structural similarity to natural products than compounds from KEGG or PubChem. MINE databases were able to propose annotations for 98.6% of a set of 667 MassBank spectra, 14% more than KEGG alone and equivalent to PubChem while returning far fewer candidates per spectra than PubChem (46 vs. 1715 median candidates). Application of MINEs to LC-MS accurate mass data enabled the identity of an unknown peak to be confidently predicted. CONCLUSIONS MINE databases are freely accessible for non-commercial use via user-friendly web-tools at http://minedatabase.mcs.anl.gov and developer-friendly APIs. MINEs improve metabolomics peak identification as compared to general chemical databases whose results include irrelevant synthetic compounds. Furthermore, MINEs complement and expand on previous in silico generated compound databases that focus on human metabolism. We are actively developing the database; future versions of this resource will incorporate transformation rules for spontaneous chemical reactions and more advanced filtering and prioritization of candidate structures. Graphical abstractMINE database construction and access methods. The process of constructing a MINE database from the curated source databases is depicted on the left. The methods for accessing the database are shown on the right.
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Affiliation(s)
- James G Jeffryes
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA ; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL USA
| | - Ricardo L Colastani
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL USA
| | | | - Tobias Kind
- West Coast Metabolomics Center, University of California, Davis, CA USA
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, CA USA ; Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL USA
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Colinas M, Fitzpatrick TB. Natures balancing act: examining biosynthesis de novo, recycling and processing damaged vitamin B metabolites. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:98-106. [PMID: 26005929 DOI: 10.1016/j.pbi.2015.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/22/2015] [Accepted: 05/01/2015] [Indexed: 05/06/2023]
Abstract
Plants use B vitamin compounds as cofactors for metabolism. Biosynthesis de novo of these metabolites in plants is almost fully elucidated. However, salvaging of precursors as well as cofactor derivatives is only being unraveled. Furthermore, processing of these compounds when damaged by cellular activities to prevent deleterious effects on metabolism is emerging. Recent investigations indicate that the role of B vitamins goes beyond metabolism and are being linked with epigenetic traits, specific developmental cues, the circadian clock, as well as abiotic and biotic stress responses. More in depth investigations on the regulation of the provision of these compounds through biosynthesis de novo, salvage and transport is suggesting that plants may share the cost of this load by division of labor.
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Affiliation(s)
- Maite Colinas
- Department of Botany and Plant Biology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
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