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Quaye JA, Gadda G. The Pseudomonas aeruginosa PAO1 metallo flavoprotein d-2-hydroxyglutarate dehydrogenase requires Zn 2+ for substrate orientation and activation. J Biol Chem 2023; 299:103008. [PMID: 36775127 PMCID: PMC10034468 DOI: 10.1016/j.jbc.2023.103008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Pseudomonas aeruginosa PAO1 d-2-hydroxyglutarate (D2HG) dehydrogenase (PaD2HGDH) oxidizes D2HG to 2-ketoglutarate during the vital l-serine biosynthesis and is a potential therapeutic target against P. aeruginosa. PaD2HGDH, which oxidizes d-malate as an alternative substrate, has been demonstrated to be a metallo flavoprotein that requires Zn2+ for activity. However, the role of Zn2+ in the enzyme has not been elucidated, making it difficult to rationalize why nature employs both a redox center and a metal ion for catalysis in PaD2HGDH and other metallo flavoenzymes. In this study, recombinant His-tagged PaD2HGDH was purified to high levels in the presence of Zn2+ or Co2+ to investigate the metal's role in catalysis. We found that the flavin reduction step was reversible and partially rate limiting for the enzyme's turnover at pH 7.4 with either D2HG or d-malate with similar rate constants for both substrates, irrespective of whether Zn2+ or Co2+ was bound to the enzyme. The steady-state pL profiles of the kcat and kcat/Km values with d-malate demonstrate that Zn2+ mediates the activation of water coordinated to the metal. Our data are consistent with a dual role for the metal, which orients the hydroxy acid substrate in the enzyme's active site and rapidly deprotonates the substrate to yield an alkoxide species for hydride transfer to the flavin. Thus, we propose a catalytic mechanism for PaD2HGDH oxidation that establishes Zn2+ as a cofactor required for substrate orientation and activation during enzymatic turnover.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Department of Biology, Georgia State University, Atlanta, Georgia, USA; Department of The Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA.
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2
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Quaye JA, Gadda G. Uncovering Zn 2+ as a cofactor of FAD-dependent Pseudomonas aeruginosa PAO1 d-2-hydroxyglutarate dehydrogenase. J Biol Chem 2023; 299:103007. [PMID: 36775126 PMCID: PMC10025160 DOI: 10.1016/j.jbc.2023.103007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Pseudomonas aeruginosa couples the oxidation of d-2-hydroxyglutarate (D2HG) to l-serine biosynthesis for survival, using d-2-hydroxyglutarate dehydrogenase from P. aeruginosa (PaD2HGDH). Knockout of PaD2HGDH impedes P. aeruginosa growth, making PaD2HGDH a potential target for therapeutics. Previous studies showed that the enzyme's activity increased with Zn2+, Co2+, or Mn2+ but did not establish the enzyme's metal composition and whether the metal is an activator or a required cofactor for the enzyme, which we addressed in this study. Comparable to the human enzyme, PaD2HGDH showed only 15% flavin reduction with D2HG or d-malate. Upon purifying PaD2HGDH with 1 mM Zn2+, the Zn2+:protein stoichiometry was 2:1, yielding an enzyme with ∼40 s-1kcat for d-malate. Treatment with 1 mM EDTA decreased the Zn2+:protein ratio to 1:1 without changing the kinetic parameters with d-malate. We observed complete enzyme inactivation for the metalloapoenzyme with 100 mM EDTA treatment, suggesting that Zn2+ is essential for PaD2HGDH activity. The presence of Zn2+ increased the flavin N3 atom pKa value to 11.9, decreased the flavin ε450 at pH 7.4 from 13.5 to 11.8 mM-1 cm-1, and yielded a charged transfer complex with a broad absorbance band >550 nm, consistent with a Zn2+-hydrate species altering the electronic properties of the enzyme-bound FAD. The exogenous addition of Zn2+, Co2+, Cd2+, Mn2+, or Ni2+ to the metalloapoenzyme reactivated the enzyme in a sigmoidal pattern, consistent with an induced fit rapid-rearrangement mechanism. Collectively, our data demonstrate that PaD2HGDH is a Zn2+-dependent metallo flavoprotein, which requires Zn2+ as an essential cofactor for enzyme activity.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Department of Biology, Georgia State University, Atlanta, Georgia, USA; The Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA.
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3
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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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Kumar Y, Singh RK, Hazra AB. Characterization of a novel mesophilic CTP-dependent riboflavin kinase and rational engineering to create its thermostable homologs. Chembiochem 2021; 22:3414-3424. [PMID: 34387404 DOI: 10.1002/cbic.202100211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/20/2021] [Indexed: 11/05/2022]
Abstract
Flavins play a central role in metabolism as molecules that catalyze a wide range of redox reactions in living organisms. Several variations in flavin biosynthesis exist among the domains of life, and their analysis has revealed many new structural and mechanistic insights till date. The cytidine triphosphate (CTP)-dependent riboflavin kinase in archaea is one such example - unlike most kinases that use adenosine triphosphate, archaeal riboflavin kinases utilize CTP to phosphorylate riboflavin and produce flavin mononucleotide. In this study, we present the characterization of a new mesophilic archaeal CTP-utilizing riboflavin kinase homolog from Methanococcus maripaludis (MmpRibK), which is linked closely in sequence to the previously characterized thermophilic Methanocaldococcus jannaschii homolog. We reconstitute the activity of MmpRibK, determine its kinetic parameters and molecular factors that contribute to its unique properties, and finally establish the residues that improve its thermostability using computation and a series of experiments. Our work advances the molecular understanding of flavin biosynthesis in archaea by the characterization of the first mesophilic CTP-dependent riboflavin kinase. Finally, it validates the role of salt bridges and rigidifying amino acid residues in imparting thermostability to this unique structural fold that characterizes archaeal riboflavin kinase enzymes, with implications in enzyme engineering and biotechnological applications.
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Affiliation(s)
- Yashwant Kumar
- IISER Pune: Indian Institute of Science Education Research Pune, Chemistry, INDIA
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5
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Ayikpoe R, Salazar J, Majestic B, Latham JA. Mycofactocin Biosynthesis Proceeds through 3-Amino-5-[( p-hydroxyphenyl)methyl]-4,4-dimethyl-2-pyrrolidinone (AHDP); Direct Observation of MftE Specificity toward MftA. Biochemistry 2018; 57:5379-5383. [PMID: 30183269 DOI: 10.1021/acs.biochem.8b00816] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structure of the ribosomally synthesized and post-translationally modified peptide product mycofactocin is unknown. Recently, the first step in mycofactocin biosynthesis was shown to be catalyzed by MftC in two S-adenosylmethionine-dependent steps. In the first step, MftC catalyzes the oxidative decarboxylation of the MftA peptide to produce the styrene-containing intermediate MftA**, followed by a subsequent C-C bond formation to yield the lactam-containing MftA*. Here, we demonstrate the subsequent biosynthetic step catalyzed by MftE is specific for MftA*. The hydrolysis of MftA* leads to the formation of MftA(1-28) and 3-amino-5-[( p-hydroxyphenyl)methyl]-4,4-dimethyl-2-pyrrolidinone (AHDP). The hydrolysis reaction is Fe2+-dependent, and addition of the metal to the reaction mixture leads to a kobs of ∼0.2 min-1. Lastly, we validate the structure of AHDP by 1H, 13C, and COSY nuclear magnetic resonance techniques as well as mass spectrometry.
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Affiliation(s)
- Richard Ayikpoe
- Department of Chemistry and Biochemistry , University of Denver , Denver , Colorado 80208 , United States
| | - Joe Salazar
- Department of Chemistry and Biochemistry , University of Denver , Denver , Colorado 80208 , United States
| | - Brian Majestic
- Department of Chemistry and Biochemistry , University of Denver , Denver , Colorado 80208 , United States
| | - John A Latham
- Department of Chemistry and Biochemistry , University of Denver , Denver , Colorado 80208 , United States
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6
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Aizat WM, Ibrahim S, Rahnamaie-Tajadod R, Loke KK, Goh HH, Noor NM. Proteomics (SWATH-MS) informed by transcriptomics approach of tropical herb Persicaria minor leaves upon methyl jasmonate elicitation. PeerJ 2018; 6:e5525. [PMID: 30186693 PMCID: PMC6118203 DOI: 10.7717/peerj.5525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Jasmonic acid (JA) and its derivative, methyl JA (MeJA) are hormonal cues released by plants that signal defense response to curb damages from biotic and abiotic stresses. To study such response, a tropical herbal plant, Persicaria minor, which possesses pungent smell and various bioactivities including antimicrobial and anticancer, was treated with MeJA. Such elicitation has been performed in hairy root cultures and plants such as Arabidopsis and rice, yet how MeJA influenced the proteome of an herbal species like P. minor is unknown. METHOD In this study, P. minor plants were exogenously elicited with MeJA and leaf samples were subjected to SWATH-MS proteomics analysis. A previously published translated transcriptome database was used as a reference proteome database for a comprehensive protein sequence catalogue and to compare their differential expression. RESULTS From this proteomics informed by transcriptomics approach, we have successfully profiled 751 proteins of which 40 proteins were significantly different between control and MeJA-treated samples. Furthermore, a correlation analysis between both proteome and the transcriptome data sets suggests that significantly upregulated proteins were positively correlated with their cognate transcripts (Pearson's r = 0.677) while a weak correlation was observed for downregulated proteins (r = 0.147). DISCUSSION MeJA treatment induced the upregulation of proteins involved in various biochemical pathways including stress response mechanism, lipid metabolism, secondary metabolite production, DNA degradation and cell wall degradation. Conversely, proteins involved in energy expensive reactions such as photosynthesis, protein synthesis and structure were significantly downregulated upon MeJA elicitation. Overall protein-transcript correlation was also weak (r = 0.341) suggesting the existence of post-transcriptional regulation during such stress. In conclusion, proteomics analysis using SWATH-MS analysis supplemented by the transcriptome database allows comprehensive protein profiling of this non-model herbal species upon MeJA treatment.
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Affiliation(s)
- Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Sarah Ibrahim
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | | | - Kok-Keong Loke
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Normah Mohd Noor
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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7
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Rodionova IA, Vetting MW, Li X, Almo SC, Osterman AL, Rodionov DA. A novel bifunctional transcriptional regulator of riboflavin metabolism in Archaea. Nucleic Acids Res 2017; 45:3785-3799. [PMID: 28073944 PMCID: PMC5397151 DOI: 10.1093/nar/gkw1331] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/20/2016] [Indexed: 12/11/2022] Open
Abstract
Riboflavin (vitamin B2) is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide, which are essential coenzymes in all free-living organisms. Riboflavin biosynthesis in many Bacteria but not in Archaea is controlled by FMN-responsive riboswitches. We identified a novel bifunctional riboflavin kinase/regulator (RbkR), which controls riboflavin biosynthesis and transport genes in major lineages of Crenarchaeota, Euryarchaeota and Thaumarchaeota. RbkR proteins are composed of the riboflavin kinase domain and a DNA-binding winged helix-turn-helix-like domain. Using comparative genomics, we predicted RbkR operator sites and reconstructed RbkR regulons in 94 archaeal genomes. While the identified RbkR operators showed significant variability between archaeal lineages, the conserved core of RbkR regulons includes riboflavin biosynthesis genes, known/predicted vitamin uptake transporters and the rbkR gene. The DNA motifs and CTP-dependent riboflavin kinase activity of two RbkR proteins were experimentally validated in vitro. The DNA binding activity of RbkR was stimulated by CTP and suppressed by FMN, a product of riboflavin kinase. The crystallographic structure of RbkR from Thermoplasma acidophilum was determined in complex with CTP and its DNA operator revealing key residues for operator and ligand recognition. Overall, this study contributes to our understanding of metabolic and regulatory networks for vitamin homeostasis in Archaea.
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Affiliation(s)
- Irina A Rodionova
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiaoqing Li
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrei L Osterman
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Dmitry A Rodionov
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051 Russia
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8
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Sarge S, Haase I, Illarionov B, Laudert D, Hohmann HP, Bacher A, Fischer M. Catalysis of an Essential Step in Vitamin B2Biosynthesis by a Consortium of Broad Spectrum Hydrolases. Chembiochem 2015; 16:2466-9. [DOI: 10.1002/cbic.201500352] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Sonja Sarge
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
| | - Ilka Haase
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
| | - Boris Illarionov
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
| | - Dietmar Laudert
- DSM Nutritional Products; P. O. Box 2676 4002 Basel Switzerland
| | | | - Adelbert Bacher
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
| | - Markus Fischer
- Hamburg School of Food Science; Institute of Food Chemistry; University of Hamburg; Grindelallee 117 20146 Hamburg Germany
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9
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Haase I, Gräwert T, Illarionov B, Bacher A, Fischer M. Recent advances in riboflavin biosynthesis. Methods Mol Biol 2014; 1146:15-40. [PMID: 24764086 DOI: 10.1007/978-1-4939-0452-5_2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Riboflavin is biosynthesized from GTP and ribulose 5-phosphate. Whereas the early reactions conducing to 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate show significant taxonomic variation, the subsequent reaction steps are universal in all taxonomic kingdoms. With the exception of a hitherto elusive phosphatase, all enzymes of the pathway have been characterized in some detail at the structural and mechanistic level. Some of the pathway enzymes (GTP cycloyhdrolase II, 3,4-dihydroxy-2-butanone 4-phosphate synthase, riboflavin synthase) have exceptionally complex reaction mechanisms. The commercial production of the vitamin is now entirely based on highly productive fermentation processes. Due to their absence in animals, the pathway enzymes are potential targets for the development of novel anti-infective drugs.
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Affiliation(s)
- Ilka Haase
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
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10
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Haase I, Sarge S, Illarionov B, Laudert D, Hohmann HP, Bacher A, Fischer M. Enzymes from the Haloacid Dehalogenase (HAD) Superfamily Catalyse the Elusive Dephosphorylation Step of Riboflavin Biosynthesis. Chembiochem 2013; 14:2272-5. [DOI: 10.1002/cbic.201300544] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Indexed: 11/09/2022]
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Sousa FL, Thiergart T, Landan G, Nelson-Sathi S, Pereira IAC, Allen JF, Lane N, Martin WF. Early bioenergetic evolution. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130088. [PMID: 23754820 PMCID: PMC3685469 DOI: 10.1098/rstb.2013.0088] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood-Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent-ocean interface via the ATP synthase, (iii) harnessing of Na(+) gradients generated by H(+)/Na(+) antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type 'reduced iron → reduced carbon' at the beginning of bioenergetic evolution.
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Affiliation(s)
- Filipa L. Sousa
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Thorsten Thiergart
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Giddy Landan
- Institute of Genomic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Inês A. C. Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - John F. Allen
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, UK
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - Nick Lane
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany
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12
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Gräwert T, Fischer M, Bacher A. Structures and reaction mechanisms of GTP cyclohydrolases. IUBMB Life 2013; 65:310-22. [PMID: 23457054 DOI: 10.1002/iub.1153] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 01/25/2013] [Indexed: 11/09/2022]
Abstract
GTP cyclohydrolases generate the first committed intermediates for the biosynthesis of certain vitamins/cofactors (folic acid, riboflavin, deazaflavin, and tetrahydrobiopterin), deazapurine antibiotics, some t-RNA bases (queuosine, archaeosine), and the phytotoxin, toxoflavin. They depend on divalent cations for hydrolytic opening of the imidazole ring of the substrate, guanosine triphosphate (GTP). Surprisingly, the ring opening reaction is not the rate-limiting step for GTP cyclohydrolases I and II whose mechanism have been studied in some detail. GTP cyclohydrolase I, Ib, and II are potential targets for novel anti-infectives. Genetic factors modulating the activity of human GTP cyclohydrolase are highly pleiotropic, since the signal transponders whose biosyntheses require their participation (nitric oxide, catecholamines) impact a very wide range of physiological phenomena. Recent studies suggest that human GTP cyclohydrolase may become an oncology target.
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Affiliation(s)
- Tobias Gräwert
- Hamburg School of Food Science, Institut für Lebensmittelchemie, Grindelallee 117, 20146 Hamburg, Germany
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13
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Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnol J 2013; 8:1070-9. [PMID: 23420771 DOI: 10.1002/biot.201200266] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/15/2013] [Accepted: 02/13/2013] [Indexed: 11/11/2022]
Abstract
Methanosarcina barkeri is an Archaeon that produces methane anaerobically as the primary byproduct of its metabolism. M. barkeri can utilize several substrates for ATP and biomass production including methanol, acetate, methyl amines, and a combination of hydrogen and carbon dioxide. In 2006, a metabolic reconstruction of M. barkeri, iAF692, was generated based on a draft genome annotation. The iAF692 reconstruction enabled the first genome-Scale simulations for Archaea. Since the publication of the first metabolic reconstruction of M. barkeri, additional genomic, biochemical, and phenotypic data have clarified several metabolic pathways. We have used this newly available data to improve the M. barkeri metabolic reconstruction. Modeling simulations using the updated model, iMG746, have led to increased accuracy in predicting gene knockout phenotypes and simulations of batch growth behavior. We used the model to examine knockout lethality data and make predictions about metabolic regulation under different growth conditions. Thus, the updated metabolic reconstruction of M. barkeri metabolism is a useful tool for predicting cellular behavior, studying the methanogenic lifestyle, guiding experimental studies, and making predictions relevant to metabolic engineering applications.
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Affiliation(s)
- Matthew C Gonnerman
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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14
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Miller D, Xu H, White RH. A New Subfamily of Agmatinases Present in Methanogenic Archaea Is Fe(II) Dependent. Biochemistry 2012; 51:3067-78. [DOI: 10.1021/bi300039f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Danielle Miller
- Department
of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
24061, United States
| | - Huimin Xu
- Department
of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
24061, United States
| | - Robert H. White
- Department
of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
24061, United States
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Phillips G, Grochowski LL, Bonnett S, Xu H, Bailly M, Haas-Blaby C, El Yacoubi B, Iwata-Reuyl D, White RH, de Crécy-Lagard V. Functional promiscuity of the COG0720 family. ACS Chem Biol 2012; 7:197-209. [PMID: 21999246 PMCID: PMC3262898 DOI: 10.1021/cb200329f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthesis of GTP derived metabolites such as tetrahydrofolate (THF), biopterin (BH(4)), and the modified tRNA nucleosides queuosine (Q) and archaeosine (G(+)) relies on several enzymes of the Tunnel-fold superfamily. A subset of these proteins includes the 6-pyruvoyltetrahydropterin (PTPS-II), PTPS-III, and PTPS-I homologues, all members of the COG0720 family that have been previously shown to transform 7,8-dihydroneopterin triphosphate (H(2)NTP) into different products. PTPS-II catalyzes the formation of 6-pyruvoyltetrahydropterin in the BH(4) pathway, PTPS-III catalyzes the formation of 6-hydroxylmethyl-7,8-dihydropterin in the THF pathway, and PTPS-I catalyzes the formation of 6-carboxy-5,6,7,8-tetrahydropterin in the Q pathway. Genes of these three enzyme families are often misannotated as they are difficult to differentiate by sequence similarity alone. Using a combination of physical clustering, signature motif, phylogenetic codistribution analyses, in vivo complementation studies, and in vitro enzymatic assays, a complete reannotation of the COG0720 family was performed in prokaryotes. Notably, this work identified and experimentally validated dual function PTPS-I/III enzymes involved in both THF and Q biosynthesis. Both in vivo and in vitro analyses showed that the PTPS-I family could tolerate a translation of the active site cysteine and was inherently promiscuous, catalyzing different reactions on the same substrate or the same reaction on different substrates. Finally, the analysis and experimental validation of several archaeal COG0720 members confirmed the role of PTPS-I in archaeosine biosynthesis and resulted in the identification of PTPS-III enzymes with variant signature sequences in Sulfolobus species. This study reveals an expanded versatility of the COG0720 family members and illustrates that for certain protein families extensive comparative genomic analysis beyond homology is required to correctly predict function.
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Affiliation(s)
- Gabriela Phillips
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Laura L. Grochowski
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Shilah Bonnett
- Department of Chemistry, Portland State University, Portland, OR 97207
| | - Huimin Xu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Marc Bailly
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Crysten Haas-Blaby
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Basma El Yacoubi
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, OR 97207
| | - Robert H. White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
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Abbas CA, Sibirny AA. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 2011; 75:321-60. [PMID: 21646432 PMCID: PMC3122625 DOI: 10.1128/mmbr.00030-10] [Citation(s) in RCA: 239] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
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Affiliation(s)
| | - Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine
- University of Rzeszow, Rzeszow 35-601, Poland
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