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Cronan JE. Lipoic acid attachment to proteins: stimulating new developments. Microbiol Mol Biol Rev 2024; 88:e0000524. [PMID: 38624243 DOI: 10.1128/mmbr.00005-24] [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] [Indexed: 04/17/2024] Open
Abstract
SUMMARYLipoic acid-modified proteins are essential for central metabolism and pathogenesis. In recent years, the Escherichia coli and Bacillus subtilis lipoyl assembly pathways have been modified and extended to archaea and diverse eukaryotes including humans. These extensions include a new pathway to insert the key sulfur atoms of lipoate, several new pathways of lipoate salvage, and a novel use of lipoic acid in sulfur-oxidizing bacteria. Other advances are the modification of E. coli LplA for studies of protein localization and protein-protein interactions in cell biology and in enzymatic removal of lipoate from lipoyl proteins. Finally, scenarios have been put forth for the evolution of lipoate assembly in archaea.
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Affiliation(s)
- John E Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
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2
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The effects of lipoic acid on respiratory diseases. Int Immunopharmacol 2023; 116. [PMCID: PMC9933494 DOI: 10.1016/j.intimp.2023.109713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Respiratory diseases, including lung cancer, pulmonary fibrosis, asthma, and the recently emerging fatal coronavirus disease-19 (COVID-19), are the leading causes of illness and death worldwide. The increasing incidence and mortality rates have attracted much attention to the prevention and treatment of these conditions. Lipoic acid (LA), a naturally occurring organosulfur compound, is not only essential for mitochondrial aerobic metabolism but also shows therapeutic potential via certain pharmacological effects (e.g., antioxidative and anti-inflammatory effects). In recent years, accumulating evidence (animal experiments and in vitro studies) has suggested a role of LA in ameliorating many respiratory diseases (e.g., lung cancer, fibrosis, asthma, acute lung injury and smoking-induced lung injury). Therefore, this review will provide an overview of the present investigational evidence on the therapeutic effect of LA against respiratory diseases in vitro and in vivo. We also summarize the corresponding mechanisms of action to inspire further basic studies and clinical trials to confirm the health benefits of LA in the context of respiratory diseases.
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Key Words
- lipoic acid
- respiratory diseases
- antioxidation
- anti-inflammatory effects
- mechanism of action
- akt, protein kinase b;
- aif, apoptosis-inducing factor;
- ampk, adenosine monophosphate-activated protein kinase;
- α-sma, alpha-smooth muscle actin;
- bcl-2, b-cell lymphoma 2;
- cox-2, cyclooxygenase-2;
- dna, deoxyribonucleic acid;
- er, endoplasmic reticulum;
- erk, extracellular-regulated kinase;
- egfr, epidermal growth factor receptor;
- gr, glutathione reductase;
- gpx, glutathione peroxidase;
- grb2, growth factor receptor-bound protein 2;
- gsh, reduced glutathione;
- gssg, oxidized glutathione;
- hif, hypoxia-inducible factor;
- ho-1, heme oxygenase 1;
- keap-1, kelch-like ech-associated protein 1;
- ig-e, immunoglobulin e;
- il, interleukin
- oct-4, octamer-binding transcription factor 4;
- parp-1, poly (adp-ribose) polymerase-1;
- pdk1, phosphoinositide-dependent kinase-1;
- pdh, pyruvate dehydrogenase;
- pi3k, phosphoinositide 3-kinase;
- pge2, prostaglandin e2;
- pgc1α, peroxisome proliferator-activated receptor‑γ co-activator 1α;
- p70s6k, p70 ribosomal protein s6 kinase;
- fak, focal adhesion kinase;
- sod, superoxide dismutase;
- mapk, mitogen-activated protein kinase;
- mtor, mammalian target of rapamycin;
- nf-κb, nuclear factor-kappa b;
- no, nitric oxide;
- nox-4, nicotinamide adenine dinucleotide phosphate (nadph) oxidase-4;
- nqo1, nadph quinone oxidoreductase 1;
- tnf-α, tumor necrosis factor-α;
- tgf-β1, transforming growth factor beta-1;
- vegf, vascular endothelial growth factor;
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3
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Lipoate protein ligase B primarily recognizes the C 8-phosphopantetheine arm of its donor substrate and weakly binds the acyl carrier protein. J Biol Chem 2022; 298:102203. [PMID: 35764173 PMCID: PMC9307952 DOI: 10.1016/j.jbc.2022.102203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 11/22/2022] Open
Abstract
Lipoic acid is a sulfur containing cofactor indispensable for the function of several metabolic enzymes. In microorganisms, lipoic acid can be salvaged from the surroundings by Lipoate protein ligase A (LplA), an ATP-dependent enzyme. Alternatively, it can be synthesized by the sequential actions of Lipoate protein ligase B (LipB) and Lipoyl synthase (LipA). LipB takes up the octanoyl chain from C8-acyl carrier protein (C8-ACP), a byproduct of the type II fatty acid synthesis pathway, and transfers it to a conserved lysine of the lipoyl domain of a dehydrogenase. However, the molecular basis of its substrate recognition is still not fully understood. Using E. coli LipB as a model enzyme, we show here that the octanoyl-transferase mainly recognizes the 4'-phosphopantetheine-tethered acyl-chain of its donor substrate and weakly binds the apo-acyl carrier protein. We demonstrate LipB can accept octanoate from its own ACP and noncognate ACPs, as well as C8-CoA. Furthermore, our 1H STD and 31P NMR studies demonstrate the binding of adenosine, as well as the phosphopantetheine arm of CoA to LipB, akin to binding to LplA. Finally, we show a conserved 71RGG73 loop, analogous to the lipoate binding loop of LplA, is required for full LipB activity. Collectively, our studies highlight commonalities between LipB and LplA in their mechanism of substrate recognition. This knowledge could be of significance in the treatment of mitochondrial fatty acid synthesis related disorders.
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Wu B, Qiu J, Zhao TV, Wang Y, Maeda T, Goronzy IN, Akiyama M, Ohtsuki S, Jin K, Tian L, Goronzy JJ, Weyand CM. Succinyl-CoA Ligase Deficiency in Pro-inflammatory and Tissue-Invasive T Cells. Cell Metab 2020; 32:967-980.e5. [PMID: 33264602 PMCID: PMC7755381 DOI: 10.1016/j.cmet.2020.10.025] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 08/09/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022]
Abstract
Autoimmune T cells in rheumatoid arthritis (RA) have a defect in mitochondrial oxygen consumption and ATP production. Here, we identified suppression of the GDP-forming β subunit of succinate-CoA ligase (SUCLG2) as an underlying abnormality. SUCLG2-deficient T cells reverted the tricarboxylic acid (TCA) cycle from the oxidative to the reductive direction, accumulated α-ketoglutarate, citrate, and acetyl-CoA (AcCoA), and differentiated into pro-inflammatory effector cells. In AcCoAhi RA T cells, tubulin acetylation stabilized the microtubule cytoskeleton and positioned mitochondria in a perinuclear location, resulting in cellular polarization, uropod formation, T cell migration, and tissue invasion. In the tissue, SUCLG2-deficient T cells functioned as cytokine-producing effector cells and were hyperinflammatory, a defect correctable by replenishing the enzyme. Preventing T cell tubulin acetylation by tubulin acetyltransferase knockdown was sufficient to inhibit synovitis. These data link mitochondrial failure and AcCoA oversupply to autoimmune tissue inflammation.
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Affiliation(s)
- Bowen Wu
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jingtao Qiu
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tuantuan V Zhao
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yanan Wang
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Toshihisa Maeda
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Mitsuhiro Akiyama
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shozo Ohtsuki
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ke Jin
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Jörg J Goronzy
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cornelia M Weyand
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Ajith TA. Alpha-lipoic acid: A possible pharmacological agent for treating dry eye disease and retinopathy in diabetes. Clin Exp Pharmacol Physiol 2020; 47:1883-1890. [PMID: 32621549 DOI: 10.1111/1440-1681.13373] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022]
Abstract
Alpha-lipoic acid (ALA) is a naturally occurring dithiol micronutrient which acts as a cofactor for mitochondrial enzyme activity. Due to its potential antioxidant activity, it is considered as "universal antioxidant". Previous studies reported the pharmacological benefits of ALA such as glycaemic control, improved insulin sensitivity and alleviation of diabetic complications such as neuropathy and cardiovascular diseases. Dry eye disease and retinopathy are prevalent in diabetic patients. Experimental studies demonstrated the beneficial effects of ALA in dry eye and diabetic retinopathy. ALA can prevent the dry eye by down regulating the expression of matrix metalloproteinase-9 in the corneal epithelial cells and activating the antioxidant status of the ocular surface. Furthermore, its direct antioxidant effect can also prevent oxidative stress-induced corneal surface erosion and lachrymal gland damage. ALA prevents diabetic retinopathy through inhibition of O-linked β-N-acetylglucosamine transferase and nuclear factor-kappa B activity and alleviation of oxidative stress. It can activate the nuclear factor erythroid-2-related factor 2 and AMP-activated protein kinase in retinal ganglion cells. Clinical trials conducted in pre-retinopathic diabetic patients showed ALA with genistein and vitamins could protect the retinal cells and decline the inflammatory effect in diabetic patients. However, studies are scant to explore its beneficial effects in dry eye disease and diabetic retinopathy. Therefore, this review article discusses an update on the role of ALA in dry eye disease and diabetic retinopathy, two ocular diseases prevalent in diabetic patients.
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Bunik VI. Redox-Driven Signaling: 2-Oxo Acid Dehydrogenase Complexes as Sensors and Transmitters of Metabolic Imbalance. Antioxid Redox Signal 2019; 30:1911-1947. [PMID: 30187773 DOI: 10.1089/ars.2017.7311] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SIGNIFICANCE This article develops a holistic view on production of reactive oxygen species (ROS) by 2-oxo acid dehydrogenase complexes. Recent Advances: Catalytic and structural properties of the complexes and their components evolved to minimize damaging effects of side reactions, including ROS generation, simultaneously exploiting the reactions for homeostatic signaling. CRITICAL ISSUES Side reactions of the complexes, characterized in vitro, are analyzed in view of protein interactions and conditions in vivo. Quantitative data support prevalence of the forward 2-oxo acid oxidation over the backward NADH oxidation in feeding physiologically significant ROS production by the complexes. Special focus on interactions between the active sites within 2-oxo acid dehydrogenase complexes highlights the central relevance of the complex-bound thiyl radicals in regulation of and signaling by complex-generated ROS. The thiyl radicals arise when dihydrolipoyl residues of the complexes regenerate FADH2 from the flavin semiquinone coproduced with superoxide anion radical in 1e- oxidation of FADH2 by molecular oxygen. FUTURE DIRECTIONS Interaction of 2-oxo acid dehydrogenase complexes with thioredoxins (TRXs), peroxiredoxins, and glutaredoxins mediates scavenging of the thiyl radicals and ROS generated by the complexes, underlying signaling of disproportional availability of 2-oxo acids, CoA, and NAD+ in key metabolic branch points through thiol/disulfide exchange and medically important hypoxia-inducible factor, mammalian target of rapamycin (mTOR), poly (ADP-ribose) polymerase, and sirtuins. High reactivity of the coproduced ROS and thiyl radicals to iron/sulfur clusters and nitric oxide, peroxynitrite reductase activity of peroxiredoxins and transnitrosylating function of thioredoxin, implicate the side reactions of 2-oxo acid dehydrogenase complexes in nitric oxide-dependent signaling and damage.
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Affiliation(s)
- Victoria I Bunik
- 1 Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.,2 Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
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Protein moonlighting elucidates the essential human pathway catalyzing lipoic acid assembly on its cognate enzymes. Proc Natl Acad Sci U S A 2018; 115:E7063-E7072. [PMID: 29987032 DOI: 10.1073/pnas.1805862115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The lack of attachment of lipoic acid to its cognate enzyme proteins results in devastating human metabolic disorders. These mitochondrial disorders are evident soon after birth and generally result in early death. The mutations causing specific defects in lipoyl assembly map in three genes, LIAS, LIPT1, and LIPT2 Although physiological roles have been proposed for the encoded proteins, only the LIPT1 protein had been studied at the enzyme level. LIPT1 was reported to catalyze only the second partial reaction of the classical lipoate ligase mechanism. We report that the physiologically relevant LIPT1 enzyme activity is transfer of lipoyl moieties from the H protein of the glycine cleavage system to the E2 subunits of the 2-oxoacid dehydrogenases required for respiration (e.g., pyruvate dehydrogenase) and amino acid degradation. We also report that LIPT2 encodes an octanoyl transferase that initiates lipoyl group assembly. The human pathway is now biochemically defined.
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An Eight-Residue Deletion in Escherichia coli FabG Causes Temperature-Sensitive Growth and Lipid Synthesis Plus Resistance to the Calmodulin Inhibitor Trifluoperazine. J Bacteriol 2017; 199:JB.00074-17. [PMID: 28264990 DOI: 10.1128/jb.00074-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/24/2017] [Indexed: 11/20/2022] Open
Abstract
FabG performs the NADPH-dependent reduction of β-keto acyl-acyl carrier protein substrates in the elongation cycle of fatty acid synthesis. We report the characterization of a temperature-sensitive mutation (fabGΔ8) in Escherichia colifabG that results from an in-frame 8-amino-acid residue deletion in the α6/α7 subdomain. This region forms part of one of the two dimerization interfaces of this tetrameric enzyme and is reported to undergo significant conformational changes upon cofactor binding, which define the entrance to the active-site cleft. The activity of the mutant enzyme is extremely thermolabile and is deficient in forming homodimers at nonpermissive temperatures with a corresponding decrease in fatty acid synthesis both in vivo and in vitro Surprisingly, the fabGΔ8 strain reverts to temperature resistance at a rate reminiscent of that of a point mutant with intragenic pseudorevertants located either on the 2-fold axes of symmetry or at the mouth of the active-site cleft. The fabGΔ8 mutation also confers resistance to the calmodulin inhibitor trifluoperazine and renders the enzyme extremely sensitive to Ca2+in vitro We also observed a significant alteration in the lipid A fatty acid composition of fabGΔ8 strains but only in an lpxC background, probably due to alterations in the permeability of the outer membrane. These observations provide insights into the structural dynamics of FabG and hint at yet another point of regulation between fatty acid and lipid A biosynthesis.IMPORTANCE Membrane lipid homeostasis and its plasticity in a variety of environments are essential for bacterial survival. Since lipid biosynthesis in bacteria and plants is fundamentally distinct from that in animals, it is an ideal target for the development of antibacterial therapeutics. FabG, the subject of this study, catalyzes the first cofactor-dependent reduction in this pathway and is active only as a tetramer. This study examines the interactions responsible for tetramerization through the biochemical characterization of a novel temperature-sensitive mutation caused by a short deletion in an important helix-turn-helix motif. The mutant strain has altered phospholipid and lipid A compositions and is resistant to trifluoperazine, an inhibitor of mammalian calmodulin. Understanding its structural dynamics and its influence on lipid A synthesis also allows us to explore lipid homeostasis as a mechanism for antibiotic resistance.
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Engineering Escherichia coli to produce branched-chain fatty acids in high percentages. Metab Eng 2016; 38:148-158. [DOI: 10.1016/j.ymben.2016.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/04/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022]
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α-Lipoic acid promotes α-tubulin hyperacetylation and blocks the turnover of mitochondria through mitophagy. Biochem J 2016; 473:1821-30. [PMID: 27099338 DOI: 10.1042/bcj20160281] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 04/20/2016] [Indexed: 11/17/2022]
Abstract
Lysine acetylation is tightly coupled to the nutritional status of the cell, as the availability of its cofactor, acetyl-CoA, fluctuates with changing metabolic conditions. Recent studies have demonstrated that acetyl-CoA levels act as an indicator of cellular nourishment, and increased abundance of this metabolite can block the induction of cellular recycling programmes. In the present study we investigated the cross-talk between mitochondrial metabolic pathways, acetylation and autophagy, using chemical inducers of mitochondrial acetyl-CoA production. Treatment of cells with α-lipoic acid (αLA), a cofactor of the pyruvate dehydrogenase complex, led to the unexpected hyperacetylation of α-tubulin in the cytosol. This acetylation was blocked by pharmacological inhibition of mitochondrial citrate export (a source for mitochondria-derived acetyl-CoA in the cytosol), was dependent on the α-tubulin acetyltransferase (αTAT) and was coupled to a loss in function of the cytosolic histone deacetylase, HDAC6. We further demonstrate that αLA slows the flux of substrates through autophagy-related pathways, and severely limits the ability of cells to remove depolarized mitochondria through PTEN-associated kinase 1 (PINK1)-mediated mitophagy.
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Assembly of Lipoic Acid on Its Cognate Enzymes: an Extraordinary and Essential Biosynthetic Pathway. Microbiol Mol Biol Rev 2016; 80:429-50. [PMID: 27074917 DOI: 10.1128/mmbr.00073-15] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Although the structure of lipoic acid and its role in bacterial metabolism were clear over 50 years ago, it is only in the past decade that the pathways of biosynthesis of this universally conserved cofactor have become understood. Unlike most cofactors, lipoic acid must be covalently bound to its cognate enzyme proteins (the 2-oxoacid dehydrogenases and the glycine cleavage system) in order to function in central metabolism. Indeed, the cofactor is assembled on its cognate proteins rather than being assembled and subsequently attached as in the typical pathway, like that of biotin attachment. The first lipoate biosynthetic pathway determined was that of Escherichia coli, which utilizes two enzymes to form the active lipoylated protein from a fatty acid biosynthetic intermediate. Recently, a more complex pathway requiring four proteins was discovered in Bacillus subtilis, which is probably an evolutionary relic. This pathway requires the H protein of the glycine cleavage system of single-carbon metabolism to form active (lipoyl) 2-oxoacid dehydrogenases. The bacterial pathways inform the lipoate pathways of eukaryotic organisms. Plants use the E. coli pathway, whereas mammals and fungi probably use the B. subtilis pathway. The lipoate metabolism enzymes (except those of sulfur insertion) are members of PFAM family PF03099 (the cofactor transferase family). Although these enzymes share some sequence similarity, they catalyze three markedly distinct enzyme reactions, making the usual assignment of function based on alignments prone to frequent mistaken annotations. This state of affairs has possibly clouded the interpretation of one of the disorders of human lipoate metabolism.
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.
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The structure of lipoyl synthase, a remarkable enzyme that performs the last step of an extraordinary biosynthetic pathway. Biochem J 2015; 464:e1-3. [PMID: 25341020 DOI: 10.1042/bj20141061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Lipoic acid is assembled on its cognate proteins (e.g. the E2 subunit of pyruvate dehydrogenase). An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthetase to a specific lysine residue of the cognate protein followed by sulfur insertion at C6 and C8 of the octanoyl chain. The challenging chemistry of this last step is performed by the radical S-adenosylmethionine (SAM) enzyme lipoyl synthase (LipA). In this issue of the Biochemical Journal, Harmer et al. report the first crystal structure of a lipoyl synthase and demonstrate that it contains two [4Fe-4S] clusters, the canonical radical SAM cluster plus a second auxiliary cluster having an unprecedented serine ligand. The structure provides strong support for the model in which the auxiliary cluster donates the lipoate sulfur atoms.
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Frohnecke N, Klein S, Seeber F. Protein-protein interaction studies provide evidence for electron transfer from ferredoxin to lipoic acid synthase in Toxoplasma gondii. FEBS Lett 2014; 589:31-6. [PMID: 25433292 DOI: 10.1016/j.febslet.2014.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 01/08/2023]
Abstract
The only known redox system in the apicoplast, a plastid-like organelle of apicomplexan parasites, is ferredoxin and ferredoxin-associated reductase. Ferredoxin donates electrons to different enzymes, presumably including lipoate synthase (LipA), which is essential for fatty acid biosynthesis. We recombinantly expressed and characterized LipA from the protozoan parasite Toxoplasma gondii, generated LipA-specific antibodies and confirmed the apicoplast localization of LipA. Electron transfer from ferredoxin to LipA would require direct protein-protein interaction. Such a robust interaction between the two proteins was demonstrated in both yeast and bacterial two-hybrid systems. Taken together, our results provide strong evidence for a role of ferredoxin as an electron donor to LipA.
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Affiliation(s)
- Nora Frohnecke
- FG16 Parasitologie, Robert Koch-Institut, 13353 Berlin, Germany
| | - Sandra Klein
- FG16 Parasitologie, Robert Koch-Institut, 13353 Berlin, Germany
| | - Frank Seeber
- FG16 Parasitologie, Robert Koch-Institut, 13353 Berlin, Germany.
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Hermes FA, Cronan JE. An NAD synthetic reaction bypasses the lipoate requirement for aerobic growth of Escherichia coli strains blocked in succinate catabolism. Mol Microbiol 2014; 94:10.1111/mmi.12822. [PMID: 25303731 PMCID: PMC4393350 DOI: 10.1111/mmi.12822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2014] [Indexed: 11/30/2022]
Abstract
The lipoate coenzyme is essential for function of the pyruvate (PDH) and 2-oxoglutarate (OGDH) dehydrogenases and thus for aerobic growth of Escherichia coli. LipB catalyzes the first step in lipoate synthesis, transfer of an octanoyl moiety from the fatty acid synthetic intermediate, octanoyl-ACP, to PDH and OGDH. E. coli also encodes LplA, a ligase that in presence of exogenous octanoate (or lipoate) can bypass loss of LipB. LplA imparts ΔlipB strains with a 'leaky' growth phenotype on aerobic glucose minimal medium supplemented with succinate (which bypasses the OGDH-catalyzed reaction), because it scavenges an endogenous octanoate pool to activate PDH. Here we characterize a ΔlipB suppressor strain that did not require succinate supplementation, but did require succinyl-CoA ligase, confirming the presence of alternative source(s) of cytosolic succinate. We report that suppression requires inactivation of succinate dehydrogenase (SDH), which greatly reduces the cellular requirement for succinate. In the suppressor strain succinate is produced by three enzymes, any one of which will suffice in the absence of SDH. These three enzymes are: trace levels of OGDH, the isocitrate lyase of the glyoxylate shunt and an unanticipated source, aspartate oxidase, the enzyme catalyzing the first step of nicotinamide biosynthesis.
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Affiliation(s)
- Fatemah A. Hermes
- Department of Microbiology, University of Illinois at Urbana-Champaign
| | - John E. Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign
- Department of Biochemistry, University of Illinois at Urbana-Champaign
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Gomes MB, Negrato CA. Alpha-lipoic acid as a pleiotropic compound with potential therapeutic use in diabetes and other chronic diseases. Diabetol Metab Syndr 2014; 6:80. [PMID: 25104975 PMCID: PMC4124142 DOI: 10.1186/1758-5996-6-80] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/11/2014] [Indexed: 02/07/2023] Open
Abstract
Alpha-lipoic acid is a naturally occurring substance, essential for the function of different enzymes that take part in mitochondria's oxidative metabolism. It is believed that alpha-lipoic acid or its reduced form, dihydrolipoic acid have many biochemical functions acting as biological antioxidants, as metal chelators, reducers of the oxidized forms of other antioxidant agents such as vitamin C and E, and modulator of the signaling transduction of several pathways. These above-mentioned actions have been shown in experimental studies emphasizing the use of alpha-lipoic acid as a potential therapeutic agent for many chronic diseases with great epidemiological as well economic and social impact such as brain diseases and cognitive dysfunctions like Alzheimer disease, obesity, nonalcoholic fatty liver disease, burning mouth syndrome, cardiovascular disease, hypertension, some types of cancer, glaucoma and osteoporosis. Many conflicting data have been found concerning the clinical use of alpha-lipoic acid in the treatment of diabetes and of diabetes-related chronic complications such as retinopathy, nephropathy, neuropathy, wound healing and diabetic cardiovascular autonomic neuropathy. The most frequent clinical condition in which alpha-lipoic acid has been studied was in the management of diabetic peripheral neuropathy in patients with type 1 as well type 2 diabetes. Considering that oxidative stress, a imbalance between pro and antioxidants with excessive production of reactive oxygen species, is a factor in the development of many diseases and that alpha-lipoic acid, a natural thiol antioxidant, has been shown to have beneficial effects on oxidative stress parameters in various tissues we wrote this article in order to make an up-to-date review of current thinking regarding alpha-lipoic acid and its use as an antioxidant drug therapy for a myriad of diseases that could have potential benefits from its use.
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Affiliation(s)
- Marilia Brito Gomes
- />Department of Internal Medicine, Diabetes Unit, State University Hospital of Rio de Janeiro, Avenida 28 de Setembro, 77, 3° andar CEP 20.551-030, Rio de Janeiro, Brazil
| | - Carlos Antonio Negrato
- />Department of Internal Medicine, Bauru’s Diabetics Association, 17012-433 Bauru, São Paulo, Brazil
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Saikia RR, Deka S. Removal of hydrocarbon from refinery tank bottom sludge employing microbial culture. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:9026-9033. [PMID: 23764986 DOI: 10.1007/s11356-013-1888-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 05/30/2013] [Indexed: 06/02/2023]
Abstract
Accumulation of oily sludge is becoming a serious environmental threat, and there has not been much work reported for the removal of hydrocarbon from refinery tank bottom sludge. Effort has been made in this study to investigate the removal of hydrocarbon from refinery sludge by isolated biosurfactant-producing Pseudomonas aeruginosa RS29 strain and explore the biosurfactant for its composition and stability. Laboratory investigation was carried out with this strain to observe its efficacy of removing hydrocarbon from refinery sludge employing whole bacterial culture and culture supernatant to various concentrations of sand-sludge mixture. Removal of hydrocarbon was recorded after 20 days. Analysis of the produced biosurfactant was carried out to get the idea about its stability and composition. The strain could remove up to 85 ± 3 and 55 ± 4.5 % of hydrocarbon from refinery sludge when whole bacterial culture and culture supernatant were used, respectively. Maximum surface tension reduction (26.3 mN m(-1)) was achieved with the strain in just 24 h of time. Emulsification index (E24) was recorded as 100 and 80 % with crude oil and n-hexadecane, respectively. The biosurfactant was confirmed as rhamnolipid containing C8 and C10 fatty acid components and having more mono-rhamnolipid congeners than the di-rhamnolipid ones. The biosurfactant was stable up to 121 °C, pH 2-10, and up to a salinity value of 2-10 % w/v. To our knowledge, this is the first report showing the potentiality of a native strain from the northeast region of India for the efficient removal of hydrocarbon from refinery sludge.
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Affiliation(s)
- Rashmi Rekha Saikia
- Environmental Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science & Technology (IASST), Paschim Boragaon, Guwahati, 781 035, Assam, India,
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Post-translational modification in the archaea: structural characterization of multi-enzyme complex lipoylation. Biochem J 2013; 449:415-25. [PMID: 23116157 DOI: 10.1042/bj20121150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multi-enzyme complexes, is essential for metabolism in aerobic bacteria and eukarya. In Escherichia coli, lipoylation is catalysed by LplA (lipoate protein ligase) or by LipA (lipoic acid synthetase) and LipB [lipoyl(octanoyl) transferase] combined. Whereas bacterial and eukaryotic LplAs comprise a single two-domain protein, archaeal LplA function typically involves two proteins, LplA-N and LplA-C. In the thermophilic archaeon Thermoplasma acidophilum, LplA-N and LplA-C are encoded by overlapping genes in inverted orientation (lpla-c is upstream of lpla-n). The T. acidophilum LplA-N structure is known, but the LplA-C structure is unknown and LplA-C's role in lipoylation is unclear. In the present study, we have determined the structures of the substrate-free LplA-N-LplA-C complex and E2lipD (dihydrolipoyl acyltransferase lipoyl domain) that is lipoylated by LplA-N-LplA-C, and carried out biochemical analyses of this archaeal lipoylation system. Our data reveal the following: (i) LplA-C is disordered but folds upon association with LplA-N; (ii) LplA-C induces a conformational change in LplA-N involving substantial shortening of a loop that could repress catalytic activity of isolated LplA-N; (iii) the adenylate-binding region of LplA-N-LplA-C includes two helices rather than the purely loop structure of varying order observed in other LplA structures; (iv) LplAN-LplA-C and E2lipD do not interact in the absence of substrate; (v) LplA-N-LplA-C undergoes a conformational change (the details of which are currently undetermined) during lipoylation; and (vi) LplA-N-LplA-C can utilize octanoic acid as well as lipoic acid as substrate. The elucidated functional inter-dependence of LplA-N and LplA-C is consistent with their evolutionary co-retention in archaeal genomes.
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Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, Methé BA. A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). PLoS One 2012; 7:e29044. [PMID: 22719821 PMCID: PMC3374610 DOI: 10.1371/journal.pone.0029044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 11/16/2011] [Indexed: 01/23/2023] Open
Abstract
As metagenomic studies continue to increase in their number, sequence volume and complexity, the scalability of biological analysis frameworks has become a rate-limiting factor to meaningful data interpretation. To address this issue, we have developed JCVI Metagenomics Reports (METAREP) as an open source tool to query, browse, and compare extremely large volumes of metagenomic annotations. Here we present improvements to this software including the implementation of a dynamic weighting of taxonomic and functional annotation, support for distributed searches, advanced clustering routines, and integration of additional annotation input formats. The utility of these improvements to data interpretation are demonstrated through the application of multiple comparative analysis strategies to shotgun metagenomic data produced by the National Institutes of Health Roadmap for Biomedical Research Human Microbiome Project (HMP) (http://nihroadmap.nih.gov). Specifically, the scalability of the dynamic weighting feature is evaluated and established by its application to the analysis of over 400 million weighted gene annotations derived from 14 billion short reads as predicted by the HMP Unified Metabolic Analysis Network (HUMAnN) pipeline. Further, the capacity of METAREP to facilitate the identification and simultaneous comparison of taxonomic and functional annotations including biological pathway and individual enzyme abundances from hundreds of community samples is demonstrated by providing scenarios that describe how these data can be mined to answer biological questions related to the human microbiome. These strategies provide users with a reference of how to conduct similar large-scale metagenomic analyses using METAREP with their own sequence data, while in this study they reveal insights into the nature and extent of variation in taxonomic and functional profiles across body habitats and individuals. Over one thousand HMP WGS datasets and the latest open source code are available at http://www.jcvi.org/hmp-metarep.
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Affiliation(s)
- Johannes Goll
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - Sahar Abubucker
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Curtis Huttenhower
- Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Shibu Yooseph
- The J. Craig Venter Institute, San Diego, California, United States of America
| | - Barbara A. Methé
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
- * E-mail:
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Saikia RR, Deka S, Deka M, Sarma H. Optimization of environmental factors for improved production of rhamnolipid biosurfactant by Pseudomonas aeruginosa RS29 on glycerol. J Basic Microbiol 2011; 52:446-57. [PMID: 22144225 DOI: 10.1002/jobm.201100228] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 09/09/2011] [Indexed: 11/11/2022]
Abstract
A biosurfactant producing Pseudomonas aeruginosa RS29 (identified on the basis of 16S rDNA analysis) with good foaming and emulsification properties has been isolated from crude oil contaminated sites. Optimization of different environmental factors was carried out with an objective to achieve maximum production of biosurfactant. Production of biosurfactant was estimated in terms of surface tension reduction and emulsification (E24) index. It was recorded that the isolated strain produced highest biosurfactant after 48 h of incubation at 37.5 °C, with a pH range of 7-8 and at salinity <0.8% (w/v). Ammonium nitrate used in the experiment was the best nitrogen source for the growth of biomass of P. aeruginosa RS29. On the other hand sodium and potassium nitrate enhanced the production of biosurfactant (Surface tension, 26.3 and 26.4 mN/m and E24 index, 80 and 79% respectively). The CMC of the biosurfactant was 90 mg/l. Maximum biomass (6.30 g/l) and biosurfactant production (0.80 g/l) were recorded at an optimal C/N ratio of 12.5. Biochemical analysis and FTIR spectra confirmed that the biosurfactant was rhamnolipid in nature. GC-MS analysis revealed the presence of C(8) and C(10) fatty acid components in the purified biosurfactant.
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Affiliation(s)
- Rashmi Rekha Saikia
- Environmental Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science & Technology, Paschim Boragaon, Guwahati, Assam, India.
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Casteel J, Miernyk JA, Thelen JJ. Mapping the lipoylation site of Arabidopsis thaliana plastidial dihydrolipoamide S-acetyltransferase using mass spectrometry and site-directed mutagenesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:1355-1361. [PMID: 21798751 DOI: 10.1016/j.plaphy.2011.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/05/2011] [Indexed: 05/31/2023]
Abstract
Catalytic enhancement achieved by the pyruvate dehydrogenase complex (PDC) results from a combination of substrate channeling plus active-site coupling. The mechanism for active-site coupling involves lipoic acid prosthetic groups covalently attached to Lys in the primary sequence of the dihydrolipoyl S-acetyltransferase (E2) component. Arabidopsis thaliana plastidial E2 (AtplE2-1A-His(6)) was expressed in Escherichia coli. Analysis of recombinant protein by SDS-PAGE revealed a Mr 59,000 band. Supplementation of bacterial culture medium with l-lipoic acid (LA) shifted the band to Mr 57,000. Intact mass determinations using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) revealed the faster migrating E2 species was 189 Da larger than the slower migrating form, exactly the difference that would result from addition of a single lipoamide group. Results from systematic MALDI-TOF analysis of Lys-containing tryptic peptides derived from purified recombinant AtplE2-1A indicate that Lys96 is the site of lipoyl-addition. Analysis of Lys96 site-directed mutant proteins showed that they migrated as single species during SDS-PAGE when expressed in either the absence or presence of supplemental LA. Results from both intact and tryptic peptide mass determinations by MALDI-TOF MS confirmed that the mutant proteins were not lipoylated. The A. thaliana plastidial E2 subunit includes a single lipoyl-prosthetic group covalently attached to Lys96. Despite low primary sequence identity with bacterial E2, the plant E2 protein was recognized and modified by E. coli E2 lipoyl-addition system. Results from meta-genomic analysis suggest a β-turn is more important in defining the site for LA addition than a conserved sequence motif.
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Affiliation(s)
- Jill Casteel
- Department of Biochemistry, Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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Christensen QH, Hagar JA, O'Riordan MXD, Cronan JE. A complex lipoate utilization pathway in Listeria monocytogenes. J Biol Chem 2011; 286:31447-56. [PMID: 21768091 DOI: 10.1074/jbc.m111.273607] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Although a complete pathway of lipoic acid metabolism has been established in Escherichia coli, lipoic acid metabolism in other bacteria is more complex and incompletely understood. Listeria monocytogenes has been shown to utilize two lipoate-protein ligases for lipoic acid scavenging, whereas only one of the ligases can function in utilization of host-derived lipoic acid-modified peptides. We report that lipoic acid scavenging requires not only ligation of lipoic acid but also a lipoyl relay pathway in which an amidotransferase transfers lipoyl groups to the enzyme complexes that require the cofactor for activity. In addition, we provide evidence for a new lipoamidase activity that could allow utilization of lipoyl peptides by lipoate-protein ligase. These data support a model of an expanded, three-enzyme pathway for lipoic acid scavenging that seems widespread in the Firmicutes phylum of bacteria.
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Affiliation(s)
- Quin H Christensen
- Department of Microbiology, University of Illinois, Urbana, Illinois 61801, USA
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