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Niehus R, Picot A, Oliveira NM, Mitri S, Foster KR. The evolution of siderophore production as a competitive trait. Evolution 2017; 71:1443-1455. [DOI: 10.1111/evo.13230] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/03/2017] [Accepted: 03/12/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Rene Niehus
- Department of Zoology; University of Oxford; South Parks Road OX1 3PS Oxford United Kingdom
- Mahidol Oxford Tropical Medicine Research Unit (MORU); 10400 Bangkok Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine; University of Oxford; Oxford United Kingdom
| | - Aurore Picot
- Department of Zoology; University of Oxford; South Parks Road OX1 3PS Oxford United Kingdom
- Sorbonne Universités, UPMC Univ Paris 6, UPEC, Univ Paris Diderot, Univ Paris-Est Créteil, CNRS, INRA, IRD; Institute of Ecology and Environmental Sciences-Paris (iEES Paris); 7 quai Saint-Bernard 75 252 Paris France
| | - Nuno M. Oliveira
- Department of Zoology; University of Oxford; South Parks Road OX1 3PS Oxford United Kingdom
- Department of Applied Mathematics and Theoretical Physics (DAMTP); Centre for Mathematical Sciences; Wilberforce Road Cambridge CB3 0WA United Kingdom
| | - Sara Mitri
- Department of Fundamental Microbiology; University of Lausanne; CH-1015 Lausanne Switzerland
| | - Kevin R. Foster
- Department of Zoology; University of Oxford; South Parks Road OX1 3PS Oxford United Kingdom
- Oxford Centre for Integrative Systems Biology; University of Oxford; South Parks Road Oxford OX1 3QU United Kingdom
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Maindad DV, Kasture VM, Chaudhari H, Dhavale DD, Chopade BA, Sachdev DP. Characterization and Fungal Inhibition Activity of Siderophore from Wheat Rhizosphere Associated Acinetobacter calcoaceticus Strain HIRFA32. Indian J Microbiol 2014; 54:315-22. [PMID: 24891739 PMCID: PMC4039728 DOI: 10.1007/s12088-014-0446-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/15/2014] [Indexed: 10/25/2022] Open
Abstract
Acinetobacter calcoaceticus HIRFA32 from wheat rhizosphere produced catecholate type of siderophore with optimum siderophore (ca. 92 % siderophore units) in succinic acid medium without FeSO4 at 28 °C and 24 h of incubation. HPLC purified siderophore appeared as pale yellow crystals with molecular weight [M(+1)] m/z 347.18 estimated by LCMS. The structure elucidated by (1)H NMR, (13)C NMR, HMQC, HMBC, NOESY and decoupling studies, revealed that siderophore composed of 2,3-dihydroxybenzoic acid with hydroxyhistamine and threonine as amino acid subunits. In vitro study demonstrated siderophore mediated mycelium growth inhibition (ca. 46.87 ± 0.5 %) of Fusarium oxysporum. This study accounts to first report on biosynthesis of acinetobactin-like siderophore by the rhizospheric strain of A. calcoaceticus and its significance in inhibition of F. oxysporum.
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Affiliation(s)
- D. V. Maindad
- />Institute of Bioinformatics and Biotechnology, University of Pune, Pune, 411007 India
| | - V. M. Kasture
- />Department of Chemistry, University of Pune, Pune, 411007 India
| | - H. Chaudhari
- />Institute of Bioinformatics and Biotechnology, University of Pune, Pune, 411007 India
| | - D. D. Dhavale
- />Department of Chemistry, University of Pune, Pune, 411007 India
| | - B. A. Chopade
- />Department of Microbiology, University of Pune, Pune, 411007 India
| | - D. P. Sachdev
- />Institute of Bioinformatics and Biotechnology, University of Pune, Pune, 411007 India
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Heemstra JR, Walsh CT, Sattely ES. Enzymatic tailoring of ornithine in the biosynthesis of the Rhizobium cyclic trihydroxamate siderophore vicibactin. J Am Chem Soc 2009; 131:15317-29. [PMID: 19778043 PMCID: PMC2783850 DOI: 10.1021/ja9056008] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To acquire iron, the N(2)-fixing, symbiotic bacterium Rhizobium sp. produce the cyclic trihydroxamate siderophore vicibactin, containing a 30-membered trilactone scaffold. Herein we report the overproduction and purification of the six proteins VbsACGOLS in the bacterial host Escherichia coli and the reconstitution of the biosynthesis of vicibactin from primary metabolites. The flavoprotein VbsO acts as a pathway-initiating l-ornithine N(5)-hydroxylase, followed by VbsA, which transfers (R)-3-hydroxybutyryl- from the CoA thioester to N(5)-hydroxyornithine to yield N(5)-((R)-3-hydroxybutyryl)-N(5)-hydroxy-l-ornithine. VbsL is a PLP-dependent epimerase acting at C(2) of the 10 atom monomer unit. VbsS, a nonribosomal peptide synthetase free-standing module, then activates N(5)-((R)-3-hydroxybutyryl)-N(5)-hydroxy-d-ornithine as the AMP anhydride on the way to cyclotrimerization to the vicibactin scaffold. The last step, tris-acetylation of the C(2) amino group of desacetyl-d-vicibactin to the mature siderophore vicibactin, is catalyzed distributively by VbsC, using three molecules of acetyl-CoA.
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Affiliation(s)
- John R. Heemstra
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Christopher T. Walsh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Elizabeth S. Sattely
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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Battistoni F, Platero R, Duran R, Cerveñansky C, Battistoni J, Arias A, Fabiano E. Identification of an iron-regulated, hemin-binding outer membrane protein in Sinorhizobium meliloti. Appl Environ Microbiol 2002; 68:5877-81. [PMID: 12450806 PMCID: PMC134414 DOI: 10.1128/aem.68.12.5877-5881.2002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2002] [Accepted: 08/29/2002] [Indexed: 11/20/2022] Open
Abstract
Rhizobia are soil bacteria that are able to establish symbiotic associations with leguminous hosts. In iron-limited environments these bacteria can use iron present in heme or heme compounds (hemoglobin, leghemoglobin). Here we report the presence in Sinorhizobium meliloti of an iron-regulated outer membrane protein that is able to bind hemin but not hemoglobin. Protein assignment was done by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Tryptic peptides correlated with the mass measurements obtained accounted for 54% of the translated sequence of a putative heme receptor gene present in the chromosome of S. meliloti 1021. The results which we obtained suggest that this protein (designated ShmR for Sinorhizobium heme receptor) is involved in high-affinity heme-mediated iron transport.
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Affiliation(s)
- Federico Battistoni
- Laboratorio de Ecología Microbiana. Unidad de Bioquímica Analítica, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE-MEC), Montevideo 11600, Uruguay
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Carter RA, Worsley PS, Sawers G, Challis GL, Dilworth MJ, Carson KC, Lawrence JA, Wexler M, Johnston AWB, Yeoman KH. The vbs genes that direct synthesis of the siderophore vicibactin in Rhizobium leguminosarum: their expression in other genera requires ECF sigma factor RpoI. Mol Microbiol 2002; 44:1153-66. [PMID: 12028377 DOI: 10.1046/j.1365-2958.2002.02951.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A cluster of eight genes, vbsGSO, vbsADL, vbsC and vbsP, are involved in the synthesis of vicibactin, a cyclic, trihydroxamate siderophore made by the symbiotic bacterium Rhizobium leguminosarum. None of these vbs genes was required for symbiotic N2 fixation on peas or Vicia. Transcription of vbsC, vbsGSO and vbsADL (but not vbsP) was enhanced by growth in low levels of Fe. Transcription of vbsGSO and vbsADL, but not vbsP or vbsC, required the closely linked gene rpoI, which encodes an ECF sigma factor of RNA polymerase. Transfer of the cloned vbs genes, plus rpoI, to Rhodobacter, Paracoccus and Sinorhizobium conferred the ability to make vicibactin on these other genera. We present a biochemical genetic model of vicibactin synthesis, which accommodates the phenotypes of different vbs mutants and the homologies of the vbs gene products. In this model, VbsS, which is similar to many non-ribosomal peptide synthetase multienzymes, has a central role. It is proposed that VbsS activates L-N5-hydroxyornithine via covalent attachment as an acyl thioester to a peptidyl carrier protein domain. Subsequent VbsA-catalysed acylation of the hydroxyornithine, followed by VbsL-mediated epimerization and acetylation catalysed by VbsC, yields the vicibactin subunit, which is then trimerized and cyclized by the thioesterase domain of VbsS to give the completed siderophore.
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Affiliation(s)
- R A Carter
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Johnston AW, Yeoman KH, Wexler M. Metals and the rhizobial-legume symbiosis--uptake, utilization and signalling. Adv Microb Physiol 2002; 45:113-56. [PMID: 11450108 DOI: 10.1016/s0065-2911(01)45003-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this review, we consider how the nitrogen-fixing root nodule bacteria, the 'rhizobia', acquire various metals, paying particular attention to the uptake of iron. We also review the literature pertaining to the roles of molybdenum and nickel in the symbiosis with legumes. We highlight some gaps in our knowledge, for example the lack of information on how rhizobia acquire molybdenum. We examine the means whereby different metals affect rhizobial physiology and the role of metals as signals for gene regulation. We describe the ways in which genetics has shown (or not) if, and how, particular metal uptake and/or metal-mediated signalling pathways are required for the symbiotic interaction with legumes.
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Affiliation(s)
- A W Johnston
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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Yeoman KH, Wisniewski-Dye F, Timony C, Stevens JB, deLuca NG, Downie JA, Johnston AWB. Analysis of the Rhizobium leguminosarum siderophore-uptake gene fhuA: differential expression in free-living bacteria and nitrogen-fixing bacteroids and distribution of an fhuA pseudogene in different strains. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 4):829-837. [PMID: 10784041 DOI: 10.1099/00221287-146-4-829] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A mutation was isolated in the Rhizobium leguminosarum gene fhuA, which appears to specify the outer-membrane receptor for the siderophore vicibactin. The mutant was defective in iron uptake and accumulated the siderophore vicibactin in the extracellular medium. Expression of fhuA was regulated by Fe3+, transcription being higher in iron-depleted cells. Transcription of fhuA was independent of a functional copy of rpol, a neighbouring gene that specifies a putative ECF sigma factor of RNA polymerase and which is involved in siderophore production in Rhizobium. Mutations in fhuA did not detectably affect symbiotic N2 fixation on peas. An fhuA::gus fusion was expressed by bacteria in the meristematic zone of pea nodules but not in mature bacteroids. Some other strains of R. leguminosarum also contain a pseudogene version of fhuA. The sequences of some of these and the 'real' fhuA genes were determined.
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Affiliation(s)
- Kay H Yeoman
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK1
| | | | - Christopher Timony
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK1
| | - James B Stevens
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK1
| | - Nicola G deLuca
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK1
| | - J Allan Downie
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK2
| | - Andrew W B Johnston
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK1
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Dhul M, Suneja S, Dadarwal K. Role of siderophores in chickpea (Cicer arietinum L.) — Rhizobium symbiosis. Microbiol Res 1998. [DOI: 10.1016/s0944-5013(98)80020-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Dilworth MJ, Carson KC, Giles RGF, Byrne LT, Glenn AR. Rhizobium leguminosarum bv. viciae produces a novel cyclic trihydroxamate siderophore, vicibactin. Microbiology (Reading) 1998; 144:781-791. [DOI: 10.1099/00221287-144-3-781] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trihydroxamate siderophores were isolated from iron-deficient cultures of three strains of Rhizobium leguminosarum biovar viciae, two from Japan (WSM709, WSM710) and one from the Mediterranean (WU235), and from a Tn5-induced mutant of WSM710 (MNF7101). The first three all produced the same compound (vicibactin), which was uncharged and could be purified by solvent extraction into benzyl alcohol. The gallium and ferric complexes of vicibactin were extractable into benzyl alcohol at pH 5.0, while metal-free vicibactin could be extracted with good yield at pH 8.0. The trihydroxamate from MNF7101 (vicibactin 7101) could not be extracted into benzyl alcohol, but its cationic nature permitted purification by chromatography on Sephadex CM-25 (NH+
4 form). Relative molecular masses and empirical formulae were obtained from fast-atom-bombardment MS. The structures were derived from one- and two-dimensional 1H and 13C NMR spectroscopy, using DQF-COSY, NOESY, HMQC and HMBC techniques on the compounds dissolved in methanol-d
4 and DMSO-d
6. Vicibactin proves to be a cyclic molecule containing three residues each of (R)-2,5-diamino-N
2-acetyl-N
5-hydroxypentanoic acid (N
2-acetyl-N
5-hydroxy-D-ornithine) and (R)-3-hydroxybutanoic acid, arranged alternately, with alternating ester and peptide bonds. Vicibactin 7101 differed only in lacking the acetyl substitution on the N2 of the N
5-hydroxyornithine, resulting in net positive charge; it was still functional as a siderophore and promoted 55Fe uptake by iron-starved cells of WSM710 in the presence of an excess of phosphate. The rate of vicibactin biosynthesis by iron-deficient cells of WSM710 was essentially constant between pH 5.5 and 7.0, but much decreased at pH 5.0. When iron-starved cultures were supplemented with potential precursors for vicibactin, the rates of its synthesis were consistent with both β-hydroxybutyrate and ornithine being precursors. At least three genes seem likely to be involved in synthesis of vicibactin from ornithine and β-hydroxybutyrate: a hydroxylase adding the -OH group to the N5 of ornithine, an acetylase adding the acetyl group to the N2 of ornithine, and a peptide synthetase system.
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Affiliation(s)
- Michael J. Dilworth
- Centre for Rhizobium Studies, School of Biological Sciences & Biotechnology, Division of Science, Murdoch University, Murdoch, Western Australia 6150
| | - Kerry C. Carson
- Centre for Rhizobium Studies, School of Biological Sciences & Biotechnology, Division of Science, Murdoch University, Murdoch, Western Australia 6150
| | - Robin G. F. Giles
- Chemistry Department, School of Mathematical & Physical Sciences, Division of Science, Murdoch University, Murdoch, Western Australia 6150
| | - Lindsay T. Byrne
- Department of Chemistry, The University of Western Australia, Nedlands, Western Australia 6009
| | - Andrew R. Glenn
- Centre for Rhizobium Studies, School of Biological Sciences & Biotechnology, Division of Science, Murdoch University, Murdoch, Western Australia 6150
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Poole RK, Rogers NJ, D'mello RAM, Hughes MN, Orii Y. Escherichia coli flavohaemoglobin (Hmp) reduces cytochrome c and Fe(III)-hydroxamate K by electron transfer from NADH via FAD: sensitivity of oxidoreductase activity to haem-bound dioxygen. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 5):1557-1565. [PMID: 9168606 DOI: 10.1099/00221287-143-5-1557] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Escherichia coli flavohaemoglobin (Hmp) reduced purified mitochondrial cytochrome c aerobically in a reaction that was not substantially inhibited by superoxide dismutase, demonstrating that superoxide anion, the product of O2 reduction by Hmp, did not contribute markedly to cytochrome c reduction. Cytochrome c was reduced by Hmp even in the presence of 0.5 mM CO, when the haem B was locked in the ferrous, low-spin state, demonstrating that electron transfer to cytochrome c from NADH was via FAD, not haem. Hmp also reduced the ferrisiderophore complex Fe(III)-hydroxamate K from Rhizobium leguminosarum bv. viciae anaerobically in a CO-insensitive manner, but at low rates and with low affinity for this substrate. The NADH-cytochrome c oxidoreductase activity of Hmp was slightly sensitive to the binding and reduction of O2 at the haem. The Vmax of cytochrome c reduction fell from 7.1 s-1 in the presence of 0.5 mM CO to 5.0 s-1 in the presence of 100 microM O2, with no significant change in K(m) for cytochrome c (6.8 to 7.3 microM, respectively). O2 at near-micromolar concentrations diminished cytochrome c reduction to a similar extent as did 100 microM O2. Thus, Hmp acts as a reductase of broad specificity, apparently without involvement of electron transfer via the globin-like haem. These data are consistent with the hypothesis that Hmp could act as an intracellular sensor of O2 since, in the absence of O2, electron flux from FAD to other electron acceptors increases. However, the nature of such acceptors in vivo is not known and alternative models for O2 sensing are also considered.
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Affiliation(s)
- Robert K Poole
- Division of Life Sciences, King's College London, Campden Hill Road, London W8 7AH, UK
| | - Nicola J Rogers
- Chemistry Department, King's College London, Strand, London WC2R 2LS, UK
- Division of Life Sciences, King's College London, Campden Hill Road, London W8 7AH, UK
| | - Rita A M D'mello
- Division of Life Sciences, King's College London, Campden Hill Road, London W8 7AH, UK
| | - Martin N Hughes
- Chemistry Department, King's College London, Strand, London WC2R 2LS, UK
| | - Yutaka Orii
- Department of Public Health, Graduate School of Medicine, Kyoto University, Kyoto 606, Japan
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LeVier K, Guerinot ML. The Bradyrhizobium japonicum fegA gene encodes an iron-regulated outer membrane protein with similarity to hydroxamate-type siderophore receptors. J Bacteriol 1996; 178:7265-75. [PMID: 8955412 PMCID: PMC178643 DOI: 10.1128/jb.178.24.7265-7275.1996] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Iron is important in the symbiosis between soybean and its nitrogen-fixing endosymbiont Bradyrhizobium japonicum, yet little is known about rhizobial iron acquisition strategies. Analysis of outer membrane proteins (OMPs) from B. japonicum 61A152 identified three iron-regulated OMPs in the size range of several known receptors for Fe(III)-scavenging siderophores. One of the iron-regulated proteins, FegA, was purified and microsequenced, and a reverse genetics approach was used to clone a fegA-containing DNA fragment. Sequencing of this fragment revealed a single open reading frame of 750 amino acids. A putative N-terminal signal sequence of 14 amino acids which would result in a mature protein of 736 amino acids with a molecular mass of 80,851 Da was predicted. FegA shares significant amino acid similarity with several Fe(III)-siderophore receptors from gram-negative bacteria and has greater than 50% amino acid similarity and 33% amino acid identity with two [corrected] bacterial receptors for hydroxamate-type Fe(III)-siderophores. A dendrogram describing total inferred sequence similarity among 36 TonB-dependent OMPs was constructed; FegA grouped with Fe(III)-hydroxamate receptors. The transcriptional start site of fegA was mapped by primer extension analysis, and a putative Fur-binding site was found in the promoter. Primer extension and RNA slot blot analysis demonstrated that fegA was expressed only in cells grown under iron-limiting conditions. This is the first report of the cloning of a gene encoding a putative Fe(III)-siderophore receptor from nitrogen-fixing rhizobia.
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Affiliation(s)
- K LeVier
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
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