A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex.


Journal

Protein science : a publication of the Protein Society
ISSN: 1469-896X
Titre abrégé: Protein Sci
Pays: United States
ID NLM: 9211750

Informations de publication

Date de publication:
Jun 2024
Historique:
revised: 25 03 2024
received: 28 12 2023
accepted: 21 04 2024
medline: 15 5 2024
pubmed: 15 5 2024
entrez: 15 5 2024
Statut: ppublish

Résumé

A heterodisulfide reductase-like complex (sHdr) and novel lipoate-binding proteins (LbpAs) are central players of a wide-spread pathway of dissimilatory sulfur oxidation. Bioinformatic analysis demonstrate that the cytoplasmic sHdr-LbpA systems are always accompanied by sets of sulfur transferases (DsrE proteins, TusA, and rhodaneses). The exact composition of these sets may vary depending on the organism and sHdr system type. To enable generalizations, we studied model sulfur oxidizers from distant bacterial phyla, that is, Aquificota and Pseudomonadota. DsrE3C of the chemoorganotrophic Alphaproteobacterium Hyphomicrobium denitrificans and DsrE3B from the Gammaproteobacteria Thioalkalivibrio sp. K90mix, an obligate chemolithotroph, and Thiorhodospira sibirica, an obligate photolithotroph, are homotrimers that donate sulfur to TusA. Additionally, the hyphomicrobial rhodanese-like protein Rhd442 exchanges sulfur with both TusA and DsrE3C. The latter is essential for sulfur oxidation in Hm. denitrificans. TusA from Aquifex aeolicus (AqTusA) interacts physiologically with AqDsrE, AqLbpA, and AqsHdr proteins. This is particularly significant as it establishes a direct link between sulfur transferases and the sHdr-LbpA complex that oxidizes sulfane sulfur to sulfite. In vivo, it is unlikely that there is a strict unidirectional transfer between the sulfur-binding enzymes studied. Rather, the sulfur transferases form a network, each with a pool of bound sulfur. Sulfur flux can then be shifted in one direction or the other depending on metabolic requirements. A single pair of sulfur-binding proteins with a preferred transfer direction, such as a DsrE3-type protein towards TusA, may be sufficient to push sulfur into the sink where it is further metabolized or needed.

Identifiants

pubmed: 38747384
doi: 10.1002/pro.5014
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

e5014

Subventions

Organisme : Deutscher Akademischer Austauschdienst/Hubert Curien Procope program
ID : 57388731
Organisme : Deutscher Akademischer Austauschdienst/Hubert Curien Procope program
ID : 40444VM
Organisme : Studienstiftung des Deutschen Volkes
Organisme : Deutsche Forschungsgemeinschaft
ID : 351/13-1

Informations de copyright

© 2024 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.

Références

Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood‐based approximation schemes. Syst Biol. 2011;60:685–699.
Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One. 2009;4:e4345.
Aussignargues C, Giuliani MC, Infossi P, Lojou E, Guiral M, Giudici‐Orticoni MT, et al. Rhodanese functions as sulfur supplier for key enzymes in sulfur energy metabolism. J Biol Chem. 2012;287:19936–19948.
Ausubel FA, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, et al. Current protocols in molecular biology. New York: John Wiley & Sons; 1997.
Balleste‐Delpierre C, Fernandez‐Orth D, Ferrer‐Navarro M, Diaz‐Pena R, Odena‐Caballol A, Oliveira E, et al. First insights into the pleiotropic role of vrf (yedF), a newly characterized gene of Salmonella Typhimurium. Sci Rep. 2017;7:15291.
Bertani G. Lysogeny at mid‐twentieth century: P1, P2, and other experimental systems. J Bacteriol. 2004;186:595–600.
Bordo D, Bork P. The rhodanese/Cdc25 phosphatase superfamily—sequence–structure–function relations. EMBO Rep. 2002;3:741–746.
Boughanemi S, Infossi P, Giudici‐Orticoni MT, Schoepp‐Cothenet B, Guiral M. Sulfite oxidation by the quinone‐reducing molybdenum sulfite dehydrogenase SoeABC from the bacterium Aquifex aeolicus. Biochim Biophys Acta Bioenerg. 2020;1861:148279.
Boughanemi S, Lyonnet J, Infossi P, Bauzan M, Kosta A, Lignon S, et al. Microbial oxidative sulfur metabolism: biochemical evidence of the membrane‐bound heterodisulfide reductase‐like complex of the bacterium Aquifex aeolicus. FEMS Microbiol Lett. 2016;363:fnw156.
Bryantseva IA, Gorlenko VM, Kompantseva EI, Imhoff JF, Süling J, Mityushina L. Thiorhodospira sibirica gen. nov., sp. nov., a new alkaliphilic purple sulfur bacterium from a Siberian soda lake. Int J Syst Bacteriol. 1999;49:697–703.
Cao X, Koch T, Steffens L, Finkensieper J, Zigann R, Cronan JE, et al. Lipoate‐binding proteins and specific lipoate‐protein ligases in microbial sulfur oxidation reveal an atypical role for an old cofactor. eLife. 2018;7:e37439.
Criscuolo A, Gribaldo S. BMGE (block mapping and gathering with entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol Biol. 2010;10:210.
Dahl C. Insertional gene inactivation in a phototrophic sulphur bacterium: APS‐reductase‐deficient mutants of Chromatium vinosum. Microbiology. 1996;142:3363–3372.
Dahl C. Cytoplasmic sulfur trafficking in sulfur‐oxidizing prokaryotes. IUBMB Life. 2015;67:268–274.
Dahl C. Sulfur metabolism in phototrophic bacteria. In: Hallenbeck PC, editor. Modern topics in the phototrophic prokaryotes: metabolism, bioenergetics and omics. Cham: Springer International Publishing; 2017. pp. 27–66.
Dahl C. A biochemical view on the biological sulfur cycle. In: Lens P, editor. (2020) Environmental technologies to treat sulfur pollution: principles and engineering. IWA Publishing, London, pp. 55–96.
Dahl JU, Radon C, Buhning M, Nimtz M, Leichert LI, Denis Y, et al. The sulfur carrier protein TusA has a pleiotropic role in Escherichia coli that also affects molybdenum cofactor biosynthesis. J Biol Chem. 2013;288:5426–5442.
Dahl C, Schulte A, Stockdreher Y, Hong C, Grimm F, Sander J, et al. Structural and molecular genetic insight into a wide‐spread bacterial sulfur oxidation pathway. J Mol Biol. 2008;384:1287–1300.
Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, et al. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 1998;392:353–358.
Ernst C, Kayashta K, Koch T, Venceslau SS, Pereira IAC, Demmer U, et al. Structural and spectroscopic characterization of a HdrA‐like subunit from Hyphomicrobium denitrificans. FEBS J. 2021;288:1664–1678.
Geoghegan KF, Dixon HBF, Rosner PJ, Hoth LR, Lanzetti AJ, Borzilleri KA, et al. Spontaneous α‐N‐6‐phosphogluconoylation of a “His Tag” in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins. Anal Biochem. 1999;267:169–184.
Gojon G. On H2S prodrugs. Antioxid Redox Signal. 2020;33:999–1002.
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum‐likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–321.
Guiral M, Prunetti L, Lignon S, Lebrun R, Moinier D, Giudici‐Orticoni MT. New insights into the respiratory chains of the chemolithoautotrophic and hyperthermophilic bacterium Aquifex aeolicus. J Proteome Res. 2009;8:1717–1730.
Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, et al. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. bioRxiv. 2022;04:04:08e487609. https://doi.org/10.1101/2022.04.08.487609
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35:518–522.
Horton RM. PCR mediated recombination and mutagenesis: SOEing together tailor‐made genes. Mol Biotechnol. 1995;3:93–99.
Hug LA, Castelle CJ, Wrighton KC, Thomas BC, Sharon I, Frischkorn KR, et al. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome. 2013;1:22.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.
Ikeda S, Satake H, Hisano T, Terazawa T. Potentiometric argentimetric method for the successive titration of sulphide and dissolved sulphur in polysulphide solutions. Talanta. 1972;19:1650–1654.
Ikei M, Miyazaki R, Monden K, Naito Y, Takeuchi A, Takahashi YS, et al. YeeD is an essential partner for YeeE‐mediated thiosulfate uptake in bacteria and regulates thiosulfate ion decomposition. PLoS Biol. 2024;22(4):e3002601. https://doi.org/10.1371/journal.pbio.3002601
Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell. 2006;21:97–108.
Ishii Y, Yamada H, Yamashino T, Ohashi K, Katoh E, Shindo H, et al. Deletion of the yhhP gene results in filamentous cell morphology in Escherichia coli. Biosci Biotech Bioch. 2000;64:799–807.
Jaffe AL, Castelle CJ, Matheus Carnevali PB, Gribaldo S, Banfield JF. The rise of diversity in metabolic platforms across the candidate phyla radiation. BMC Biol. 2020;18:69.
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596:583–589.
Justice NB, Norman A, Brown CT, Singh A, Thomas BC, Banfield JF. Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics. 2014;15:1107.
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–589.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–780.
Kessler D. Enzymatic activation of sulfur for incorporation into biomolecules in prokaryotes. FEMS Microbiol Rev. 2006;30:825–840.
Koch T, Dahl C. A novel bacterial sulfur oxidation pathway provides a new link between the cycles of organic and inorganic sulfur compounds. ISME J. 2018;12:2479–2491.
Krishna SS, Tautz L, Xu Q, McMullan D, Miller MD, Abdubek P, et al. Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 Å resolution provides a structural scaffold for nonclassical, eukaryotic‐like phosphatases. Proteins. 2007;69:415–421.
Kümpel C, Grosser M, Tanabe TS, Dahl C. Fe/S proteins in microbial sulfur oxidation. Biochim Biophys Acta. 2024;1871:119732.
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293–W296.
Li J, Koch J, Flegler W, Garcia Ruiz L, Hager N, Ballas A, et al. A metabolic puzzle: consumption of C1 compounds and thiosulfate in Hyphomicrobium denitrificans XT. Biochim Biophys Acta Bioenerget. 2023;1864:148932.
Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, et al. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res. 2021;49:D1020–D1028.
Li J, Törkel K, Tanabe TS, Hsu HY, Dahl C. In the Alphaproteobacterium Hyphomicrobium denitrificans SoxR serves as a sulfane sulfur‐responsive repressor of sulfur oxidation. Antioxidants. 2023;12:1620.
Liu LJ, Stockdreher Y, Koch T, Sun ST, Fan Z, Josten M, et al. Thiosulfate transfer mediated by DsrE/TusA homologs from acidothermophilic sulfur‐oxidizing archaeon Metallosphaera cuprina. J Biol Chem. 2014;289:26949–26959.
Liu LJ, You XY, Guo X, Liu SJ, Jiang CY. Metallosphaera cuprina sp. nov., an acidothermophilic, metal‐mobilizing archaeon. Int J Syst Evol Microbiol. 2011;61:2395–2400.
Mirdita M, Steinegger M, Söding J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics. 2019;35:2856–2858.
Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 2021;49:D412–D419.
Mueller EG. Trafficking in persulfides: delivering sulfur in biosynthetic pathways. Nat Chem Biol. 2006;2:185–194.
Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Foster B, Sun H, et al. Complete genome sequence of Thioalkalivibrio sp. K90mix. Stand Genomic Sci. 2011;5:341–355. https://doi.org/10.4056/sigs.2315092
Neukirchen S, Pereira IAC, Sousa FL. Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction. ISME J. 2023;17:1680–1692.
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ‐TREE: a fast and effective stochastic algorithm for estimating maximum‐likelihood phylogenies. Mol Biol Evol. 2015;32:268–274.
Norris PR, Clark DA, Owen JP, Waterhouse S. Characteristics of Sulfobacillus acidophilus sp. nov. and other moderately thermophilic mineral‐sulphide‐oxidizing bacteria. Microbiology. 1996;142:775–783.
Prioretti L, D'Ermo G, Infossi P, Kpebe A, Lebrun R, Bauzan M, et al. Carbon fixation in the chemolithoautotrophic bacterium Aquifex aeolicus involves two low‐potential ferredoxins as partners of the PFOR and OGOR enzymes. Life. 2023;13:627.
Ran M, Li Q, Xin Y, Ma S, Zhao R, Wang M, et al. Rhodaneses minimize the accumulation of cellular sulfane sulfur to avoid disulfide stress during sulfide oxidation in bacteria. Redox Biol. 2022;53:102345.
Ray WK, Zeng G, Potters MB, Mansuri AM, Larson TJ. Characterization of a 12‐kilodalton rhodanese encoded by glpE of Escherichia coli and its interaction with thioredoxin. J Bacteriol. 2000;182:2277–2284.
Shi R, Proteau A, Villarroya M, Moukadiri I, Zhang LH, Trempe JF, et al. Structural basis for Fe–S cluster assembly and tRNA thiolation mediated by IscS protein–protein interactions. PLoS Biol. 2010;8:e1000354.
Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35:1026–1028.
Stockdreher Y, Sturm M, Josten M, Sahl HG, Dobler N, Zigann R, et al. New proteins involved in sulfur trafficking in the cytoplasm of Allochromatium vinosum. J Biol Chem. 2014;289:12390–12403.
Stockdreher Y, Venceslau SS, Josten M, Sahl HG, Pereira IAC, Dahl C. Cytoplasmic sulfurtransferases in the purple sulfur bacterium Allochromatium vinosum: evidence for sulfur transfer from DsrEFH to DsrC. PLoS One. 2012;7:e40785.
Szajli E, Feher T, Medzihradszky KF. Investigating the quantitative nature of MALDI‐TOF MS. Mol Cell Proteomics. 2008;7:2410–2418.
Tanabe TS, Dahl C. HMS‐S‐S: a tool for the identification of sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies. Mol Ecol Resour. 2022;22:2758–2774.
Tanabe TS, Dahl C. HMSS2: an advanced tool for the analysis of sulfur metabolism, including organosulfur compound transformation, in genome and metagenome assemblies. Mol Ecol Resour. 2023;23:1930–1945.
Tanabe TS, Grosser M, Hahn L, Kümpel C, Hartenfels H, Vtulkin E, et al. Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes. PLoS Biol. 2023;21:e3002177.
Tanabe TS, Leimkühler S, Dahl C. The functional diversity of the prokaryotic sulfur carrier protein TusA. Adv Microb Physiol. 2019;75:233–277.
Tanaka Y, Yoshikaie K, Takeuchi A, Ichikawa M, Mori T, Uchino S, et al. Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake. Sci Adv. 2020;6:eaba7637.
Wagner T, Koch J, Ermler U, Shima S. Methanogenic heterodisulfide reductase (HdrABC‐MvhAGD) uses two noncubane [4Fe‐4S] clusters for reduction. Science. 2017;357:699–703.
Watanabe T, Kojima H, Umezawa K, Hori C, Takasuka TE, Kato Y, et al. Genomes of neutrophilic sulfur‐oxidizing chemolithoautotrophs representing 9 proteobacterial species from 8 genera. Front Microbiol. 2019;10:316.
Westley J. Rhodanese. Adv Enzymol Relat Areas Mol Biol. 1973;39:327–368.
Xin Y, Liu H, Cui F, Liu H, Xun L. Recombinant Escherichia coli with sulfide:quinone oxidoreductase and persulfide dioxygenase rapidly oxidises sulfide to sulfite and thiosulfate via a new pathway. Environ Microbiol. 2016;18:5123–5136.
Yildiz T, Leimkühler S. TusA is a versatile protein that links translation efficiency to cell division in Escherichia coli. J Bacteriol. 2021;203(1):659‐20.
Zhang X, Liu X, Liang Y, Guo X, Xiao Y, Ma L, et al. Adaptive evolution of extreme acidophile Sulfobacillus thermosulfidooxidans potentially driven by horizontal gene transfer and gene loss. Appl Environ Microbiol. 2017;83:e03098–e03116.

Auteurs

Tomohisa Sebastian Tanabe (TS)

Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
Division of Microbial Ecology, University of Vienna, Wien, Austria.

Elena Bach (E)

Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.

Giulia D'Ermo (G)

CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, Marseille, France.

Marc Gregor Mohr (MG)

Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.

Natalie Hager (N)

Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.

Niklas Pfeiffer (N)

Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.

Marianne Guiral (M)

CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, Marseille, France.

Christiane Dahl (C)

Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.

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