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Study of Fe-S Cluster Proteins in Methanococcus maripaludis , a Model Archaeal Organism

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Fe-S Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2353))

Abstract

Iron-sulfur (Fe-S) clusters are among the oldest and most versatile cofactors present in all domains of life. Many bacterial and eukaryotic Fe-S proteins have been well-characterized, whereas the archaeal ones are less studied. Fe-S proteins are particularly abundant and play essential roles in methanogenic archaea. Methanococcus maripaludis is a model methanogen with available genetic tools. Here, we describe the techniques for anaerobic cultivation of M. maripaludis with formate, liposome-mediated transformation, expression and anoxic affinity purification of Fe-S proteins, Fe-S cluster reconstitution, and analysis of Fe-S proteins by UV-visible absorption spectroscopy.

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References

  1. Eck RV, Dayhoff MO (1966) Evolution of the structure of ferredoxin based on living relics of primitive amino acid sequences. Science 152(3720):363–366. https://doi.org/10.1126/science.152.3720.363

    Article  CAS  PubMed  Google Scholar 

  2. Meyer J (2008) Iron-sulfur protein folds, iron-sulfur chemistry, and evolution. J Biol Inorg Chem 13(2):157–170. https://doi.org/10.1007/s00775-007-0318-7

    Article  CAS  PubMed  Google Scholar 

  3. Johnson DC, Dean DR, Smith AD, Johnson MK (2005) Structure, function, and formation of biological iron-sulfur clusters. Annu Rev Biochem 74:247–281. https://doi.org/10.1146/annurev.biochem.74.082803.133518

    Article  CAS  PubMed  Google Scholar 

  4. Pain D, Dancis A (2016) Roles of Fe-S proteins: from cofactor synthesis to iron homeostasis to protein synthesis. Curr Opin Genet Dev 38:45–51. https://doi.org/10.1016/j.gde.2016.03.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Imlay JA (2006) Iron-Sulphur clusters and the problem with oxygen. Mol Microbiol 59(4):1073–1082. https://doi.org/10.1111/j.1365-2958.2006.05028.x

    Article  PubMed  Google Scholar 

  6. Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125:171–189. https://doi.org/10.1196/annals.1419.019

    Article  CAS  PubMed  Google Scholar 

  7. Buan NR (2018) Methanogens: pushing the boundaries of biology. Emerg Top Life Sci 2(4):629–646. https://doi.org/10.1042/ETLS20180031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Lyu Z, Shao N, Akinyemi T, Whitman WB (2018) Methanogenesis. Curr Biol 28(13):R727–R732. https://doi.org/10.1016/j.cub.2018.05.021

    Article  CAS  PubMed  Google Scholar 

  9. Lyu Z, Liu Y (2019) Diversity and taxonomy of methanogens. In: Stams AJM, Sousa D (eds) Biogenesis of hydrocarbons. Springer International Publishing, Cham, pp 19–77. https://doi.org/10.1007/978-3-319-53114-4_5-1

    Chapter  Google Scholar 

  10. Liu Y, Sieprawska-Lupa M, Whitman WB, White RH (2010) Cysteine is not the sulfur source for iron-sulfur cluster and methionine biosynthesis in the methanogenic archaeon Methanococcus maripaludis. J Biol Chem 285(42):31923–31929. https://doi.org/10.1074/jbc.M110.152447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Wagner T, Ermler U, Shima S (2016) The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters. Science 354(6308):114–117. https://doi.org/10.1126/science.aaf9284

    Article  CAS  PubMed  Google Scholar 

  12. Wagner T, Koch J, Ermler U, Shima S (2017) Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science 357(6352):699–703. https://doi.org/10.1126/science.aan0425

    Article  CAS  PubMed  Google Scholar 

  13. Long F, Wang L, Lupa B, Whitman WB (2017) A flexible system for cultivation of Methanococcus and other formate-utilizing methanogens. Archaea 2017:7046026. https://doi.org/10.1155/2017/7046026

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Leigh JA, Albers SV, Atomi H, Allers T (2011) Model organisms for genetics in the domain archaea: methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiol Rev 35(4):577–608. https://doi.org/10.1111/j.1574-6976.2011.00265.x

    Article  CAS  PubMed  Google Scholar 

  15. Sarmiento F, Leigh JA, Whitman WB (2011) Genetic systems for hydrogenotrophic methanogens. Methods Enzymol 494:43–73. https://doi.org/10.1016/B978-0-12-385112-3.00003-2

    Article  CAS  PubMed  Google Scholar 

  16. Lyu Z, Whitman WB (2019) Transplanting the pathway engineering toolbox to methanogens. Curr Opin Biotechnol 59:46–54. https://doi.org/10.1016/j.copbio.2019.02.009

    Article  CAS  PubMed  Google Scholar 

  17. Xia Q, Hendrickson EL, Zhang Y, Wang T, Taub F, Moore BC, Porat I, Whitman WB, Hackett M, Leigh JA (2006) Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol Cell Proteomics 5(5):868–881. https://doi.org/10.1074/mcp.M500369-MCP200

    Article  CAS  PubMed  Google Scholar 

  18. Hendrickson EL, Haydock AK, Moore BC, Whitman WB, Leigh JA (2007) Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic archaea. Proc Natl Acad Sci U S A 104(21):8930–8934. https://doi.org/10.1073/pnas.0701157104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hendrickson EL, Liu Y, Rosas-Sandoval G, Porat I, Söll D, Whitman WB, Leigh JA (2008) Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J Bacteriol 190(6):2198–2205. https://doi.org/10.1128/JB.01805-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Xia Q, Wang T, Hendrickson EL, Lie TJ, Hackett M, Leigh JA (2009) Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis. BMC Microbiol 9:149. https://doi.org/10.1186/1471-2180-9-149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Yoon SH, Reiss DJ, Bare JC, Tenenbaum D, Pan M, Slagel J, Moritz RL, Lim S, Hackett M, Menon AL, Adams MWW, Barnebey A, Yannone SM, Leigh JA, Baliga NS (2011) Parallel evolution of transcriptome architecture during genome reorganization. Genome Res 21(11):1892–1904. https://doi.org/10.1101/gr.122218.111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Sarmiento F, Mrázek J, Whitman WB (2013) Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis. Proc Natl Acad Sci U S A 110(12):4726–4731. https://doi.org/10.1073/pnas.1220225110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Walters AD, Smith SE, Chong JP (2011) Shuttle vector system for Methanococcus maripaludis with improved transformation efficiency. Appl Environ Microbiol 77(7):2549–2551. https://doi.org/10.1128/AEM.02919-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Lyu Z, Chou C-W, Shi H, Wang L, Ghebreab R, Phillips D, Yan Y, Duin EC, Whitman WB (2018) Assembly of methyl coenzyme M reductase in the methanogenic archaeon Methanococcus maripaludis. J Bacteriol 200(7):e00746–e00717. https://doi.org/10.1128/JB.00746-17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Zhao C, Lyu Z, Long F, Akinyemi T, Manakongtreecheep K, Söll D, Whitman WB, Vinyard DJ, Liu Y (2020) The Nbp35/ApbC homolog acts as a nonessential [4Fe-4S] transfer protein in methanogenic archaea. FEBS Lett 594(5):924–932. https://doi.org/10.1002/1873-3468.13673

    Article  CAS  PubMed  Google Scholar 

  26. Liu Y, Vinyard DJ, Reesbeck ME, Suzuki T, Manakongtreecheep K, Holland PL, Brudvig GW, Söll D (2016) A [3Fe-4S] cluster is required for tRNA thiolation in archaea and eukaryotes. Proc Natl Acad Sci U S A 113(45):12703–12708. https://doi.org/10.1073/pnas.1615732113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Ollagnier de Choudens S, Barras F (2017) Genetic, biochemical, and biophysical methods for studying FeS proteins and their assembly. Methods Enzymol 595:1–32. https://doi.org/10.1016/bs.mie.2017.07.015

    Article  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA

    Cuiping Zhao

  2. Astrix Technology Group, Red Bank, NJ, USA

    Christina A. Roberts

  3. Corporate Strategic Research, ExxonMobil Research & Engineering Company, Annandale, NJ, USA

    Ian J. Drake & Yuchen Liu

Authors
  1. Cuiping Zhao
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  2. Christina A. Roberts
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  3. Ian J. Drake
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  4. Yuchen Liu
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Corresponding author

Correspondence to Yuchen Liu .

Editor information

Editors and Affiliations

  1. Department of Chemistry, Wake Forest University, Winston Salem, NC, USA

    Patricia C. Dos Santos

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Zhao, C., Roberts, C.A., Drake, I.J., Liu, Y. (2021). Study of Fe-S Cluster Proteins in Methanococcus maripaludis , a Model Archaeal Organism. In: Dos Santos, P.C. (eds) Fe-S Proteins. Methods in Molecular Biology, vol 2353. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1605-5_2

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  • DOI: https://doi.org/10.1007/978-1-0716-1605-5_2

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1604-8

  • Online ISBN: 978-1-0716-1605-5

  • eBook Packages: Springer Protocols

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