Early Origin of Iron-Sulfur Cluster Biosynthesis Machinery Before Earth Oxygenation

  • Fontecave, M. Iron-sulfur groups: expanding roles. nat. Chem. Biol. 2171-174 (2006).

    CAS
    Article – Commodity

    Google Scholar

  • Roche, b. et al. Reprint: Iron/sulfur protein biogenesis in prokaryotes: composition, organization, and diversity. Biochem Biophysics. Acta 187923-937 (2013).

    Article – Commodity

    Google Scholar

  • Braymer, J. J., Freibert, SA, Rakwalska-Bange, M. & Lill, R. Mechanistic concepts of iron and sulfur protein biosynthesis in biology. Biochem Biophysics. Acta Mall. cell accuracy. 1868118863 (2021).

  • Tsaousis, AD On the origin of iron/sulfur cluster biosynthesis in eukaryotes. Frontal microbiol. 102478 (2019).

  • Py, B. & Barras, F. Constructing Fe-S proteins: bacterial strategies. nat. Rev. Microbiol. 8436-446 (2010).

    CAS
    Article – Commodity

    Google Scholar

  • Gao, F. Iron-sulfur cluster biogenesis and iron homeostasis in cyanobacteria. Frontal microbiol. 11165 (2020).

  • Wächtershäuser, G. The essential works of evolutionary biochemistry: the world of iron and sulfur. prog. Biovise. mall. Biol. 5885-201 (1992).

  • Imlay, JA. Iron-sulfur groups and the oxygen problem. mall. microbiol; 591073-1082 (2006).

    Article – Commodity

    Google Scholar

  • Andreini, C., Rosato, A. & Banci, L. The relationship between environmental dioxygen and iron-sulfur proteins has been explored at the genome level. PLUS ONE 12e0171279 (2017).

  • Tokumoto, U., Kitamura, S., Fukuyama, K. & Takahashi, Y. Interchangeability and characteristic properties of bacterial Fe–S cluster assembly systems: functional substitution of isc and suf factors in Escherichia coli With a nifSU-like operator from Helicobacter pylori. J. Biochem. 136199 – 209 (2004).

    CAS
    Article – Commodity

    Google Scholar

  • Boyd, E.S., Thomas, KM, Dai, Y., Boyd, JM & Outten, F.W. Interaction between oxygen and Fe–S cluster biogenesis: insights from the Suf pathway. Biochemistry 535834-5847 (2014).

    CAS
    Article – Commodity

    Google Scholar

  • Deere, T. M., Prakash, D., Lessner, F. H., Duin, E. C. & Lessner, DJ Methanosarcina acetivorans Contains a functional ISC system for biosynthesis of iron-sulfur cluster. BMC Microbiol. 20323 (2020).

  • Olson, J. W., Agar, J. N., Johnson, M. K. & Maier, R. J. Characterization of NifU and NifS Fe-S cluster-forming proteins essential for survival in Helicobacter pylori. Biochemistry 3916213-16219 (2000).

    CAS
    Article – Commodity

    Google Scholar

  • Hug, Los Angeles et al. A new view of the tree of life. nat. microbiol; 116048 (2016).

  • Dombrowski, N., Lee, JH, Williams, TA, Offre, P. & Spang, A. Genetic diversity, lifestyles, and evolutionary origins of the DPANN archaea. FEMS Microbiol. Lett. 366fnz008 (2019).

  • Liu, Y., Sieprawska-Lupa, M., Whitman, W. B. & White, R. H. Cysteine ​​is not a sulfur source for iron-sulfur agglomeration and methionine biosynthesis in trace methanogens. Methanococcus maripaludis. J. Biol. Chem. 28531923-31929 (2010).

    CAS
    Article – Commodity

    Google Scholar

  • Trotter, in et al. CsdA cysteine ​​desulfurase promotes Fe/S biogenesis by recruiting Suf components and participating in the new sulfur transport pathway by recruiting CsdL (ex-YgdL), a ubiquitin-like protein. mall. microbiol; 741527-1542 (2009).

    CAS
    Article – Commodity

    Google Scholar

  • Gribaldo, S., Talla, E. & Brochier-Armanet, C. Evolution of the haem copper oxidase family: a rooting story. Biochem directions. Sciences. 34375-381 (2009).

    CAS
    Article – Commodity

    Google Scholar

  • Brochier-Armanet, C., Talla, E. & Gribaldo, S. The multiple evolutionary history of dioxygen reductase: implications for the origin and evolution of aerobic respiration. mall. Biol. Evol. 26285-297 (2009).

    CAS
    Article – Commodity

    Google Scholar

  • Jabłońska, J. & Tawfik, D. S. The evolution of oxygen-utilizing enzymes indicates early biosphere oxygenation. nat. Ecol. Evol. 5442-448 (2021).

    Article – Commodity

    Google Scholar

  • Hayat, Dr. et al. Prodigal: recognition of prokaryotic genes and determination of the translation initiation site. BMC Bioinf. 11119 (2010).

  • Jain, C., Rodriguez-R, LM, Phillippy, AM, Konstantinidis, KT & Aluru, S. High-throughput ANI analysis of 90,000 prokaryotic genomes reveals clear species boundaries. nat. subscriber. 95114 (2018).

  • Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: Accelerated next-generation sequencing data collection. bioinformatics 283150–3152 (2012).

    CAS
    Article – Commodity

    Google Scholar

  • Alchul, SF et al. Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Software. Res nucleic acids. 253389–3402 (1997).

    CAS
    Article – Commodity

    Google Scholar

  • Katoh, K. & Standley, DM MAFFT Multi Sequence Alignment Software version 7: Performance and usability improvements. mall. Biol. Evol. 30772-780 (2013).

    CAS
    Article – Commodity

    Google Scholar

  • Eddy, SR Quick search for an HMM file. PLoS Comput. Biol. 7e1002195 (2011).

    CAS
    Article – Commodity

    Google Scholar

  • Price, MN, Dehal, PS & Arkin, AP FastTree 2 – Trees with nearly maximum probability of large alignment. PLUS ONE 5e9490 (2010).

  • Criscuolo, A. & Gribaldo, S. BMGE (Block Mapping and Gathering with Entropy): A new program for selecting phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 10210 (2010).

  • Leigh, J. W., Schliep, K., Lopez, P. & Bapteste, E. Let them fall where they can: congruence analysis in huge data sets from the phylogenetic phylogeny. mall. Biol. Evol. 282773–2785 (2011).

    CAS
    Article – Commodity

    Google Scholar

  • Adam, Bess; Borrell, c. and Gribaldo, S.; The evolutionary history of the carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. Brooke. Acad Natel. knows the United States of America 115E1166-E1173 (2018).

    CAS
    Article – Commodity

    Google Scholar

  • Coleman, GA et al. Evolution of root phylogeny solves early bacterial evolution. Sciences 372eabe0511 (2021).

  • Raymann, K., Brochier-Armanet, C. & Gribaldo, S. The two-scaled tree of life is associated with a new rootstock for archaea. Brooke. Acad Natel. knows the United States of America 1126670 – 6675 (2015).

    CAS
    Article – Commodity

    Google Scholar

  • Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and efficient randomized algorithm for estimating high-likelihood strains. mall. Biol. Evol. 32268-274 (2015).

    CAS
    Article – Commodity

    Google Scholar

  • Wang, HC, Minh, B.Q., Susko, E. & Roger, A. J. Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenetic estimation. the system. Biol. 67216 – 235 (2018).

    CAS
    Article – Commodity

    Google Scholar

  • Garcia, PS, Jauffrit, F., Grangeasse, C. & Brochier-Armanet, C. GeneSpy, an easy-to-use and flexible genomic context visualizer. bioinformatics 35329 – 331 (2019).

    CAS
    Article – Commodity

    Google Scholar

  • Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v4: Latest Updates and New Developments. Res nucleic acids. 47W256–W259 (2019).

    CAS
    Article – Commodity

    Google Scholar

  • Wahl, A., My, L., Dumoulin, R., Sturgis, J. N. & Bouveret, E. Escherichia coli. mall. microbiol; 801260–1275 (2011).

    CAS
    Article – Commodity

    Google Scholar

  • Gully, D. & Bouveret, E. A protein network for phospholipid synthesis revealed by a variant of the tandem affinity purification method in Escherichia coli. proteomics 6282-293 (2006).

    CAS
    Article – Commodity

    Google Scholar

  • Fish, WW Accurate rapid chromatography method for the determination of the amount of iron complex in biological samples. enzyme methods. 158357–364 (1988).

    CAS
    Article – Commodity

    Google Scholar

  • Beinert, H. Semi-accurate methods for the analysis of variable sulfides and variable sulfides plus sulfur in extraordinarily stable iron and sulfur proteins. anal. Biochem. 131373-378 (1983).

    CAS
    Article – Commodity

    Google Scholar

  • Gardner, P. R. & Fridovich, I. Inactivation—reactivation of aconitase in Escherichia coli. Superoxide radical meter. J. Biol. Chem. 2678757 – 8763 (1992).

    CAS
    Article – Commodity

    Google Scholar

  • Karimova, G., Pidoux, J., Ullmann, A. & Ladant, D. A bacterial dihybrid system based on a reconstituted signal transduction pathway. Brooke. Acad Natel. knows the United States of America 955752-5756 (1998).

    CAS
    Article – Commodity

    Google Scholar