Letter

Microbial metalloproteomes are largely uncharacterized

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Accepted:
Published online:

Abstract

Metal ion cofactors afford proteins virtually unlimited catalytic potential, enable electron transfer reactions and have a great impact on protein stability1,2. Consequently, metalloproteins have key roles in most biological processes, including respiration (iron and copper), photosynthesis (manganese) and drug metabolism (iron). Yet, predicting from genome sequence the numbers and types of metal an organism assimilates from its environment or uses in its metalloproteome is currently impossible because metal coordination sites are diverse and poorly recognized2,3,4. We present here a robust, metal-based approach to determine all metals an organism assimilates and identify its metalloproteins on a genome-wide scale. This shifts the focus from classical protein-based purification to metal-based identification and purification by liquid chromatography, high-throughput tandem mass spectrometry (HT-MS/MS) and inductively coupled plasma mass spectrometry (ICP-MS) to characterize cytoplasmic metalloproteins from an exemplary microorganism (Pyrococcus furiosus). Of 343 metal peaks in chromatography fractions, 158 did not match any predicted metalloprotein. Unassigned peaks included metals known to be used (cobalt, iron, nickel, tungsten and zinc; 83 peaks) plus metals the organism was not thought to assimilate (lead, manganese, molybdenum, uranium and vanadium; 75 peaks). Purification of eight of 158 unexpected metal peaks yielded four novel nickel- and molybdenum-containing proteins, whereas four purified proteins contained sub-stoichiometric amounts of misincorporated lead and uranium. Analyses of two additional microorganisms (Escherichia coli and Sulfolobus solfataricus) revealed species-specific assimilation of yet more unexpected metals. Metalloproteomes are therefore much more extensive and diverse than previously recognized, and promise to provide key insights for cell biology, microbial growth and toxicity mechanisms.

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Acknowledgements

This research is part of the MAGGIE (Molecular Assemblies, Genes and Genomes Integrated Efficiently) project supported by Department of Energy grant (DE-FG0207ER64326). We thank S. Hammond, L. Wells, R. Hopkins and D. Phillips for help with in-gel MS analyses.

Author information

Author notes

    • Aleksandar Cvetkovic
    • , Angeli Lal Menon
    •  & Michael P. Thorgersen

    These authors contributed equally to this work.

    • Francis E. Jenney Jr

    Present address: Philadelphia College of Osteopathic Medicine, Suwanee, Georgia 30024, USA (F.E.J.).

Affiliations

  1. Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA

    • Aleksandar Cvetkovic
    • , Angeli Lal Menon
    • , Michael P. Thorgersen
    • , Joseph W. Scott
    • , Farris L. Poole II
    • , Francis E. Jenney Jr
    • , W. Andrew Lancaster
    • , Jeremy L. Praissman
    • , Saratchandra Shanmukh
    • , Brian J. Vaccaro
    •  & Michael W. W. Adams
  2. Scripps Center for Mass Spectrometry and the Departments of Molecular Biology and Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA

    • Sunia A. Trauger
    • , Ewa Kalisiak
    • , Junefredo V. Apon
    •  & Gary Siuzdak
  3. Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA

    • Steven M. Yannone
    •  & John A. Tainer

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Contributions

A.C., A.L.M., M.P.T. and J.W.S. grew and fractionated P. furiosus; A.L.M. carried out cytoplasmic washes; A.L.M. and S.M.Y. grew and fractionated S. solfataricus; A.L.M. and M.P.T. grew and fractionated E. coli; A.C. and S.S. performed ICP-MS analyses; S.A.T., E.K., J.V.A. and G.S. performed HT-MS/MS analyses; A.L.M. purified PF0056; J.W.S. purified PF1972 and PF0086; M.P.T. and B.J.V. purified PF0742; M.T.P. purified PF1587, PF0215, PF1343 and PF0257; W.A.L., J.L.P. and F.L.P. carried out metal-protein bioinformatic analyses; A.C., A.L.M., F.E.J., F.L.P., M.P.T. and J.A.T. and M.W.W.A. contributed to experimental design and data analyses, and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Michael W. W. Adams.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Figures S1-S16 with legends, Supplementary Tables S1-S13 and References.

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