CoChat
Sign Up
Cited by 147Bacterial Genetics and BiotechnologyMetalloenzymes and iron-sulfur proteinsPorphyrin Metabolism and Disorders

Bacterial sensors define intracellular free energies for correct enzyme metalation

Open access
Osman, Deenah, Martini, Maria Alessandra, Foster, Andrew W., Chen, Junjun, Scott, Andrew J. P., Morton, Richard J., Steed, Jonathan W., Lurie-Luke, Elena +6 more·2019·Nature Chemical Biology
DOI 10.1038/s41589-018-0211-4PMC PMC6420079
Open this paper in CoChat — free accountOpen PDF

Abstract

There is a challenge for metalloenzymes to acquire their correct metals because some inorganic elements form more stable complexes with proteins than do others. These preferences can be overcome provided some metals are more available than others. However, while the total amount of cellular metal can be readily measured, the available levels of each metal have been more difficult to define. Metal-sensing transcriptional regulators are tuned to the intracellular availabilities of their cognate ions. Here we have determined the standard free energy for metal complex formation to which each sensor, in a set of bacterial metal sensors, is attuned: the less competitive the metal, the less favorable the free energy and hence the greater availability to which the cognate allosteric mechanism is tuned. Comparing these free energies with values derived from the metal affinities of a metalloprotein reveals the mechanism of correct metalation exemplified here by a cobalt chelatase for vitamin B 12.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41589-018-0211-4

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The brackets in Figure 2 denote the range of free metal concentrations corresponding to a 10-90% change in gene expression for the indicated metalloregulators purified from Salmonella and the MgtE riboswitch from B. subtilis.

    “The brackets denote the range of free metal concentrations corresponding to a 10–90% change in gene expression as calculated for the indicated metalloregulators purified from Salmonella(4) and the MgtE riboswitch from B. subtilis.29”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [4]

    The Results section (‘Low buffered cytosolic metal relative to metal cell−1’; page unavailable) calculates Salmonella metalloregulator responses across buffered metal concentrations. The Online Methods (‘Mathematical calculations’; page unavailable) specifies that these responses are normalized DNA-promoter occupancy, not a 10–90% change in gene expression; our copy does not give that range. The MgtE riboswitch is attached to a separate citation (29), so it is not judged against this source. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • The best estimates of the free Fe2+ pool are on the order of <1 μM.

    “The best estimates of the free Fe2+ pool are on the order of <1 μM.4”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [4]

    The Results section, “Low buffered cytosolic metal relative to metal cell−1” (page not available), says sensor-derived cytosolic metal availabilities are far below total cellular metal and mostly imply negligible free, fully hydrated metal. It does not give a specific estimate below 1 μM for free Fe²⁺, and its measurements concern Salmonella rather than free Fe²⁺ pools generally. (LLM, conf=0.77)

    Experimental — accuracy not yet measured

  • Within the complex milieu of the cytosol, the biochemically determined metal sensitivity of metalloregulatory proteins and metal-sensing riboswitches provides a useful proxy for free metal concentrations and defines the biological set-point for specific genetic changes.

    “Within the more complex milieu of the cytosol, the biochemically determined metal sensitivity of metalloregulatory proteins and metal-sensing riboswitches provides a useful proxy3,4 and defines the biological set-point for specific genetic changes (Figure 2).4,24”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [4]

  • Metal binding to metalloregulators often affects DNA affinity, and the converse is also true; these effects need to be considered when assessing sensitivity.

    “Further, since metal binding to metalloregulators often affects DNA affinity, the converse is also true,26 and these effects need to be considered when assessing sensitivity.3,4”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [4]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 52

  1. [1]Waldron KJ Rutherford JC Ford D Robinson NJ Metalloproteins and metal sensing Nature 2009 460 823 830 19675642
  2. [2]Tottey S Protein-folding location can regulate manganese-binding versus copper- or zinc-binding Nature 2008 455 1138 1142 18948958
  3. [3]Fraústo da Silva JJR Williams RJP The Biological Chemistry of the Elements: The Inorganic Chemistry of Life Oxford University Press Oxford 1991
  4. [5]Chandrangsu P Rensing C Helmann JD Metal homeostasis and resistance in bacteria Nat Rev Microbiol 2017 15 338 350 28344348 PMC5963929
  5. [6]Reyes-Caballero H Campanello GC Giedroc DP Metalloregulatory proteins: metal selectivity and allosteric switching Biophys Chem 2011 156 103 114 21511390 PMC3097251
  6. [7]Giedroc DP Arunkumar AI Metal sensor proteins: nature's metalloregulated allosteric switches Dalton Trans 2007 3107 3120 17637984
  7. [8]Foster AW A tight tunable range for Ni(II) sensing and buffering in cells Nat Chem Biol 2017 13 409 414 28166209 PMC5365139
  8. [10]Carter KP Young AM Palmer AE Fluorescent sensors for measuring metal ions in living systems Chem Rev 2014 114 4564 4601 24588137 PMC4096685
  9. [11]Osman D Fine control of metal concentrations is necessary for cells to discern zinc from cobalt Nat Commun 2017 8 1884 PMC5709419 29192165
  10. [12]Ansari AZ Chael ML O'Halloran TV Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-MerR Nature 1992 355 87 89 1731201
  11. [13]Ikeda JS Janakiraman A Kehres DG Maguire ME Slauch JM Transcriptional regulation of sitABCD of Salmonella enterica serovar Typhimurium by MntR and Fur J Bacteriol 2005 187 912 922 15659669 PMC545731
  12. [14]Osman D Copper homeostasis in Salmonella is atypical and copper-CueP is a major periplasmic metal complex J Biol Chem 2010 285 25259 25268 20534583 PMC2919089
  13. [15]O'Halloran T Walsh C Metalloregulatory DNA-binding protein encoded by the merR gene: isolation and characterization Science 1987 235 211 214 3798107
  14. [16]Iwig JS Rowe JL Chivers PT Nickel homeostasis in Escherichia coli – the rcnR-rcnA efflux pathway and its linkage to NikR function Mol Microbiol 2006 62 252 262 16956381
  15. [17]Iwig JS Leitch S Herbst RW Maroney MJ Chivers PT Ni(II) and Co(II) sensing by Escherichia coli RcnR J Am Chem Soc 2008 130 7592 7606 18505253 PMC2435081
  16. [22]Schreiter ER Crystal structure of the nickel-responsive transcription factor NikR Nat Struct Biol 2003 10 794 799 12970756
  17. [23]Osman D Generating a metal-responsive transcriptional regulator to test what confers metal sensing in cells J Biol Chem 2015 290 19806 19822 26109070 PMC4528141
  18. [24]Pi H Helmann JD Sequential induction of Fur-regulated genes in response to iron limitation in Bacillus subtilis Proc Natl Acad Sci U S A 2017 114 12785 12790 29133393 PMC5715773
  19. [25]Record MT Jr Ha JH Fisher MA Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA Methods Enzymol 1991 208 291 343 1779839
  20. [26]Campanello GC Allosteric inhibition of a zinc-sensing transcriptional repressor: insights into the arsenic repressor (ArsR) family J Mol Biol 2013 425 1143 1157 23353829 PMC3602352
  21. [27]Epstein W Schultz SG Cation Transport in Escherichia coli: V. Regulation of cation content J Gen Physiol 1965 49 221 234 19873561 PMC2195484
  22. [28]Su J Gong H Lai J Main A Lu S The potassium transporter Trk and external potassium modulate Salmonella enterica protein secretion and virulence Infect Immun 2009 77 667 675 19001074 PMC2632022
  23. [29]Stickle DF Vossen KM Riley DA Fried MG Free DNA concentration in E. coli estimated by an analysis of competition for DNA binding proteins J Theor Biol 1994 168 1 12 8022188
  24. [30]Gilston BA Structural and mechanistic basis of zinc regulation across the E. coli Zur regulon PLOS Biol 2014 12 e1001987 25369000 PMC4219657
  25. [31]Shin J-H Helmann JD Molecular logic of the Zur-regulated zinc deprivation response in Bacillus subtilis Nat Commun 2016 7 12612 PMC5007448 27561249
  26. [32]Ma Z Gabriel SE Helmann JD Sequential binding and sensing of Zn(II) by Bacillus subtilis Zur Nucleic Acids Res 2011 39 9130 9138 21821657 PMC3241647
  27. [33]Natori Y A fail-safe system for the ribosome under zinc-limiting conditions in Bacillus subtilis Mol Microbiol 2007 63 294 307 17163968
  28. [34]Dalecki AG Crawford CL Wolschendorf F Copper and Antibiotics: Discovery, Modes of Action, and Opportunities for Medicinal Applications Adv Microb Physiol 2017 70 193 260 28528648
  29. [35]Foster AW Osman D Robinson NJ Metal preferences and metallation J Biol Chem 2014 289 28095 28103 25160626 PMC4192464
  30. [36]Warren MJ Raux E Schubert HL Escalante-Semerena JC The biosynthesis of adenosylcobalamin (vitamin B12) Nat Prod Rep 2002 19 390 412 12195810
  31. [37]Frank S Anaerobic synthesis of vitamin B12: characterization of the early steps in the pathway Biochem Soc Trans 2005 33 811 814 16042604
  32. [38]Raux E Thermes C Heathcote P Rambach A Warren MJ A role for Salmonella typhimurium cbiK in cobalamin (vitamin B12) and siroheme biosynthesis J Bacteriol 1997 179 3202 3212 9150215 PMC179098
  33. [39]Lobo SA Two distinct roles for two functional cobaltochelatases (CbiK) in Desulfovibrio vulgaris hildenborough Biochemistry 2008 47 5851 5857 18457416
  34. [40]Martin JE Lisher JP Winkler ME Giedroc DP Perturbation of manganese metabolism disrupts cell division in Streptococcus pneumoniae Mol Microbiol 2017 104 334 348 28127804 PMC5380469
  35. [41]Brown DR The cellular prion protein binds copper in vivo Nature 1997 390 684 687 9414160
  36. [42]Bush AI The metallobiology of Alzheimer's disease Trends Neurosci 2003 26 207 214 12689772
  37. [43]McCarthy RC Kosman DJ Iron transport across the blood–brain barrier: development, neurovascular regulation and cerebral amyloid angiopathy Cell Mol Life Sci 2015 72 709 727 25355056 PMC4312246
  38. [44]Xiao T Copper regulates rest-activity cycles through the locus coeruleus-norepinephrine system Nat Chem Biol 2018 14 655 663 29867144 PMC6008210
  39. [46]Lisher JP Giedroc DP Manganese acquisition and homeostasis at the host-pathogen interface Front Cell Infect Microbiol 2013 3 91 24367765 PMC3851752
  40. [47]Wilks A Burkhard KA Heme and virulence: how bacterial pathogens regulate, transport and utilize heme Nat Prod Rep 2007 24 511 522 17534527
  41. [48]Djoko KY Ong C-lY Walker MJ McEwan AG The role of copper and zinc toxicity in innate immune defense against bacterial pathogens J Biol Chem 2015 290 18954 18961 26055706 PMC4521016
  42. [49]Damo SM Molecular basis for manganese sequestration by calprotectin and roles in the innate immune response to invading bacterial pathogens Proc Natl Acad Sci USA 2013 110 3841 3846 23431180 PMC3593839
  43. [50]Lemire JA Harrison JJ Turner RJ Antimicrobial activity of metals: mechanisms, molecular targets and applications Nat Rev Microbiol 2013 11 371 384 23669886
  44. [51]Chivers PT Benanti EL Heil-Chapdelaine V Iwig JS Rowe JL Identification of Ni-(L-His)2 as a substrate for NikABCDE-dependent nickel uptake in Escherichia coli Metallomics 2012 4 1043 1050 22885853
  45. [52]Livak KJ Schmittgen TD Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method Methods 2001 25 402 408 11846609
  46. [53]Ramakers C Ruijter JM Deprez RHL Moorman AFM Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data Neurosci Lett 2003 339 62 66 12618301
  47. [54]Chivers PT Sauer RT NikR repressor: high-affinity nickel binding to the C-terminal domain regulates binding to operator DNA Chem Biol 2002 9 1141 1148 12401498
  48. [55]Romao CV Evolution in a family of chelatases facilitated by the introduction of active site asymmetry and protein oligomerization Proc Natl Acad Sci U S A 2011 108 97 102 21173279 PMC3017170
  49. [57]Dainty SJ Patterson CJ Waldron KJ Robinson NJ Interaction between cyanobacterial copper chaperone Atx1 and zinc homeostasis J Biol Inorg Chem 2010 15 77 19543924
  50. [58]Kuzmic P Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase Anal Biochem 1996 237 260 273 8660575
  51. [59]Reyes-Caballero H Lee CW Giedroc DP Mycobacterium tuberculosis NmtR harbors a nickel sensing site with parallels to Escherichia coli RcnR Biochemistry 2011 50 7941 7952 21819125 PMC3225088
  52. [60]Xiao Z Unification of the copper(I) binding affinities of the metallo-chaperones Atx1, Atox1, and related proteins: detection probes and affinity standards J Biol Chem 2011 286 11047 11055 21258123 PMC3064159

Cited by

Sorted by citations

Authors
Osman, D., Martini, M. A., Foster, A. W., Chen, J., Scott, A. J. P., Morton, R. J., Steed, J. W., Lurie-Luke, E., Huggins, T. G., Lawrence, A. D., Deery, E., Warren, M. J., Chivers, P. T., & Robinson, N. J.
Affiliations
  • Durham University (GB)
  • Procter & Gamble (United States) (US)
  • Northumbria University (GB)
  • University of Kent (GB)
Corresponding author
  • Chivers, Peter T.
  • Robinson, Nigel J.
ORCID
Venue
Nature Chemical Biology
Publisher
Springer Science and Business Media LLC
Published
2019-01-28
Volume
15
Issue
3
Pages
241-249
ISSN
  • 1552-4450 (ISSN-L)
  • 1552-4469
DOI
10.1038/s41589-018-0211-4
PMC
PMC6420079
OpenAlex
W2911831757
Cited by
147
References
6
Citations by year
2026: 10 · 2025: 23 · 2024: 13 · 2023: 17 · 2022: 24 · 2021: 19 · 2020: 26 · 2019: 15
FWCI
12.50
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature Chemical Biology (publishedVersion)
  • PubMed (publishedVersion)
  • Kent Academic Repository (University of Kent) (acceptedVersion)
  • Northumbria Research Link (Northumbria University) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Durham Research Online (Durham University) (acceptedVersion)
  • Durham Research Online (Durham University) (submittedVersion, cc-by)
  • ePrints Soton (University of Southampton) (submittedVersion)
  • UEA Digital Repository (University of East Anglia) (submittedVersion)
Funders
  • Procter and Gamble
  • University of Oxford
  • Durham University
  • Directorate for Biological Sciences
  • Biotechnology and Biological Sciences Research Council (BB/S002197/1, BB/L010208/1, BB/R002118/1, BB/L009226/1, BB/J017787/1, BB/L013711/1)
  • Mathematical Institute, University of Oxford
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Physical Sciences › Energy › Renewable Energy, Sustainability and the Environment › Metalloenzymes and iron-sulfur proteins
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Porphyrin Metabolism and Disorders
Keywords
metal availability, vitamin B12 biosynthesis, allosteric regulation, metal homeostasis
MeSH terms
Affinity Labels, Bacteria, Bacterial Proteins, Energy Transfer, Metalloproteins, Metals, Salmonella, Bacterial Physiological Phenomena

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review