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A tight tunable range for Ni(II) sensing and buffering in cells

Abstract

The metal affinities of metal-sensing transcriptional regulators co-vary with cellular metal concentrations over more than 12 orders of magnitude. To understand the cause of this relationship, we determined the structure of the Ni(II) sensor InrS and then created cyanobacteria (Synechocystis PCC 6803) in which transcription of genes encoding a Ni(II) exporter and a Ni(II) importer were controlled by InrS variants with weaker Ni(II) affinities. Variant strains were sensitive to elevated nickel and contained more nickel, but the increase was small compared with the change in Ni(II) affinity. All of the variant sensors retained the allosteric mechanism that inhibits DNA binding following metal binding, but a response to nickel in vivo was observed only when the sensitivity was set to respond in a relatively narrow (less than two orders of magnitude) range of nickel concentrations. Thus, the Ni(II) affinity of InrS is attuned to cellular metal concentrations rather than the converse.

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Figure 1: DNA-binding Ni(II)-sensor InrS.
Figure 2: Weak Ni(II)-affinity sensors with altered predicted sensitivities.
Figure 3: The tight Ni(II) affinity of InrS was needed to regulate nrsD.
Figure 4: InrS also regulates nikM.
Figure 5: InrS competes for Ni(II) with metabolites at cellular concentrations.

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Acknowledgements

We thank M.K. Grøftehauge for support in crystal structure determination, J.E. Frías (Universidad de Sevilla) for plasmid pCSE120 and C. Eckert (National Renewable Energy Laboratory) for hox Synechocystis PCC 6803. This research was funded by BBSRC grants BB/K00817X/1, BB/H006052/2 and BB/L009226/1 to N.J.R. R. Pal is a Royal Society University Research Fellow. We also thank the Diamond Light Source and the staff of beamline I02.

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Contributions

A.W.F. was involved in all aspects of data interpretation, iterative experimental design and, along with R. Pernil, contributed equally to the experiments. C.J.P. generated crystals, and P.T.C. and A.J.P.S. supported Ni(II)-binding studies in a synthetic cytoplasm. L.-O.P. and R. Pal analyzed Ni(II) with Newport Green, I.C. performed the metabolomics analyses, and E.P. generated the X-ray crystal structure. All of the authors contributed to drafting the manuscript. N.J.R. planned, managed and had overall responsibility for the program, data interpretation and writing the manuscript.

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Correspondence to Nigel J Robinson.

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Foster, A., Pernil, R., Patterson, C. et al. A tight tunable range for Ni(II) sensing and buffering in cells. Nat Chem Biol 13, 409–414 (2017). https://doi.org/10.1038/nchembio.2310

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