The third pillar of metal homeostasis in Cupriavidus metallidurans CH34: preferences are controlled by extracytoplasmic function sigma factors

Abstract

The role of extracytoplasmic function (ECF) sigma factors in multiple metal homeostasis of the metallophilic bacterium Cupriavidus metallidurans was studied. RNA sequencing was used to predict 3084 operons in the genome of this bacterium, including 11 for ECF sigma factors, and to measure transcript abundances. Mutants carrying multiple deletions in genes for ECF sigma factors were constructed and characterized. Mutants and parent were challenged with a metal mix, changes in the global gene expression profile and the overall metal content determined. All 11 ECF sigma factors were involved in metal homeostasis. The three ECF sigma factors RpoI, RpoJ and RpoK synchronized iron homeostasis with that of other divalent metal cations, RpoO, RpoL and RpoM magnesium and phosphorous homeostasis with that of zinc and with cadmium resistance. Factors RpoE, CnrH and RpoP controlled the response to nickel and cobalt, RpoQ and RpoR may be assigned to the thiol and sulfide metabolism. All 11 ECF sigma factors overlap in their function and control gene expression involved in metal homeostasis, however, except CnrH, no other ECF sigma factor was needed for up-regulation of 63 predicted operons responding to metal shock, 48 of these encoding metal efflux pumps. Moreover, disturbance of the cellular metal content resulting from missing sigma factors also affected silencing and un-silencing of genomic islands. Together, these data demonstrate on a global and systemic level how a robust network of ECF sigma factors and other regulators allow C. metallidurans to handle a mixture of toxic transition metal cations, which are conditions the bacterium faces in its natural environment. Iron homeostasis is to be maintained at any cost, followed by the necessity for magnesium, phosphorous and zinc homeostasis on the second level, and cobalt plus nickel coming last.