Fe-S cluster assembly pathways in bacteria

Abstract

Iron-sulfur (Fe-S) clusters are required for critical biochemical pathways, including respiration, photosynthesis, and nitrogen fixation. Assembly of these iron cofactors is a carefully controlled process in cells to avoid toxicity from free iron and sulfide. Multiple Fe-S cluster assembly pathways are present in bacteria to carry out basal cluster assembly, stress-responsive cluster assembly, and enzyme-specific cluster assembly. Although biochemical and genetic characterization is providing a partial picture of in vivo Fe-S cluster assembly, a number of mechanistic questions remain unanswered. Furthermore, new factors involved in Fe-S cluster assembly and repair have recently been identified and are expanding the complexity of current models. Here we attempt to summarize recent advances and to highlight new avenues of research in the field of Fe-S cluster assembly.

FIG. 1.

Current model for Fe-S cluster assembly on the IscU scaffold. IscS donates sulfur liberated from l-cysteine, and iron is donated from an iron chaperone (such as CyaY) or by direct iron binding to IscU. Sequential iron and sulfur donations result in assembly of one [2Fe-2S] cluster, which is transferred to an apoprotein with the assistance of the HscAB molecular chaperone system. Further assembly of a second [2Fe-2S] cluster occurs, setting the stage for reductive coupling to form a [4Fe-4S] cluster. IscFdx may mediate reductive coupling in vivo through a one-electron reduction of each cluster (only one IscFdx molecule is shown for simplicity). The [4Fe-4S] cluster can be transferred to an apoprotein or can react with oxygen to degrade to a single [2Fe-2S] cluster.

FIG. 2.

Structural comparison of E. coli SufE (PDB accession no. 1MZG) with H. influenza IscU (PDB accession no. 1R9P). (A) Overlay of the carbon backbone of SufE (blue) with that of IscU (mauve), demonstrating the high degree of structural similarity. Relevant Cys side chains are shown for orientation. (B) Enlargement of the overlaid structures in the vicinity of SufE Cys51 and IscU Cys37, Cys63, and Cys106. SufE Cys51 is located in a similar region to that of the conserved IscU Cys37 residue but is oriented deeper into the protein interior and is not solvent exposed. Cys63 and Cys106 are not present in SufE. The superposition of SufE and IscU was performed using lsqkab from the CCP4 suite and DaliLite pairwise structure comparison. Figures were generated using PyMOL.

FIG. 3.

Current model for Fe-S cluster assembly by the Suf system. (A) SufS and SufE mobilize sulfur for donation to SufB (as part of SufBCD) and SufA. (B) An Fe-S cluster can form on both SufA and SufB. The Fe-S cluster on SufA can be transferred to an apoprotein. The SufB Fe-S cluster could be transferred to an apoprotein or could participate in redox processes during cluster assembly (e⁻). Dotted arrows indicate possible donation of iron by SufD or by direct binding to SufA. The exact role of SufC ATPase activity is unknown.

FIG. 4.

Regulation of Fe-S cluster assembly pathways in E. coli under normal growth conditions. Holo-IscR and apo-IscR will be present in an equilibrium that is dependent on the amount of Isc proteins available for cluster synthesis. Holo-IscR will repress isc transcription when there is sufficient cluster assembly capacity (i.e., when the Isc proteins are not titrated away for cluster assembly in other proteins). Under normal growth conditions, suf transcription will be low due to repression by Fe²⁺-Fur.

FIG. 5.

Regulation of Fe-S cluster assembly pathways in E. coli under stress conditions. During oxidative stress or iron starvation, apo-IscR will predominate as the Isc proteins are titrated away by increased demand for cluster assembly. This will relieve isc repression and induce the operon. Simultaneously, apo-IscR will activate suf transcription as Fur repression is relieved. Under hydrogen peroxide stress, OxyR will also activate suf transcription in an integration host factor-dependent manner. Under iron starvation conditions, induction of the RyhB small RNA will lead to posttranscriptional repression of the Isc system so that Suf becomes the predominant Fe-S cluster pathway.