Fe-S cluster homeostasis and beyond: The multifaceted roles of IscR

Abstract

The role of IscR in regulating the transcription of genes involved in Fe-S cluster homeostasis has been well established for the model organism Escherichia coli K12. In this bacterium, IscR coordinates expression of the Isc and Suf Fe-S cluster assembly pathways to meet cellular Fe-S cluster demands shaped by a variety of environmental cues. However, since its initial discovery nearly 25 years ago, there has been growing evidence that IscR function extends well beyond Fe-S cluster homeostasis, not only in E. coli, but in bacteria of diverse lifestyles. Notably, pathogenic bacteria have exploited the ability of IscR to respond to changes in oxygen tension, oxidative and nitrosative stress, and iron availability to navigate their trajectory in their respective hosts as changes in these cues are frequently encountered during host infection. In this review, we highlight these broader roles of IscR in different cellular processes and, in particular, discuss the importance of IscR as a virulence factor for many bacterial pathogens.

Figure 1.

E. coli IscR is a dimeric, Rrf2 transcription factor that possesses a winged helix-turn-helix DNA binding domain and a [2Fe-2S] cluster binding domain. Shown is the crystal structure of an apoprotein variant of IscR, in which the Cys cluster ligands were substituted with Ala, bound to its type 2 recognition motif from the hyaA promoter. One IscR subunit is colored gray, the other is presented in rainbow colors, and the DNA is colored blue. Marked in magenta are the residues involved in [2Fe-2S] cluster binding: His107 and residues 92, 98, and 104 that are Cys in wild-type IscR. Side chains making specific contacts with PhyaA are shown as sticks. This figure was prepared with PyMOL using the structure (accession code 4HF1) available in the Research Collaboratory for Structural Bioinformatics Protein Data Bank.

Figure 2.

IscR differentially regulates gene expression through binding two types of DNA motifs. Shown are the proposed consensus DNA binding motifs for E. coli IscR. [2Fe-2S]-IscR binds with high affinity to type 1 motifs, while both holo- and apo-forms of IscR bind with similar high affinity to type 2 motifs. A, T, C, and G represent adenine, thymine, cytosine, and guanine, respectively; R represents A or G, Y represents C or T, W represents A or T, and x is undefined. Example promoters containing type 1 motifs are iscR, erpA, and nfuA, whereas those containing type 2 motifs are sufA, hyaA, and ydiU.

Figure 3.

In E. coli, IscR coordinates transcription of isc and suf operons to accommodate the demand for Fe-S biogenesis under various growth conditions. Upon acquiring its [2Fe-2S] cluster from the Isc machinery, holo-IscR can bind type 1 motifs to repress transcription of isc. Due to this negative autoregulation and decreased Fe-S needs under anaerobic conditions, the cellular concentration of IscR is low, and primarily in the [2Fe-2S]-containing form. Consequently, there is minimal suf transcription occurring under anaerobic conditions. Under aerobic conditions, the Fe-S demand increases due to the instability of some clusters by O₂ or ROS, causing competition between IscR and apoprotein targets for the Isc machinery. This results in partial derepression of isc and elevated levels of apo-IscR that bind type 2 motifs to activate suf transcription. Finally, conditions of extreme oxidative or nitrosative stress, iron limitation, or toxic metal exposure, further propagate apo-IscR levels, thereby enabling high expression of both Isc and Suf pathways.

Figure 4.

Alignment of Rrf2 family members. Clustal Omega was used to align the relevant Rrf2 family members discussed in this review. Conserved structural features [helix-turn helix (red), cluster ligands (green) and dimerization domain (blue)] are inferred from E. coli IscR, highlighted in grey. Orthologs are A0A4Y6C491_MYXXA, Myxococcus xanthus; Q8P749_XANCP, Xanthomonas campestris pv. campestris; A0A127EK09_CLOPF, Clostridium perfringens; A0A0H2WEW8_BURMA, Burkholderia mallei; Q9HXI7_PSEAE, Pseudomonas aeruginosa; A0A8I2W602_HAEIF, Haemophilus influenzae; ISCR_VIBVY, Vibrio vulnificus; W8URH5_KLEPN, Klebsiella pneumoniae; A0A8E6JFT1_SALTM, Salmonella enterica subsp. enterica serovar Typhimurium; A0A6N3QRV3_SHIFL, Shigella flexneri CDC 796–83; ISCR_ECOLI, Escherichia coli K12; H3RGK7_PANSE, Pantoea stewartii subsp. stewartii DC283; ISCR_YERPS, Yersinia pseudotuberculosis serotype I; ISCR_YERPS, E0SAX8_DICD3, Dickeya dadantii.