IscR of Rhodobacter sphaeroides functions as repressor of genes for iron‐sulfur metabolism and represents a new type of iron‐sulfur‐binding protein

Abstract

IscR proteins are known as transcriptional regulators for Fe–S biogenesis. In the facultatively phototrophic bacterium, Rhodobacter sphaeroides IscR is the product of the first gene in the isc-suf operon. A major role of IscR in R. sphaeroides iron-dependent regulation was suggested in a bioinformatic study (Rodionov et al., PLoS Comput Biol 2:e163, 2006), which predicted a binding site in the upstream regions of several iron uptake genes, named Iron-Rhodo-box. Most known IscR proteins have Fe–S clusters featuring (Cys)3(His)1 ligation. However, IscR proteins from Rhodobacteraceae harbor only a single-Cys residue and it was considered unlikely that they can ligate an Fe–S cluster. In this study, the role of R. sphaeroides IscR as transcriptional regulator and sensor of the Fe–S cluster status of the cell was analyzed. A mutant lacking IscR is more impaired in growth under iron limitation than the wild-type and exhibits significantly increased ROS levels in iron-replete and iron-deplete conditions. Expression studies reveal that R. sphaeroides IscR in its cluster-bound form functions as transcriptional repressor of genes involved in iron metabolism by direct binding to the promoter region of genes preceded by the motif. A total of 110 genes are directly or indirectly affected by IscR. Furthermore, IscR possesses a unique Fe–S cluster ligation scheme with only a single cysteine involved.

Multiple Sense and Antisense Promoters Contribute to the Regulated Expression of the isc-suf Operon for Iron-Sulfur Cluster Assembly in Rhodobacter

“…R. sphaeroides serves as a model organism to elucidate the response of photosynthetic bacteria to singlet oxygen [24][25][26][27][28][29] and has also been analyzed in regard to its response to iron limitation in oxic and anoxic environments [20,23,30,31]. The Fur ortholog (Fur/Mur) of R. sphaeroides is involved in both iron and manganese homeostasis [23].…”

Rhodobacter sphaeroides CryB is a bacterial cryptochrome with (6–4) photolyase activity

“…Instead, one wide single peak of lower absorption emerged. This shape with its absorption maximum at approximately 400 nm resembles that of other iron–sulfur cluster‐containing proteins, for example IscR of R. sphaeroides or XPD helicase of Sulfolobus acidocaldarius , and it is likely that upon loss of the otherwise spectroscopically predominant FAD the absorption of the iron–sulfur cluster of CryB becomes visible.…”

Ecotype diversification of an abundant Roseobacter lineage

“…This 19‐base palindromic consensus sequence resembles the ‘Iron‐Rhodo‐box’ motif (Rodionov et al ., ) (Supporting Information Table S6). IscR is known to act as an activator of iron uptake genes preceded by the specific Iron‐Rhodo‐box in Rhodobacter sphaeroides (Remes et al ., ), and thus may similarly regulate fecBCDE in roseobacters, which are known to be closely related to Rhodobacter . At downstream of fecBCDE in the Antarctic genome, we identified a gene encoding iron‐regulated protein A ( IrpA ; AB‐661‐I11_01070; Fig.…”

“…sphaeroides (Remes et al, 2015), and thus may similarly regulate fecBCDE in roseobacters, which are known to be closely related to Rhodobacter. At downstream of fecBCDE in the Antarctic genome, we identified a gene encoding iron-regulated protein A (IrpA; AB-661-I11_01070; Fig.…”