26
Fe
Iron
55.845
Essential:
almost all organisms
Iron
Major functions in cells:
-Cytochromes and other heme proteins
-Fe/S clusters
-Mononuclear, di-iron, and other non-heme Fe proteins
Environmental and health impacts:
-Limitation affects oceanic primary production, agriculture, human health.
-Both C and N fixation are Fe-intensive processes
- Iron deficiency is common health problem in humans
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(1) Iron: A Required Element in Almost All Cells
Iron is required for growth in nearly all cells. The only known exceptions to this general requirement are certain bacteria that grow in severely Fe-limited environments. Lactobacilli (Weinberg, 1997) and the spirochete Borrelia burgdorferi (Posey and Gherardini, 2000) are thought not to require Fe. In addition to dispensing with heme and Fe/S proteins, enzymes that in other organisms often require Fe for catalytic activity use a different metal in these systems. For example, in both Lactobacillus plantarum and B. burgdorferi, peptide deformylase contains a catalytically essential Zn in place of what would normally be Fe (Nguyen et al., 2007).
(2) Iron Sparing Response
Many organisms, including E. coli, B. subtilis, and S. cerevisiae, have iron sparing responses. The Fe-sparing response reduces the requirement for Fe-containing proteins by synthesizing alternative enzymes using either organic cofactors or other metal ions in place of Fe, and concurrently shutting off the synthesis of low-priority Fe proteins. Low priority proteins are not absolutely essential for growth or can be functionally replaced by other proteins and pathways.
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Metalloregulators:
Acclimation to Fe limitation requires, first, that cells have mechanisms to monitor their Fe status and alter gene expression appropriately. In Bacteria, iron homeostasis is regulated by specific Fe-sensing metalloregulatory proteins, such as the ferric uptake repressor (Fur) and the diphtheria toxin repressor (DtxR), which serve to sense the cytosolic availability of Fe(II) (Hantke, 2001) (Andrews et al., 2003). In S. cerevisiae, Fe-acclimation responses are coordinated by functionally equivalent metalloregulatory proteins such as Aft1 and Aft2 (Philpott and Protchenko, 2008), whereas C. reinhardtii may use orthologs of the regulatory proteins found in Arabidopsis (Long et al., 2010).
Fur is representative of a large group of metalloregulators that sense metal ions such as Fe, Zn, Mn, and Ni to regulate metal homeostasis (Lee and Helmann, 2007). Typically, Fur family regulators act as metal-dependent transcriptional repressors (Delany et al., 2004). Under Fe-replete conditions, Fur binds Fe(II) and represses the expression of uptake function and activates the expression of Fe storage proteins. Conversely, when Fe levels drop, iron uptake functions are derepressed and pathways contributing to acclimation are induced. These pathways include iron acquisition systems and mobilization of intracellular stores.
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E. coli Iron Sparing Response:
Bacterial iron homeostasis in E. coli, regulated by Fur, is exceptionally well understood in E. coli (Hantke, 2001). Fur contributes to Fe homeostasis in numerous ways:
1. Fur directly represses, under replete conditions, Fe acquisition pathways.
2. Fur indirectly activates synthesis of the Fe-storage protein ferritin under Fe-replete conditions (Nandal et al., 2010).
3. Fur regulates RyhB, a small noncoding RNA (sRNA), with wide-ranging effects, which serves to remodel the proteome as part of a global Fe-sparing response. When cells are Fe limited, the Fur repressor is inactive and RyhB accumulates (Masse and Gottesman, 2002). RyhB, in turn, downregulates the synthesis of several abundant Fe-containing proteins.
4. Fur regulates the expression of enzymes that can substitute for what would otherwise be Fe-dependent pathways. This substitution includes replacing FeRNR with MnRNR and FeSOD with MnSOD (see #3 below).
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B. subtilis Iron Sparing Response:
B. subtilis also responds to Fe limitation with derepression of a large and complex regulon of genes controlled by Fur (Baichoo et al., 2002). The induced operons lead to the synthesis of siderophore (bacillibactin) and expression of transport systems for ferric-bacillibactin and other siderophores (Ollinger et al., 2006). In addition to these acquisition mechanisms, other operons function in Fe sparing by encoding proteins that can substitute for functions that might be disabled under Fe limitation. B. subtilis substitutes ferredoxins for flavodoxins.
B. subtilis has a robust Fe-sparing response that is dependent on an sRNA designated FsrA, which is repressed by Fur and similar in function to RhyB (Gaballa et al., 2008). Some of the notable FsrA-regulated targets that are downregulated
include SDH, and several other Fe/S-containing enzymes including aconitase, a lactate oxidase complex, glutamate synthase, and dehydratases involved in branched chain amino acid biosynthesis.
The B. subtilis Fe-sparing response differs from that of the enteric bacteria in that it also involves three small, basic (positively charged) proteins named FbpA, B, and C, which are postulated to function as Fur-regulated RNA chaperones. Fur, FsrA, Fbp proteins overlap in their specificity, and several FsrA targets are coregulated by one or more Fbp.
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S. cerevisiae Iron Sparing Response:
The primary response to Fe deprivation is the activation of the Aft1 and Aft2 transcription factors, which coordinate a multifaceted acclimation response that can reduce the cellular Fe quota by twofold or more. Most genes activated by Fe deprivation are under the transcriptional control of Aft1, which is translocated to the nucleus in response to declining Fe status. Aft1 coordinates the activation of a complex and multilayered Fe-sparing response:
1. Aft1 activates the transcription of genes for Fe acquisition and mobilization (Philpott and Protchenko, 2008), including many encoding high-affinity transporters for Fe-chelates and elemental Fe, as well as heme oxygenase Hmx1 that degrades heme.
2. Aft1 activates transcription of two RNA-binding proteins, Cth1 and Cth2, that target numerous mRNAs for functional inactivation (Puig et al., 2005, 2008). Cth2 downregulates many Fe-consuming processes including TCA cycle enzymes, mitochondrial respiration, fatty acid synthesis, heme biosynthesis, and Fe/S proteins. This spares Fe for more essential processes, likely including the synthesis of Fe/S cluster enzymes and an Fe-dependent RNR.
3. The metabolic changes resulting from both the direct and indirect effects of Aft1 alter the activity of other regulons in the cell that may also impact Fe homeostasis (Ihrig et al., 2010). For example, decreasing heme availability leads to downregulation of cytochrome c. Similarly, decreased activity of Fe/S-containing biosynthetic enzymes can lead to changes in metabolite pools that alter gene expression.
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(3) Substitution Mechanisms of the Iron Sparing Response
Ferrodoxins to Flavodoxins:
Perhaps the most widespread acclimation strategy for Fe limitation is replacement of the electron carrier protein ferredoxin with an Fe-free alternative, flavodoxin. The substitution of ferredoxin with flavodoxin allows the former to be actively degraded in order to release and recycle Fe for maintenance of pyruvate synthase, an Fe/S protein (Schönheit et al., 1979).
In Prochlorococcus, strains in very low Fe environments have reduced the number of ferredoxins and other Fe-requiring proteins encoded in the genome (Rusch et al., 2010).
However, a more common evolutionary strategy is to retain the genes for both ferredoxins and flavodoxins, but only express the former when Fe is relatively abundant. The Fe-regulated substitution of ferredoxin with flavodoxin as a major electron carrier has been noted in numerous organisms including a chlorophyte alga, several cyanobacterial species, cryptomonads, and diatoms. Although this Fe-sparing mechanism is widespread in microbes, it appears to have been lost in land plants, even though Fe can be a limiting nutrient in the soil environment (Yi and Guerinot, 1996).
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FeSOD to MnSOD and NiSOD:
The replacement of FeSOD by MnSOD is another widespread Fe-sparing mechanism in bacteria, algae, and diatoms. The two SODs evolved from a common ancestor and are structurally highly similar. In organisms adapted to the low Fe content of the open ocean, the use of MnSOD may contribute to their higher Mn quota (Peers and Price, 2004).
An adaptation that has emerged in some organisms faced with chronic Fe limitation is the evolution of NiSOD (SodN), a structurally distinct protein that can functionally replace FeSOD. Genes encoding SodN are widespread in the marine cyanobacteria and are correlated with the presence of urease, another Ni-requiring enzyme. Together, these two enzymes contribute to a Ni requirement for bacteria in the ocean (Dupont et al., 2008) while reducing the Fe quota.
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FeRNR to MnRNR:
The synthesis of deoxyribonucleotides is essential for DNA replication, and most bacterial RNRs contain Fe as an essential catalytic cofactor. In Fe-deficient E. coli cells, a Fur-regulated substitution pathway is used in which the nrdEF operon encodes an alternative, Mn-utilizing RNR to replace the Fe-dependent RNR that requires an Fe2S2 ferredoxin (Andrews, 2011). The Mn-dependent enzyme instead requires a flavodixin as an oxidant (Cotruvo and Stubbe, 2008).
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Biotin Synthesis to Transport:
In S. cerevisiae, the primary response to Fe deprivation is the activation of the Aft1 and Aft2 transcription factors, which coordinate a multifaceted acclimation response that can reduce the cellular Fe quota by twofold or more. One example of an Fe-sparing mechanism in this pathway is that Aft1 upregulates a biotin importer, which compensates for the transcriptional repression of biotin biosynthetic functions (including the Fe/S-containing Bio2 protein) under Fe deprivation.
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(4) Recycling Iron between N2 and Photosynthetic Enzymes
In many photosynthetic diazotrophs, photosynthesis and N2 fixation are separated in space or in time. In Crocosphaera watsonii, temporal separation of the two processes reduces the Fe quota. The sharing of intracellular Fe between nitrogenous metalloproteins and the Psa proteins of PSI and cytochromes by daily degradation of the iron proteins and recycling of the released Fe reduces the Fe requirement by 40% (Saito et al., 2011).
(5) Degradation of Fdx and PSI
The substitution of ferredoxin with flavodoxin allows the former to be actively degraded in order to release and recycle Fe for maintenance of pyruvate synthase (another Fe/S protein) (Schönheit et al., 1979).
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In C. reinhardtii, Fe is required for both photosynthesis (PSI) and respiration (ferredoxins). In a situation of respiratory growth, a program of Fe sparing in the chloroplast is activated (Moseley et al., 2002). This involves drastic loss of PS I and cytochrome complexes, as well as a less significant loss of ferredoxin. This is because ferredoxin is a high priority function, and C. reinhardtii does not encode a flavodoxin.