The mycobacterial IdeR protein is a metal-dependent regulator of the DtxR (diphtheria toxin repressor) family. In the presence of iron, it binds to a specific DNA sequence in the promoter regions of the genes that it regulates, thus controlling their transcription. In this study, we provide evidence that ideR is an essential gene in Mycobacterium tuberculosis. ideR cannot normally be disrupted in this mycobacterium in the absence of a second functional copy of the gene. However, a rare ideR mutant was obtained in which the lethal effects of ideR inactivation were alleviated by a second-site suppressor mutation and which exhibited restricted iron assimilation capacity. Studies of this strain and a derivative in which IdeR expression was restored allowed us to identify phenotypic effects resulting from ideR inactivation. Using DNA microarrays, the iron-dependent transcriptional profiles of the wild-type, ideR mutant, and ideR-complemented mutant strains were analyzed, and the genes regulated by iron and IdeR were identified. These genes encode a variety of proteins, including putative transporters, proteins involved in siderophore synthesis and iron storage, members of the PE/PPE family, a membrane protein involved in virulence, transcriptional regulators, and enzymes involved in lipid metabolism.

The proteins belonging to the Fur family are global regulators of gene expression involved in the response to several environmental stresses and to the maintenance of divalent cation homeostasis. The Mycobacterium tuberculosis genome encodes two Fur-like proteins, FurA and a protein formerly annotated FurB. Since in this paper we show that it represents a zinc uptake regulator, we refer to it as Zur. The gene encoding Zur is found in an operon together with the gene encoding a second transcriptional regulator (Rv2358). In a previous work we demonstrated that Rv2358 is responsible for the zinc-dependent repression of the Rv2358-zur operon, favoring the hypothesis that these genes represent key regulators of zinc homeostasis. In this study we generated a zur mutant in M. tuberculosis, examined its phenotype, and characterized the Zur regulon by DNA microarray analysis. Thirty-two genes, presumably organized in 16 operons, were found to be upregulated in the zur mutant. Twenty-four of them belonged to eight putative transcriptional units preceded by a conserved 26-bp palindrome. Electrophoretic mobility shift experiments demonstrated that Zur binds to this palindrome in a zinc-dependent manner, suggesting its direct regulation of these genes. The proteins encoded by Zurregulated genes include a group of ribosomal proteins, three putative metal transporters, the proteins belonging to early secretory antigen target 6 (ESAT-6) cluster 3, and three additional proteins belonging to the ESAT-6/culture filtrate protein 10 (CFP-10) family known to contain immunodominant epitopes in the T-cell response to M. tuberculosis infection.Mycobacterium tuberculosis is a human pathogen that infects and replicates within macrophages. This microorganism lives in phagosomes that fail to fuse with lysosomes and has adapted its lifestyle to survive and replicate in the changing environment within the endosomal system (20).The long-recognized phenomenon of nutritional immunity, in which sequestration of iron and possibly other metals occurs as a nonspecific host response to infection (2), hints in general terms at the possibility of a keen competition between host and parasite for essential metal ions. A critical point is the bacterial ability to compete with the host for nutrients, and the acquisition of metal ions has important implications for intracellular survival.Pathogenic bacteria respond to such limitations by inducing metabolic functions that overcome nutritional deficiencies and/or inducing virulence functions required for immediate survival and spread to subsequent anatomical sites of infection. The outcome of this competition between the host cell and the microorganism is certainly one of the most important factors determining the ability of pathogens to multiply and cause disease (41).Metalloregulatory proteins sense the intracellular levels of specific metal ions and mediate a transcriptional response aimed at restoring homeostasis when these levels are altered. In prokaryotes, these transcriptional regulators are clustered...

Iron availability affects the course of tuberculosis infection, and the ability to acquire this metal is known to be essential for replication of Mycobacterium tuberculosis in human macrophages. M. tuberculosis overcomes iron deficiency by producing siderophores. The relevance of siderophore synthesis for iron acquisition by M. tuberculosis has been demonstrated, but the molecules involved in iron uptake are currently unknown. We have identified two genes (irtA and irtB) encoding an ABC transporter similar to the YbtPQ system involved in iron transport in Yersinia pestis. Inactivation of the irtAB system decreases the ability of M. tuberculosis to survive iron-deficient conditions. IrtA and -B do not participate in siderophore synthesis or secretion but are required for efficient utilization of iron from Fe-carboxymycobactin, as well as replication of M. tuberculosis in human macrophages and in mouse lungs. We postulate that IrtAB is a transporter of Fe-carboxymycobactin. The irtAB genes are located in a chromosomal region previously shown to contain genes regulated by iron and the major iron regulator IdeR. Taken together, our results and previous observations made by other groups regarding two other genes in this region indicate that this gene cluster is dedicated to siderophore synthesis and transport in M. tuberculosis.

In this work, we characterize genes in Mycobacterium tuberculosis that are regulated by IdeR (iron‐dependent regulator), an iron‐responsive DNA‐binding protein of the DtxR family that has been shown to regulate iron acquisition in Mycobacterium smegmatis. To identify some of the genes that constitute the IdeR regulon, we searched the M. tuberculosis genome for promoter regions containing the consensus IdeR/DxR binding sequence. Genes preceded by IdeR boxes included a set encoding proteins necessary for iron acquisition, such as the biosynthesis of siderophores (mbtA, mbtB, mbtI), aromatic amino acids (pheA, hisE, hisB‐like) and others annotated to be involved in the synthesis of iron‐storage proteins (bfrA, bfrB). Some putative IdeR‐regulated genes identified in this search encoded proteins predicted to be engaged in the biosynthesis of lipopolysaccharide (LPS)‐like molecules (rv3402c), lipids (acpP) and peptidoglycan (murB). We analysed four promoter regions containing putative IdeR boxes, mbtA–mbtB, mbI, rv3402c and bfrA–bfd, for interaction with IdeR and for iron‐dependent expression. Gel retardation experiments and DNase footprinting analyses with purified IdeR showed that IdeR binds to these IdeR boxes in vitro. Analysis of the promoters by primer extension indicated that the IdeR boxes are located near the −10 position of each promoter, suggesting that IdeR acts as a transcriptional repressor by blocking RNA polymerase binding. Using quantitative reverse transcriptase–polymerase chain reaction (RT–PCR) coupled to molecular beacons, we showed that mRNA levels of mbtA, mbtB, mbtI, rv3402c and bfd are induced 14‐ to 49‐fold in cultures of M. tuberculosis starved for iron, whereas mRNA levels of bfrA decreased about threefold. We present evidence that IdeR not only acts as a transcriptional repressor but also functions as an activator of bfrA. Three of the IdeR‐ and iron‐repressed genes, mbtB, mbtI and rv3402c, were induced during M. tuberculosis infection of human THP‐1 macrophages.

dMycobacterium tuberculosis releases membrane vesicles packed with molecules that can modulate the immune response. Because environmental conditions often influence the production and content of bacterial vesicles, this study examined M. tuberculosis microvesicles released under iron limitation, a common condition faced by pathogens inside the host. The findings indicate that M. tuberculosis increases microvesicle production in response to iron restriction and that these microvesicles contain mycobactin, which can serve as an iron donor and supports replication of iron-starved mycobacteria. Consequently, the results revealed a role of microvesicles in iron acquisition in M. tuberculosis, which can be critical for survival in the host. The production of extracellular vesicles and vesicle-mediated communication is evolutionarily conserved among unicellular and multicellular organisms. Bacteria release membrane vesicles (MVs) containing proteins, genetic material, and lipids as a way to interact with prokaryotic and eukaryotic cells in their environment. Mycobacteria, including Mycobacterium tuberculosis, the causative agent of tuberculosis, release MVs in culture, in macrophages, and in the lungs of infected mice (1). MVs released by M. tuberculosis in culture are packed with immunologically active molecules that can modulate the immune response to the benefit of the bacterium (1). MV production by M. tuberculosis has recently been shown to be under genetic control (2).Environmental factors, including those encountered by pathogens during infection, often influence the production and composition of outer membrane vesicles released by Gram-negative bacteria (3). Iron limitation is a well-recognized hallmark of the host environment. Due to its poor solubility in water in the presence of oxygen and at neutral pH, ferric iron is not found free but rather is sequestered in complexes with host iron binding proteins, such as transferrin, lactoferrin, and ferritin (4). For this reason, and because iron is essential for cell vitality, high-affinity iron acquisition systems are critical for pathogens to proliferate during infection. In fact, competition for iron deeply influences host-pathogen interactions. On one hand, rapid withdrawal of accessible iron is the most prominent example of "nutritional immunity"; on the other hand, iron deficiency in the host is a signal for pathogens to induce the expression of toxins and other virulence factors in conjunction with iron acquisition systems (5). To obtain iron, M. tuberculosis synthesizes and secretes high-affinity iron chelators or siderophores named mycobactins, which are essential for virulence (6, 7). Two forms of mycobactins are produced: carboxymycobactin, an amphiphilic molecule that is secreted into the medium, and mycobactin, a lipophilic molecule that remains cell associated (8). These two siderophores share a core but differ mainly in the length of an alkyl substitution; carboxymycobactin has a short one (2 to 9 carbons), whereas a long one (10 to 21 carbons) chara...

This study was conducted to investigate the role of iron deprivation in the persistence of Mycobacterium tuberculosis. We present evidence of iron restriction in human necrotic granulomas and demonstrate that under iron starvation M. tuberculosis persists, refractive to antibiotics and capable of restarting replication when iron is made available. Transcriptomics and metabolomic analyses indicated that the persistence of M. tuberculosis under iron starvation is dependent on strict control of endogenous Fe utilization and is associated with upregulation of pathogenicity and intrinsic antibiotic resistance determinants. M. tuberculosis mutants compromised in their ability to survive Fe starvation were identified. The findings of this study advance the understanding of the physiological settings that may underpin the chronicity of human tuberculosis (TB) and are relevant to the design of effective antitubercular therapies.

SummaryThe role of iron in mycobacteria as in other bacteria goes beyond the need for this essential cofactor. Limitation of this metal triggers an extensive response aimed at increasing iron acquisition while coping with iron deficiency. In contrast, iron-rich environments prompt these prokaryotes to induce synthesis of iron storage molecules and to increase mechanisms of protection against iron-mediated oxidative damage. The response to changes in iron availability is strictly regulated in order to maintain sufficient but not excessive and potentially toxic levels of iron in the cell. This response is also linked to other important processes such as protection against oxidative stress and virulence. In bacteria, iron metabolism is regulated by controlling transcription of genes involved in iron uptake, transport and storage. In mycobacteria, this role is fulfilled by the iron-dependent regulator IdeR. IdeR is an essential protein in Mycobacterium tuberculosis , the causative agent of human tuberculosis. It functions as a repressor of iron acquisition genes, but is also an activator of iron storage genes and a positive regulator of oxidative stress responses.

ABSTRACTIron is an essential, elusive, and potentially toxic nutrient for most pathogens, includingMycobacterium tuberculosis. Due to the poor solubility of ferric iron under aerobic conditions, free iron is not found in the host.M. tuberculosisrequires specialized iron acquisition systems to replicate and cause disease. It also depends on a strict control of iron metabolism and intracellular iron levels to prevent iron-mediated toxicity. Under conditions of iron sufficiency,M. tuberculosisrepresses iron acquisition and induces iron storage, suggesting an important role for iron storage proteins in iron homeostasis.M. tuberculosissynthesizes two iron storage proteins, a ferritin (BfrB) and a bacterioferritin (BfrA). The individual contributions of these proteins to the adaptive response ofM. tuberculosisto changes in iron availability are not clear. By generating individual knockout strains ofbfrAandbfrB, the contribution of each one of these proteins to the maintenance of iron homeostasis was determined. The effect of altered iron homeostasis, resulting from impaired iron storage, on the resistance ofM. tuberculosistoin vitroandin vivostresses was examined. The results show that ferritin is required to maintain iron homeostasis, whereas bacterioferritin seems to be dispensable for this function.M. tuberculosislacking ferritin suffers from iron-mediated toxicity, is unable to persist in mice, and, most importantly, is highly susceptible to killing by antibiotics, showing that endogenous oxidative stress can enhance the antibiotic killing of this important pathogen. These results are relevant for the design of new therapeutic strategies againstM. tuberculosis.