The crystal structure of FdxA, a 7Fe ferredoxin from Mycobacterium smegmatis

Ricagno, Stéfano; Rosa, Matteo de; Aliverti, Alessandro; Zanetti, G.; Bolognesi, Martino

doi:10.1016/j.bbrc.2007.06.013

Cited by 15 publications

(16 citation statements)

References 30 publications

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“…Ferredoxins are small, acidic proteins containing iron–sulphur clusters which act as multifunctional electron carriers in diverse redox systems. It has been suggested that M. tuberculosis FdxA protein may serve the tubercle bacteria as an electron carrier under hypoxia [18] or that it may play a role in maintaining DevS in its reduced functional state [19]. During the present study, we discovered the presence of a low‐scoring DevR binding site in the fdxA promoter in addition to the previously predicted site.…”

Section: Introductionsupporting

confidence: 66%

K182G substitution in DevR or C₈G mutation in the Dev box impairs protein–DNA interaction and abrogates DevR‐mediated gene induction in Mycobacterium tuberculosis

2011

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The DevR response regulator mediates adaptation of Mycobacterium tuberculosis to various signals that are likely to be encountered within the host such as hypoxia, nitric oxide, carbon monoxide and ascorbic acid. DevR is proposed as a promising target for developing drugs against dormant bacteria. It induces the expression of target genes by interacting with DNA motifs located in their promoter regions. An understanding of DNA–protein interactions is expected to facilitate the development of inhibitors targeting DevR. Only three amino acids in DevR, namely Lys179, Lys182 and Asn183, directly contact nucleotide bases in the DNA motif. The present study was designed to decipher the contribution of Lys182 in DevR function. M. tuberculosis fdxA (Rv2007c), a member of the DevR regulon, was selected for this analysis. Its transcriptional start point was mapped at −1 or −2 with respect to the putative translational start site suggesting that fdxA is expressed as a leaderless mRNA. DNase I footprinting led to the discovery of a secondary binding site and induction of the fdxA promoter is explained by the cooperative binding of DevR to two binding sites. Mutation of Lys182 lowers the DNA binding affinity of DevR and abrogates induction of fdxA and other regulon genes. Mutational analyses also highlight the singular importance of Lys182–G13 nucleotide interaction for DevR binding and regulon induction. Our findings demonstrate that impairment of Lys182‐mediated interactions alone abolishes DevR function and provide valuable insights for designing molecules that interfere with DevR‐mediated dormancy adaptation.

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Section: Introductionsupporting

confidence: 66%

K182G substitution in DevR or C₈G mutation in the Dev box impairs protein–DNA interaction and abrogates DevR‐mediated gene induction in Mycobacterium tuberculosis

2011

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“…The [4Fe-4S] Fds, whose cofactors can be damaged by O 2 (Hsueh et al, 2013) (Jagannathan and Golbeck, 2009), and (3) adoption of a [3Fe-4S] cluster as a redox cofactor rather than a [4Fe-4S] cluster (Tilley et al, 2001). Support for the last mechanism has come from successes in purifying Fds with [3Fe-4S] clusters that remain stable under aerobic conditions (Aono et al, 1989;Gomes et al, 1998;Ricagno et al, 2007). Additionally, some [4Fe-4S] clusters lose a single Fe atom when placed in an oxidizing atmosphere, rather than losing the entire cluster (Beinert et al, 1996;Tilley et al, 2001).…”

Section: Pec Usage Varies With Environment Nichementioning

confidence: 99%

“…PCC 6803 Fd (4KT0) (Mazor et al, 2013), Thauera aromatica Fd (1RGV) (Unciuleac et al, 2004), and Thermosynechococcus elongatus Fd (1JB0) (Jordan et al, 2001). The second mode corresponds to the hybrid [3Fe-4S][4Fe-4S] Fds in the PDB, such as Sulfolobus tokodaii Fd (1XER) (Fujii et al, 1996), Mycobacterium smegmatis Fd (2V2K) (Ricagno et al, 2007), and Azotobacter vinelandii Fd (7FDR) (Schipke et al, 1999).…”

Section: Pec Length Distributionsmentioning

confidence: 99%

Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers

2019

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Proteins from the ferredoxin (Fd) and flavodoxin (Fld) families function as low potential electrical transfer hubs in cells, at times mediating electron transfer between overlapping sets of oxidoreductases. To better understand protein electron carrier (PEC) use across the domains of life, we evaluated the distribution of genes encoding [4Fe-4S] Fd, [2Fe-2S] Fd, and Fld electron carriers in over 7,000 organisms. Our analysis targeted genes encoding small PEC genes encoding proteins having ≤200 residues. We find that the average number of small PEC genes per Archaea (∼13), Bacteria (∼8), and Eukarya (∼3) genome varies, with some organisms containing as many as 54 total PEC genes. Organisms fall into three groups, including those lacking genes encoding low potential PECs (3%), specialists with a single PEC gene type (20%), and generalists that utilize multiple PEC types (77%). Mapping PEC gene usage onto an evolutionary tree highlights the prevalence of [4Fe-4S] Fds in ancient organisms that are deeply rooted, the expansion of [2Fe-2S] Fds with the advent of photosynthesis and a concomitant decrease in [4Fe-4S] Fds, and the expansion of Flds in organisms that inhabit low-iron host environments. Surprisingly, [4Fe-4S] Fds present a similar abundance in aerobes as [2Fe-2S] Fds. This bioinformatic study highlights understudied PECs whose structure, stability, and partner specificity should be further characterized.

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“…Despite the uncertainty about the precise stimuli that stimulate MTB to enter a dormant state during human infection, recent work has shown convincingly that in vitro both hypoxia (Desjardin et al, 2001;Florczyk et al, 2001;Kendall et al, 2004a;Roberts et al, 2004a;Voskuil et al, 2004) and NO (Ohno et al, 2003;Purkayastha et al, 2002;Voskuil et al, 2003) induce ∼50 genes known as the dormancy regulon . Many of the genes of the dormancy regulon have unknown functions, but some genes have been characterized including an electron transporter, ferredoxin (fdxA) (Ricagno et al, 2007), a heat shock protein, α-crystallin (hspX or acr) (Hu et al, 2006) and an operon involved in nitrite and nitrate reduction, narK2X (Sohaskey and Wayne, 2003).…”

Section: Introductionmentioning

confidence: 99%

Mycobacterium tuberculosis Senses Host-Derived Carbon Monoxide during Macrophage Infection

Shiloh

Manzanillo

Cox

2008

Cell Host & Microbe

198

221

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Mycobacterium tuberculosis (MTB) expresses a set of genes known as the dormancy regulon in vivo. These genes are expressed in vitro in response to nitric oxide (NO) or hypoxia, conditions used to model MTB persistence in latent infection. Although NO, a macrophage product that inhibits respiration, and hypoxia are likely triggers in vivo, additional cues could activate the dormancy regulon during infection. Here, we show that MTB infection stimulates expression of heme oxygenase (HO-1) by macrophages and that the gaseous product of this enzyme, carbon monoxide (CO), activates expression of the dormancy regulon. Deletion of macrophage HO-1 reduced expression of the dormancy regulon. Furthermore, we show that the MTB DosS/DosT/DosR two-component sensory relay system is required for the response to CO. Together, these findings demonstrate that MTB senses CO during macrophage infection. CO may represent a general cue used by pathogens to sense and adapt to the host environment.

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The crystal structure of FdxA, a 7Fe ferredoxin from Mycobacterium smegmatis

Cited by 15 publications

References 30 publications

K182G substitution in DevR or C₈G mutation in the Dev box impairs protein–DNA interaction and abrogates DevR‐mediated gene induction in Mycobacterium tuberculosis

K182G substitution in DevR or C₈G mutation in the Dev box impairs protein–DNA interaction and abrogates DevR‐mediated gene induction in Mycobacterium tuberculosis

Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers

Mycobacterium tuberculosis Senses Host-Derived Carbon Monoxide during Macrophage Infection

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The crystal structure of FdxA, a 7Fe ferredoxin from Mycobacterium smegmatis

Cited by 15 publications

References 30 publications

K182G substitution in DevR or C8G mutation in the Dev box impairs protein–DNA interaction and abrogates DevR‐mediated gene induction in Mycobacterium tuberculosis

K182G substitution in DevR or C8G mutation in the Dev box impairs protein–DNA interaction and abrogates DevR‐mediated gene induction in Mycobacterium tuberculosis

Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers

Mycobacterium tuberculosis Senses Host-Derived Carbon Monoxide during Macrophage Infection

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K182G substitution in DevR or C₈G mutation in the Dev box impairs protein–DNA interaction and abrogates DevR‐mediated gene induction in Mycobacterium tuberculosis

K182G substitution in DevR or C₈G mutation in the Dev box impairs protein–DNA interaction and abrogates DevR‐mediated gene induction in Mycobacterium tuberculosis