The
            <i>Bacillus subtilis</i>
            iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins

Gaballa, Ahmed; Antelmann, Haike; Aguilar, Claudio; Khakh, Sukhjit K.; Song, Kyung-Bok; Smaldone, Gregory T.; Helmann, John D.

doi:10.1073/pnas.0711752105

Cited by 196 publications

(244 citation statements)

References 50 publications

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“…The presence of potential binding sites for other protein factors can also give clues to the regulatory process controlled by a particular RNA. For instance, for B. subtilis, this was reported for the Fur-dependent FsrA sRNA, which regulates the iron-sparing response (43), and the gluconeogenesis sRNA SR1, which is regulated by CcpA and CcpN (44).…”

Section: Clues For Predicting Regulatory Rna Functionsmentioning

confidence: 99%

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Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Mars

Nicolas

Denham

et al. 2016

Microbiol Mol Biol Rev

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SUMMARY Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans -acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5′ untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella . Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis . A recent study identified 1,583 putative regulatory RNAs in B. subtilis , whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis , and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5′ ends of mRNA molecules. These can include 5′ secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis . Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis .

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Section: Clues For Predicting Regulatory Rna Functionsmentioning

confidence: 99%

“…The sRNA FsrA/S512 is an important regulator of the ironsparing response of B. subtilis (43,100). FsrA/S512 thus serves to reduce the expression of proteins relating to iron metabolism and storage.…”

Section: Independently Expressed Small Rnas and Rna Antitoxinsmentioning

confidence: 99%

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Mars

Nicolas

Denham

et al. 2016

Microbiol Mol Biol Rev

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“…An interesting correlation has been emphasized between the number of positively charged amino acids (arginines or lysines) at the rim and the function of Hfq from Gram-positive bacteria in sRNA regulation (Panja et al 2013). Indeed, among the Hfq proteins studied in Gram-positive bacteria, L. monocytogenes Hfq carries the RKEK rim motif and stabilizes at least one sRNA-mRNA complex (Nielsen et al 2010(Nielsen et al , 2011, while B. subtilis Hfq having a RKEN motif associated with numerous RNAs was not required for sRNA regulation (Heidrich et al 2007;Gaballa et al 2008;Dambach et al 2013). The function of S. aureus Hfq carrying the KANQ rim motif remains unclear (Bohn et al 2007).…”

Section: Similarities and Differences Of Ec-hfq And Cd-hfqmentioning

confidence: 99%

Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function

Caillet

Gracia

Fontaine

et al. 2014

RNA

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A gene for the Hfq protein is present in the majority of sequenced bacterial genomes. Its characteristic hexameric ring-like core structure is formed by the highly conserved N-terminal regions. In contrast, the C-terminal forms an extension, which varies in length, lacks homology, and is predicted to be unstructured. In Gram-negative bacteria, Hfq facilitates the pairing of sRNAs with their mRNA target and thus affects gene expression, either positively or negatively, and modulates sRNA degradation. In Gram-positive bacteria, its role is still poorly characterized. Numerous sRNAs have been detected in many Gram-positive bacteria, but it is not yet known whether these sRNAs act in association with Hfq. Compared with all other Hfqs, the C. difficile Hfq exhibits an unusual C-terminal sequence with 75% asparagine and glutamine residues, while the N-terminal core part is more conserved. To gain insight into the functionality of the C. difficile Hfq (Cd-Hfq) protein in processes regulated by sRNAs, we have tested the ability of Cd-Hfq to fulfill the functions of the E. coli Hfq (Ec-Hfq) by examining various functions associated with Hfq in both positive and negative controls of gene expression. We found that Cd-Hfq substitutes for most but not all of the tested functions of the Ec-Hfq protein. We also investigated the role of the C-terminal part of the Hfq proteins. We found that the C-terminal part of both Ec-Hfq and Cd-Hfq is not essential but contributes to some functions of both the E. coli and C. difficile chaperons.

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“…Because of the importance of iron to the function of heme-containing cytochromes in the respiratory apparatus (Gaballa et al 2008), we wondered whether matrix production would be sensitive to levels of iron in the medium. While iron clearly can have many effects on cellular physiology, we reasoned that one of the effects of having low amounts of iron accessible to cells might lead to defects in the assembly of the cytochromes in the respiratory apparatus.…”

Section: Impaired Respiration Stimulates Wrinkling and Matrix Gene Exmentioning

confidence: 99%

Respiration control of multicellularity in Bacillus subtilis by a complex of the cytochrome chain with a membrane-embedded histidine kinase

Kolodkin‐Gal¹,

Elsholz²,

Muth³

et al. 2013

Genes Dev.

130

132

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Bacillussubtilis forms organized multicellular communities known as biofilms wherein the individual cells are held together by a self-produced extracellular matrix. The environmental signals that promote matrix synthesis remain largely unknown. We discovered that one such signal is impaired respiration. Specifically, high oxygen levels suppressed synthesis of the extracellular matrix. In contrast, low oxygen levels, in the absence of an alternative electron acceptor, led to increased matrix production. The response to impaired respiration was blocked in a mutant lacking cytochromes caa3 and bc and markedly reduced in a mutant lacking kinase KinB. Mass spectrometry of proteins associated with KinB showed that the kinase was in a complex with multiple components of the aerobic respiratory chain. We propose that KinB is activated via a redox switch involving interaction of its second transmembrane segment with one or more cytochromes under conditions of reduced electron transport. In addition, a second kinase (KinA) contributes to the response to impaired respiration. Evidence suggests that KinA is activated by a decrease in the nicotinamide adenine dinucleotide (NAD+)/NADH ratio via binding of NAD+ to the kinase in a PAS domain A-dependent manner. Thus, B. subtilis switches from a unicellular to a multicellular state by two pathways that independently respond to conditions of impaired respiration.

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The Bacillus subtilis iron-sparing response is mediated by a Fur-regulated small RNA and three small, basic proteins

Cited by 196 publications

References 50 publications

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Clostridium difficile Hfq can replace Escherichia coli Hfq for most of its function

Respiration control of multicellularity in Bacillus subtilis by a complex of the cytochrome chain with a membrane-embedded histidine kinase

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