Redox reactions pervade living cells. They are central to both anabolic and catabolic metabolism. The ability to maintain redox balance is therefore vital to all organisms. Various regulatory sensors continually monitor the redox state of the internal and external environments and control the processes that work to maintain redox homeostasis. In response to redox imbalance, new metabolic pathways are initiated, the repair or bypassing of damaged cellular components is coordinated and systems that protect the cell from further damage are induced. Advances in biochemical analyses are revealing a range of elegant solutions that have evolved to allow bacteria to sense different redox signals.

Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2–4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor.

We describe the identi®cation of Rex, a novel redoxsensing repressor that appears to be widespread among Gram-positive bacteria. In Streptomycescoelicolor Rex binds to operator (ROP) sites located upstream of several respiratory genes, including the cydABCD and rex-hemACD operons. The DNA-binding activity of Rex appears to be controlled by the redox poise of the NADH/NAD + pool. Using electromobility shift and surface plasmon resonance assays we show that NADH, but not NAD + , inhibits the DNAbinding activity of Rex. However, NAD + competes with NADH for Rex binding, allowing Rex to sense redox poise over a range of NAD(H) concentrations. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved. In support of this, the central glycine in the signature motif (GlyXGlyXXGly) is shown to be essential for redox sensing. Rex homologues exist in most Gram-positive bacteria, including human pathogens such as Staphylococcus aureus, Listeria monocytogenes and Streptococcus pneumoniae.

SummaryMembers of the 70 family of sigma factors are components of the RNA polymerase holoenzyme that direct bacterial or plastid core RNA polymerase to specific promoter elements that are situated 10 and 35 base-pairs upstream of transcription-initiation points. Members of the 70 family also function as contact points for some activator proteins, such as PhoB and cI, and play a role in the initiation process itself. The primary factor, which is essential for general transcription in exponentially growing cells, is reversibly associated with RNA polymerase and can be replaced by alternative factors that co-ordinately express genes involved in diverse functions, such as stress responses, morphological development and iron uptake. On the basis of gene structure and function, members of the 70 family can broadly be divided into four main groups. Sequence alignments of the 70 family members reveal that they have four conserved regions, although the highest conservation is found in regions 2 and 4, which are involved in binding to RNA polymerase, recognizing promoters and separating DNA strands (so-called 'DNA melting'). The division of the linear sequence of 70 factors into four regions is largely supported by recent structural data indicating that primary factors have three stable domains that incorporate regions 2, 3 and 4. Furthermore, structures of the RNA polymerase holoenzyme have revealed that these domains of 70 are spread out across one face of RNA polymerase. These structural data are starting to illuminate the mechanistic role of factors in transcription initiation. Gene organization and evolutionary historyThe bacterial core RNA polymerase complex, which consists of five subunits (␤␤␣ 2 ), is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme. The vast majority of factors belong to the so-called 70 family, reflecting their relationship to the principal factor of Escherichia coli, 70 . A second family of factors, the 54 family, comprises proteins that are functionally similar to, but structurally distinct from, 70 of E. coli. Here, we limit ourselves to the 70 family.Members of the 70 family direct RNA polymerase to specific promoter elements that are usually 5-6 base-pairs (bp) in length and are centred 10 and 35 bp upstream (positions -10 and -35) of the transcription initiation site. They also function in the melting of promoter DNA and the early stages of elongation of transcripts. The discovery of the factor as a dissociable RNA polymerase subunit [1] heralded the subsequent finding that RNA polymerase recruits alternative factors as a means of switching on specific regulons [2]. Multiple members of the 70 family have since been discovered in most bacteria, with up to 63 encoded by a single genome, in the case of the antibiotic-producing bacterium Streptomyces coelicol...

We have identified an RNA polymerase sigma factor, sigmaR, that is part of a system that senses and responds to thiol oxidation in the Gram-positive, antibiotic-producing bacterium Streptomyces coelicolor A3(2). Deletion of the gene (sigR) encoding sigmaR caused sensitivity to the thiol-specific oxidant diamide and to the redox cycling compounds menadione and plumbagin. This correlated with reduced levels of disulfide reductase activity and an inability to induce this activity on exposure to diamide. The trxBA operon, encoding thioredoxin reductase and thioredoxin, was found to be under the direct control of sigmaR. trxBA is transcribed from two promoters, trxBp1 and trxBp2, separated by 5-6 bp. trxBp1 is transiently induced at least 50-fold in response to diamide treatment in a sigR-dependent manner. Purified sigmaR directed transcription from trxBp1 in vitro, indicating that trxBp1 is a target for sigmaR. Transcription of sigR itself initiates at two promoters, sigRp1 and sigRp2, which are separated by 173 bp. The sigRp2 transcript was undetectable in a sigR-null mutant, and purified sigmaR could direct transcription from sigRp2 in vitro, indicating that sigR is positively autoregulated. Transcription from sigRp2 was also transiently induced (70-fold) following treatment with diamide. We propose a model in which sigmaR induces expression of the thioredoxin system in response to cytoplasmic disulfide bond formation. Upon reestablishment of normal thiol levels, sigmaR activity is switched off, resulting in down-regulation of trxBA and sigR. We present evidence that the sigmaR system also functions in the actinomycete pathogen Mycobacterium tuberculosis.