Specialized osmotic stress response systems involve multiple SigB-like sigma factors in Streptomyces coelicolor

Machine-Learning Analysis of Streptomyces coelicolor Transcriptomes Reveals a Transcription Regulatory Network Encompassing Biosynthetic Gene Clusters

Streptomyces produces diverse secondary metabolites of biopharmaceutical importance, yet the rate of biosynthesis of these metabolites is often hampered by complex transcriptional regulation. Therefore, a fundamental understanding of transcriptional regulation in Streptomyces is key to fully harness its genetic potential. Here, independent component analysis (ICA) of 454 high-quality gene expression profiles of the model species Streptomyces coelicolor is performed, of which 249 profiles are newly generated for S. coelicolor cultivated on 20 different carbon sources and 64 engineered strains with overexpressed sigma factors. ICA of the transcriptome dataset reveals 117 independently modulated groups of genes (iModulons), which account for 81.6% of the variance in the dataset. The genes in each iModulon are involved in specific cellular responses, which are often transcriptionally controlled by specific regulators. Also, iModulons accurately predict 25 secondary metabolite biosynthetic gene clusters encoded in the genome. This systemic analysis leads to reveal the functions of previously uncharacterized genes, putative regulons for 40 transcriptional regulators, including 30 sigma factors, and regulation of secondary metabolism via phosphate- and iron-dependent mechanisms in S. coelicolor. ICA of large transcriptomic datasets thus enlightens a new and fundamental understanding of transcriptional regulation of secondary metabolite synthesis along with interconnected metabolic processes in Streptomyces.

Multiple SigB homologues govern the transcription of the ssgBp promoter in the sporulation-specific ssgB gene in Streptomyces coelicolor A3(2)

Unlike Bacillus subtilis, Streptomyces coelicolor contains nine SigB homologues of the stress-response sigma factor SigB. By using a two-plasmid system, we previously identified promoters recognized by these sigma factors. Almost all promoters were recognized by several SigB homologues. However, no specific sequences of these promoters were found. One of these promoters, ssgBp, was selected to examine this cross-recognition in the native host. It controls the expression of the sporulation-specific gene ssgB. Using a luciferase reporter, the activity of this promoter in S. coelicolor and nine mutant strains lacking individual sigB homologous genes showed that sgBp is dependent on three sigma factors, SigH, SigN, and SigI. To determine which nucleotides in the-10 region are responsible for the selection of a specific SigB homologue, promoters mutated at the last three nucleotide positions were tested in the two-plasmid system. Some mutant promoters were specifically recognized by a distinct set of SigB homologues. Analysis of these mutant promoters in the native host showed the role of these nucleotides. A conserved nucleotide A at position 5 was essential for promoter activity, and two variable nucleotides at positions 4 and 6 were responsible for the partial selectivity of promoter recognition by SigB homologues.

Sigma Factor Engineering in Actinoplanes sp. SE50/110: Expression of the Alternative Sigma Factor Gene ACSP50_0507 (σHAs) Enhances Acarbose Yield and Alters Cell Morphology

Sigma factors are transcriptional regulators that are part of complex regulatory networks for major cellular processes, as well as for growth phase-dependent regulation and stress response. Actinoplanes sp. SE50/110 is the natural producer of acarbose, an α-glucosidase inhibitor that is used in diabetes type 2 treatment. Acarbose biosynthesis is dependent on growth, making sigma factor engineering a promising tool for metabolic engineering. ACSP50_0507 is a homolog of the developmental and osmotic-stress-regulating Streptomyces coelicolor σHSc. Therefore, the protein encoded by ACSP50_0507 was named σHAs. Here, an Actinoplanes sp. SE50/110 expression strain for the alternative sigma factor gene ACSP50_0507 (sigHAs) achieved a two-fold increased acarbose yield with acarbose production extending into the stationary growth phase. Transcriptome sequencing revealed upregulation of acarbose biosynthesis genes during growth and at the late stationary growth phase. Genes that are transcriptionally activated by σHAs frequently code for secreted or membrane-associated proteins. This is also mirrored by the severely affected cell morphology, with hyperbranching, deformed and compartmentalized hyphae. The dehydrated cell morphology and upregulation of further genes point to a putative involvement in osmotic stress response, similar to its S. coelicolor homolog. The DNA-binding motif of σHAs was determined based on transcriptome sequencing data and shows high motif similarity to that of its homolog. The motif was confirmed by in vitro binding of recombinantly expressed σHAs to the upstream sequence of a strongly upregulated gene. Autoregulation of σHAs was observed, and binding to its own gene promoter region was also confirmed.

Osmotic stress responses and the biology of the second messenger c-di-AMP in Streptomyces

Streptomyces are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how Streptomyces react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of Streptomyces' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, S. coelicolor and S. venezuelae.

Spaceflight Changes the Production and Bioactivity of Secondary Metabolites in Beauveria bassiana

Studies on microorganism response spaceflight date back to 1960. However, nothing conclusive is known concerning the effects of spaceflight on virulence and environmental tolerance of entomopathogenic fungi; thus, this area of research remains open to further exploration. In this study, the entomopathogenic fungus Beauveria bassiana (strain SB010) was exposed to spaceflight (ChangZheng 5 space shuttle during 5 May 2020 to 8 May 2020) as a part of the Key Research and Development Program of Guangdong Province, China, in collaboration with the China Space Program. The study revealed significant differences between the secondary metabolite profiles of the wild isolate (SB010) and the spaceflight-exposed isolate (BHT021, BH030, BHT098) of B. bassiana. Some of the secondary metabolites/toxins, including enniatin A2, brevianamide F, macrosporin, aphidicolin, and diacetoxyscirpenol, were only produced by the spaceflight-exposed isolate (BHT021, BHT030). The study revealed increased insecticidal activities for of crude protein extracts of B. bassiana spaceflight mutants (BHT021 and BH030, respectively) against Megalurothrips usitatus 5 days post application when compared crude protein extracts of the wild isolate (SB010). The data obtained support the idea of using space mutation as a tool for development/screening of fungal strains producing higher quantities of secondary metabolites, ultimately leading to increased toxicity/virulence against the target insect host.

RIViT-seq enables systematic identification of regulons of transcriptional machineries

Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcription factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is laborious and not scalable. Here, we demonstrate regulon identification by in vitro transcription-sequencing (RIViT-seq) that enables systematic identification of regulons of transcription factors by combining an in vitro transcription assay and RNA-sequencing. Using this technology, target genes of 11 sigma factors were identified in Streptomyces coelicolor A3(2). The RIViT-seq data expands the transcriptional regulatory network in this bacterium, discovering regulatory cascades and crosstalk between sigma factors. Implementation of RIViT-seq with other transcription factors and in other organisms will improve our understanding of transcriptional regulatory networks across biology.

Cross-Recognition of Promoters by the Nine SigB Homologues Present in Streptomyces coelicolor A3(2)

In contrast to Bacillus subtilis, Streptomyces coelicolor A3(2) contains nine homologues of stress response sigma factor SigB with a major role in differentiation and osmotic stress response. The aim of this study was to further characterize these SigB homologues. We previously established a two-plasmid system to identify promoters recognized by sigma factors and used it to identify promoters recognized by the three SigB homologues, SigF, SigG, and SigH from S. coelicolor A3(2). Here, we used this system to identify 14 promoters recognized by SigB. The promoters were verified in vivo in S. coelicolor A3(2) under osmotic stress conditions in sigB and sigH operon mutants, indicating some cross-recognition of these promoters by these two SigB homologues. This two-plasmid system was used to examine the recognition of all identified SigB-, SigF-, SigG-, and SigH-dependent promoters with all nine SigB homologues. The results confirmed this cross-recognition. Almost all 24 investigated promoters were recognized by two or more SigB homologues and data suggested some distinguishing groups of promoters recognized by these sigma factors. However, analysis of the promoters did not reveal any specific sequence characteristics for these recognition groups. All promoters showed high similarity in the -35 and -10 regions. Immunoblot analysis revealed the presence of SigB under osmotic stress conditions and SigH during morphological differentiation. Together with the phenotypic analysis of sigB and sigH operon mutants in S. coelicolor A3(2), the results suggest a dominant role for SigB in the osmotic stress response and a dual role for SigH in the osmotic stress response and morphological differentiation. These data suggest a complex regulation of the osmotic stress response in relation to morphological differentiation in S. coelicolor A3(2).

Genome sequence and annotation of Streptomyces tendae UTMC 3329, acid and alkaline tolerant actinobacterium

BACKGROUND AND OBJECTIVES

Streptomyces tendae is one of the most prolific actinobacteria with a wide range of biotechnological applications. Genomic data can help in better understanding and exploration of important microorganisms, however, there is a few genomic information available for this species.

MATERIALS AND METHODS

Molecular identification, pH and salt tolerance of an actinobacterium, designated Streptomyces tendae UTMC 3329, isolated from a tea field soil were done. Also, genomic DNA was extracted and sequenced using Illumina platform with MPS (massively parallel sequencing) Illumina technology. Gene annotation and bioinformatic analysis were done using appropriate software and servers.

RESULTS

The draft genome is ∼8.7 megabase pairs, containing 7557 predicted coding sequences. The strain was able to grow at pH 5-12 and 0-10% NaCl. The maximum growth rate of the bacterium was obtained at pH 7. The gene clusters involved in central carbon metabolism, phosphate regulation, transport system, stress responses were revealed. It was shown the presence of gene clusters of polyketides, ribosomally and non-ribosomally synthesized peptides. Various genes were found in xenobiotic degradation pathways and heavy metal resistance.

CONCLUSION

The current genomic information which reveals biological features, as well as the biotechnological potential of this acid and alkaline tolerant actinobacterium, can be implemented for further research on the species.

Pleiotropic anti-anti-sigma factor BldG is phosphorylated by several anti-sigma factor kinases in the process of activating multiple sigma factors in Streptomyces coelicolor A3(2)

The anti-anti-sigma factor BldG has a pleiotropic function in Streptomyces coelicolor A3(2), regulating both morphological and physiological differentiation. Together with the anti-sigma factor UshX, it participates in a partner-switching activation of the sigma factor σ^H, which has a dual role in the osmotic stress response and morphological differentiation in S. coelicolor A3(2). In addition to UshX, BldG also interacts with the anti-sigma factor ApgA, although no target sigma factor has yet been identified. However, neither UshX nor ApgA phosphorylates BldG. This phosphorylation is provided by the anti-sigma factor RsfA, which is specific for the late developmental sigma factor σ^F. However, BldG is phosphorylated in the rsfA mutant, suggesting that some other anti-sigma factors containing HATPase_c kinase domain are capable to phosphorylate BldG in vivo. Bacterial two-hybrid system (BACTH) was therefore used to investigate the interactions of all suitable anti-sigma factors of S. coelicolor A3(2) with BldG. At least 15 anti-sigma factors were found to interact with BldG. These interactions were confirmed by native PAGE. In addition to RsfA, BldG is specifically phosphorylated on the conserved phosphorylation Ser57 residue by at least seven additional anti-sigma factors. However, only one of them, SCO7328, has been shown to interact with three sigma factors, σ^G, σ^K and σ^M. A mutant with deleted SCO7328 gene was prepared in S. coelicolor A3(2), however, no specific function of SCO7328 in growth, differentiation or stress response could be attributed to this anti-sigma factor. These results suggest that BldG is specifically phosphorylated by several anti-sigma factors and it plays a role in the regulation of several sigma factors in S. coelicolor A3(2). This suggests a complex regulation of the stress response and differentiation in S. coelicolor A3(2) through this pleiotropic anti-sigma factor.

Effects of spaceflight and simulated microgravity on microbial growth and secondary metabolism

Spaceflight and ground-based microgravity analog experiments have suggested that microgravity can affect microbial growth and metabolism. Although the effects of microgravity and its analogs on microorganisms have been studied for more than 50 years, plausible conflicting and diverse results have frequently been reported in different experiments, especially regarding microbial growth and secondary metabolism. Until now, only the responses of a few typical microbes to microgravity have been investigated; systematic studies of the genetic and phenotypic responses of these microorganisms to microgravity in space are still insufficient due to technological and logistical hurdles. The use of different test strains and secondary metabolites in these studies appears to have caused diverse and conflicting results. Moreover, subtle changes in the extracellular microenvironments around microbial cells play a key role in the diverse responses of microbial growth and secondary metabolisms. Therefore, "indirect" effects represent a reasonable pathway to explain the occurrence of these phenomena in microorganisms. This review summarizes current knowledge on the changes in microbial growth and secondary metabolism in response to spaceflight and its analogs and discusses the diverse and conflicting results. In addition, recommendations are given for future studies on the effects of microgravity in space on microbial growth and secondary metabolism.

Connecting Metabolic Pathways: Sigma Factors in Streptomyces spp

The gram-positive filamentous bacterium Streptomyces is one of the largest resources for bioactive metabolites, particularly antibiotics. Antibiotic production and other metabolic processes are tightly regulated at the transcriptional level. Sigma (σ) factors are components of bacterial RNA polymerases that determine promoter specificity. In Streptomyces, σ factors also play essential roles in signal transduction and in regulatory networks, thereby assisting in their survival in complex environments. However, our current understanding of σ factors in Streptomyces is still limited. In this mini-review, we demonstrate the roles of Streptomyces σ factors, illustrating that these serve as linkers of different metabolic pathways. Further investigations on σ factors may improve our knowledge of Streptomyces physiology and benefit exploitation of Streptomyces resources.

Cell-Biological Studies of Osmotic Shock Response in Streptomyces spp

Most bacteria are likely to face osmotic challenges, but there is yet much to learn about how such environmental changes affect the architecture of bacterial cells. Here, we report a cell-biological study in model organisms of the genus Streptomyces, which are actinobacteria that grow in a highly polarized fashion to form branching hyphae. The characteristic apical growth of Streptomyces hyphae is orchestrated by protein assemblies, called polarisomes, which contain coiled-coil proteins DivIVA and Scy, and recruit cell wall synthesis complexes and the stress-bearing cytoskeleton of FilP to the tip regions of the hyphae. We monitored cell growth and cell-architectural changes by time-lapse microscopy in osmotic upshift experiments. Hyperosmotic shock caused arrest of growth, loss of turgor, and hypercondensation of chromosomes. The recovery period was protracted, presumably due to the dehydrated state of the cytoplasm, before hyphae could restore their turgor and start to grow again. In most hyphae, this regrowth did not take place at the original hyphal tips. Instead, cell polarity was reprogrammed, and polarisomes were redistributed to new sites, leading to the emergence of multiple lateral branches from which growth occurred. Factors known to regulate the branching pattern of Streptomyces hyphae, such as the serine/threonine kinase AfsK and Scy, were not involved in reprogramming of cell polarity, indicating that different mechanisms may act under different environmental conditions to control hyphal branching. Our observations of hyphal morphology during the stress response indicate that turgor and sufficient hydration of cytoplasm are required for Streptomyces tip growth.

IMPORTANCE

Polar growth is an intricate manner of growth for accomplishing a complicated morphology, employed by a wide range of organisms across the kingdoms of life. The tip extension of Streptomyces hyphae is one of the most pronounced examples of polar growth among bacteria. The expansion of the cell wall by tip extension is thought to be facilitated by the turgor pressure, but it was unknown how external osmotic change influences Streptomyces tip growth. We report here that severe hyperosmotic stress causes cessation of growth, followed by reprogramming of cell polarity and rearrangement of growth zones to promote lateral hyphal branching. This phenomenon may represent a strategy of hyphal organisms to avoid osmotic stress encountered by the growing hyphal tip.

Proteomics analysis of global regulatory cascades involved in clavulanic acid production and morphological development in Streptomyces clavuligerus

The genus Streptomyces comprises bacteria that undergo a complex developmental life cycle and produce many metabolites of importance to industry and medicine. Streptomyces clavuligerus produces the β-lactamase inhibitor clavulanic acid, which is used in combination with β-lactam antibiotics to treat certain β-lactam resistant bacterial infections. Many aspects of how clavulanic acid production is globally regulated in S. clavuligerus still remains unknown. We conducted comparative proteomics analysis using the wild type strain of S. clavuligerus and two mutants (ΔbldA and ΔbldG), which are defective in global regulators and vary in their ability to produce clavulanic acid. Approximately 33.5 % of the predicted S. clavuligerus proteome was detected and 192 known or putative regulatory proteins showed statistically differential expression levels in pairwise comparisons. Interestingly, the expression of many proteins whose corresponding genes contain TTA codons (predicted to require the bldA tRNA for translation) was unaffected in the bldA mutant.

Methylatable Signaling Helix Coordinated Inhibitory Receiver Domain in Sensor Kinase Modulates Environmental Stress Response in Bacillus Cereus

σ^B, an alternative transcription factor, controls the response of the cell to a variety of environmental stresses in Bacillus cereus. Previously, we reported that RsbM negatively regulates σ^B through the methylation of RsbK, a hybrid sensor kinase, on a signaling helix (S-helix). However, RsbK comprises a C-terminal receiver (REC) domain whose function remains unclear. In this study, deletion of the C-terminal REC domain of RsbK resulted in high constitutive σ^B expression independent of environmental stimuli. Thus, the REC domain may serve as an inhibitory element. Mutagenic substitution was employed to modify the putative phospho-acceptor residue D827 in the REC domain of RsbK. The expression of RsbK_D827N and RsbK_D827E exhibited high constitutive σ^B, indicating that D827, if phosphorylatable, possibly participates in σ^B regulation. Bacterial two-hybrid analyses demonstrated that RsbK forms a homodimer and the REC domain interacts mainly with the histidine kinase (HK) domain and partly with the S-helix. In particular, co-expression of RsbM strengthens the interaction between the REC domain and the S-helix. Consistently, our structural model predicts a significant interaction between the HK and REC domains of the RsbK intradimer. Here, we demonstrated that coordinated the methylatable S-helix and the REC domain of RsbK is functionally required to modulate σ^B-mediated stress response in B. cereus and maybe ubiquitous in microorganisms encoded RsbK-type sensor kinases.

Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution

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.

A sporulation-specific, sigF-dependent protein, SspA, affects septum positioning in Streptomyces coelicolor

The RNA polymerase sigma factor SigF controls late development during sporulation in the filamentous bacterium Streptomyces coelicolor. The only known SigF-dependent gene identified so far, SCO5321, is found in the biosynthetic cluster encoding spore pigment synthesis. Here we identify the first direct target for SigF, the gene sspA, encoding a sporulation-specific protein. Bioinformatic analysis suggests that SspA is a secreted lipoprotein with two PepSY signature domains. The sspA deletion mutant exhibits irregular sporulation septation and altered spore shape, suggesting that SspA plays a role in septum formation and spore maturation. The fluorescent translational fusion protein SspA–mCherry localized first to septum sites, then subsequently around the surface of the spores. Both SspA protein and sspA transcription are absent from the sigF null mutant. Moreover, in vitro transcription assay confirmed that RNA polymerase holoenzyme containing SigF is sufficient for initiation of transcription from a single sspA promoter. In addition, in vivo and in vitro experiments showed that sspA is a direct target of BldD, which functions to repress sporulation genes, including whiG, ftsZ and ssgB, during vegetative growth, co-ordinating their expression during sporulation septation.

Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote

A computational model of gene expression was applied to a novel test set of microarray time series measurements to reveal regulatory interactions between transcriptional regulators represented by 45 sigma factors and the genes expressed during germination of a prokaryote Streptomyces coelicolor. Using microarrays, the first 5.5 h of the process was recorded in 13 time points, which provided a database of gene expression time series on genome-wide scale. The computational modeling of the kinetic relations between the sigma factors, individual genes and genes clustered according to the similarity of their expression kinetics identified kinetically plausible sigma factor-controlled networks. Using genome sequence annotations, functional groups of genes that were predominantly controlled by specific sigma factors were identified. Using external binding data complementing the modeling approach, specific genes involved in the control of the studied process were identified and their function suggested.

Rate of environmental change determines stress response specificity

Cells use general stress response pathways to activate diverse target genes in response to a variety of stresses. However, general stress responses coexist with more specific pathways that are activated by individual stresses, provoking the fundamental question of whether and how cells control the generality or specificity of their response to a particular stress. Here we address this issue using quantitative time-lapse microscopy of the Bacillus subtilis environmental stress response, mediated by σ(B). We analyzed σ(B) activation in response to stresses such as salt and ethanol imposed at varying rates of increase. Dynamically, σ(B) responded to these stresses with a single adaptive activity pulse, whose amplitude depended on the rate at which the stress increased. This rate-responsive behavior can be understood from mathematical modeling of a key negative feedback loop in the underlying regulatory circuit. Using RNAseq we analyzed the effects of both rapid and gradual increases of ethanol and salt stress across the genome. Because of the rate responsiveness of σ(B) activation, salt and ethanol regulons overlap under rapid, but not gradual, increases in stress. Thus, the cell responds specifically to individual stresses that appear gradually, while using σ(B) to broaden the cellular response under more rapidly deteriorating conditions. Such dynamic control of specificity could be a critical function of other general stress response pathways.

Signals and regulators that govern Streptomyces development

Streptomyces coelicolor is the genetically best characterized species of a populous genus belonging to the gram-positive Actinobacteria. Streptomycetes are filamentous soil organisms, well known for the production of a plethora of biologically active secondary metabolic compounds. The Streptomyces developmental life cycle is uniquely complex and involves coordinated multicellular development with both physiological and morphological differentiation of several cell types, culminating in the production of secondary metabolites and dispersal of mature spores. This review presents a current appreciation of the signaling mechanisms used to orchestrate the decision to undergo morphological differentiation, and the regulators and regulatory networks that direct the intriguing development of multigenomic hyphae first to form specialized aerial hyphae and then to convert them into chains of dormant spores. This current view of S. coelicolor development is destined for rapid evolution as data from '-omics' studies shed light on gene regulatory networks, new genetic screens identify hitherto unknown players, and the resolution of our insights into the underlying cell biological processes steadily improve.

Potato suberin induces differentiation and secondary metabolism in the genus Streptomyces

Bacteria of the genus Streptomyces are soil microorganisms with a saprophytic life cycle. Previous studies have revealed that the phytopathogenic agent S. scabiei undergoes metabolic and morphological modifications in the presence of suberin, a complex plant polymer. This paper investigates morphological changes induced by the presence of potato suberin in five species of the genus Streptomyces, with emphasis on S. scabiei. Streptomyces scabiei, S. acidiscabies, S. avermitilis, S. coelicolor and S. melanosporofaciens were grown both in the presence and absence of suberin. In all species tested, the presence of the plant polymer induced the production of aerial hyphae and enhanced resistance to mechanical lysis. The presence of suberin in liquid minimal medium also induced the synthesis of typical secondary metabolites in S. scabiei and S. acidiscabies (thaxtomin A), S. coelicolor (actinorhodin) and S. melanosporofaciens (geldanamycin). In S. scabiei, the presence of suberin modified the fatty acid composition of the bacterial membrane, which translated into higher membrane fluidity. Moreover, suberin also induced thickening of the bacterial cell wall. The present data indicate that suberin hastens cellular differentiation and triggers the onset of secondary metabolism in the genus Streptomyces.

Regulation of an alternative sigma factor σI by a partner switching mechanism with an anti-sigma factor PrsI and an anti-anti-sigma factor ArsI in Streptomyces coelicolor A3(2)

Two genes, prsI and arsI, are located divergently next to the sigI gene encoding alternative sigma factor σI of Streptomyces coelicolor A3(2). The similarity of PrsI and ArsI to anti-sigma and anti-anti-sigma factors, respectively, suggests that both putative regulators may be involved in regulation of σI. By using a combination of several approaches including bacterial two-hybrid assays, pull-down assay and visualization of the complex by native polyacrylamide electrophoresis, we demonstrated that PrsI specifically interacts with σI and ArsI. In vitro phosphorylation demonstrated that PrsI serves as a specific kinase for its putative partner, ArsI, and negatively regulates its activity. The sigI gene was deleted in the S. coelicolor M145 strain without obvious effect on growth, stress response and differentiation. Complex transcriptional analyses of sigI, prsI, and arsI revealed that sigI is directed by a single promoter induced by osmotic stress, arsI is directed by a single constitutive promoter, and prsI is directed by two tandem promoters, one constitutive and the second one induced by osmotic stress. None of the determined promoters was dependent upon σI, σB and σH. These data suggested a role of σI in the osmotic stress response and its regulation by a partner switching mechanism through the anti-sigma factor PrsI and its antagonist, anti-anti-sigma factor ArsI.

Magnetic field is the dominant factor to induce the response of Streptomyces avermitilis in altered gravity simulated by diamagnetic levitation

Background

Diamagnetic levitation is a technique that uses a strong, spatially varying magnetic field to simulate an altered gravity environment, as in space. In this study, using Streptomyces avermitilis as the test organism, we investigate whether changes in magnetic field and altered gravity induce changes in morphology and secondary metabolism. We find that a strong magnetic field (12T) inhibit the morphological development of S. avermitilis in solid culture, and increase the production of secondary metabolites.

Methodology/Principal Findings

S. avermitilis on solid medium was levitated at 0 g*, 1 g* and 2 g* in an altered gravity environment simulated by diamagnetic levitation and under a strong magnetic field, denoted by the asterix. The morphology was obtained by electromicroscopy. The production of the secondary metabolite, avermectin, was determined by OD_{245 nm}. The results showed that diamagnetic levitation could induce a physiological response in S. avermitilis. The difference between 1 g* and the control group grown without the strong magnetic field (1 g), showed that the magnetic field was a more dominant factor influencing changes in morphology and secondary metabolite production, than altered gravity.

Conclusion/Significance

We have discovered that magnetic field, rather than altered gravity, is the dominant factor in altered gravity simulated by diamagnetic levitation, therefore care should to be taken in the interpretation of results when using diamagnetic levitation as a technique to simulate altered gravity. Hence, these results are significant, and timely to researchers considering the use of diamagnetic levitation to explore effects of weightlessness on living organisms and on physical phenomena.

The dpsA gene of Streptomyces coelicolor: induction of expression from a single promoter in response to environmental stress or during development

The DpsA protein plays a dual role in Streptomyces coelicolor, both as part of the stress response and contributing to nucleoid condensation during sporulation. Promoter mapping experiments indicated that dpsA is transcribed from a single, sigB-like dependent promoter. Expression studies implicate SigH and SigB as the sigma factors responsible for dpsA expression while the contribution of other SigB-like factors is indirect by means of controlling sigH expression. The promoter is massively induced in response to osmotic stress, in part due to its sensitivity to changes in DNA supercoiling. In addition, we determined that WhiB is required for dpsA expression, particularly during development. Gel retardation experiments revealed direct interaction between apoWhiB and the dpsA promoter region, providing the first evidence for a direct WhiB target in S. coelicolor.

Forkhead-associated proteins genetically linked to the serine/threonine kinase PknB regulate carbon flux towards antibiotic biosynthesis in Streptomyces coelicolor

To date, the function of only two of the 34 predicted serine/threonine protein kinases (STPKs) of Streptomyces coelicolor has been described. Here we report functional analysis of pknB and two linked genes, fhaAB, encoding forkhead‐associated (FHA) domain proteins that are part of a highly conserved gene locus in actinobacteria. In contrast to the homologous gene of Mycobacterium tuberculosis, pknB in S. coelicolor is not essential and has no apparent role in defining cell shape. Phosphorylation of recombinant forms of both the full‐length protein and N‐terminal kinase domain suggest that PknB‐mediated signalling in S. coelicolor may be modulated by another factor(s). FhaAB are candidate interacting partners of PknB and loss of their function resulted in deregulation of central carbon metabolism, with carbon flux diverted to synthesis of the antibiotic actinorhodin. The substrate hyphae of the fhaAB mutant also exhibited an unusual cording morphology. The results indicate that inactivation of FHA ‘brake’ proteins can potentially amplify the function of STPKs and, in this case, provide a means to overproduce antibiotics.

Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases

A common bacterial strategy to cope with stressful conditions is the activation of alternative sigma factors that control specific regulons enabling targeted responses. In the human pathogen Bacillus cereus, activation of the major stress-responsive sigma factor σ(B) is controlled by a signalling route that involves the multi-sensor hybrid histidine kinase RsbK. RsbK-type kinases are not restricted to the B. cereus group, but occur in a wide variety of other bacterial species, including members of the the low-GC Gram-positive genera Geobacillus and Paenibacillus as well as the high-GC actinobacteria. Genome context and protein sequence analyses of 118 RsbK homologues revealed extreme variability in N-terminal sensory as well as C-terminal regulatory domains and suggested that RsbK-type kinases are subject to complex fine-tuning systems, including sensitization and desensitization via methylation and demethylation within the helical domain preceding the H-box. The RsbK-mediated stress-responsive sigma factor activation mechanism that has evolved in B. cereus and the other species differs markedly from the extensively studied and highly conserved RsbRST-mediated σ(B) activation route found in Bacillus subtilis and other low-GC Gram-positive bacteria. Implications for future research on sigma factor control mechanisms are presented and current knowledge gaps are briefly discussed.

Role of σ-factor (orf21) in clavulanic acid production in Streptomyces clavuligerus NRRL3585

A putative sigma factor gene, orf21, was disrupted or overexpressed in the wild-type clavulanic acid (CA) producer Streptomyces clavuligerus NRRL3585 and characterized. An orf21 mutant (Streptomyces clavuligerus HN14) of S. clavuligerus was obtained by insertional inactivation via double-crossover. Although there was little reduction of sporulation in the mutant, the growth pattern was similar between mutant and wild-type. The production was reduced by 10-15% in S. clavuligerus HN14 compared to that in wild-type. Overexpression of orf21 in wild-type cells caused hyperproduction of spores on solid medium and increased clavulanic acid production by 1.43-fold. The overexpression of orf21 in wild-type S. clavuligerus stimulated the expression of the early clavulanic acid genes, ceas2 and cas2, and the regulatory gene, ccaR, as demonstrated by RT-PCR. The elevation of the ceas2, cas2 and ccaR transcripts was consistent with the enhanced production of clavulanic acid.

The anti-anti-sigma factor BldG is involved in activation of the stress response sigma factor σ(H) in Streptomyces coelicolor A3(2)

The alternative stress response sigma factor σ(H) has a role in regulation of the osmotic stress response and in morphological differentiation in Streptomyces coelicolor A3(2). Its gene, sigH, is located in an operon with the gene that encodes its anti-sigma factor UshX (PrsH). However, no gene with similarity to an anti-anti-sigma factor which may have a role in σ(H) activation by a "partner-switching" mechanism is located in the operon. By using a combination of several approaches, including pull-down and bacterial two-hybrid assays and visualization of the complex by native polyacrylamide electrophoresis, we demonstrated a direct interaction between UshX and the pleiotropic sporulation-specific anti-anti-sigma factor BldG. Osmotic induction of transcription of the sigHp2 promoter that is specifically recognized by RNA polymerase containing σ(H) was absent in an S. coelicolor bldG mutant, indicating a role of BldG in σ(H) activation by a partner-switching-like mechanism.

The complex whiJ locus mediates environmentally sensitive repression of development of Streptomyces coelicolor A3(2)

A segment of DNA was isolated that complemented several poorly characterised sporulation-defective white-colony mutants of Streptomyces coelicolor A3(2) from an early collection (Hopwood et al., J Gen Microbiol 61: 397-408, 1970). Complementation was attributable to a gene, SCO4543, named whiJ, encoding a likely DNA-binding protein. Surprisingly, although some mutations in whiJ had a white colony phenotype, complete deletion of the wild-type or mutant gene gave a wild-type morphology. The whiJ gene is a member of a large paralogous set of S. coelicolor genes including abaAorfA, which regulates antibiotic production; and genes flanking whiJ are paralogues of other gene classes that are often associated with whiJ-like genes (Gehring et al., Proc Natl Acad Sci USA 97: 9642-9647, 2000). Thus, the small gene SCO4542 encodes a paralogue of the abaAorfD gene product, and SCO4544 encodes a paralogue of a family of likely anti-sigma factors (including the product of abaAorfB). Deletion of SCO4542 resulted in a medium-dependent bald- or white-colony phenotype, which could be completely suppressed by the simultaneous deletion of whiJ. A model is proposed in which WhiJ binds to operator sequences to repress developmental genes, with repression being released by interaction with the WhiJ-associated SCO4542 protein. It is suggested that this activity of SCO4542 protein is prevented by an unknown signal.

BldG and SCO3548 interact antagonistically to control key developmental processes in Streptomyces coelicolor

The similarity of BldG and the downstream coexpressed protein SCO3548 to anti-anti-sigma and anti-sigma factors, respectively, together with the phenotype of a bldG mutant, suggests that BldG and SCO3548 interact as part of a regulatory system to control both antibiotic production and morphological differentiation in Streptomyces coelicolor. A combination of bacterial two-hybrid, affinity purification, and far-Western analyses demonstrated that there was self-interaction of both BldG and SCO3548, as well as a direct interaction between the two proteins. Furthermore, a genetic complementation experiment demonstrated that SCO3548 antagonizes the function of BldG, similar to other anti-anti-sigma/anti-sigma factor pairs. It is therefore proposed that BldG and SCO3548 form a partner-switching pair that regulates the function of one or more sigma factors in S. coelicolor. The conservation of bldG and sco3548 in other streptomycetes demonstrates that this system is likely a key regulatory switch controlling developmental processes throughout the genus Streptomyces.

Osmoregulation in Streptomyces coelicolor: modulation of SigB activity by OsaC

As free-living non-motile saprophytes, Streptomyces need to adapt to a wide range of environmental conditions and this is reflected by an enormous diversity of regulatory proteins encoded by, for example, the genome of the model streptomycete Streptomyces coelicolor. In this organism, we have identified a new osmoregulation gene, osaC, encoding a member of a novel family of regulatory proteins. Members of the family have a predicted domain composition consisting of an N-terminal kinase domain related to anti-sigma factors, sensory Pas and Gaf domains, and a C-terminal phosphatase domain. osaC is linked to the response regulator gene osaB; expression analysis of the latter revealed that it is induced after osmotic stress in a sigma(B)-dependent manner. OsaC is required to return osaB and sigB expression back to constitutive levels after osmotic stress. From analysis of the activities of OsaC(DeltaPho), lacking the C-terminal phosphatase domain, and OsaC(N92A), with a substitution of a critical asparagine residue in the kinase domain, we infer that this N-terminal domain functions as a sigma(B) anti-sigma factor. Indeed, co-purification experiments indicate association of OsaC and sigma(B). These results support a model for post-osmotic stress modulation of sigma(B) activity by OsaC.

A possible extended family of regulators of sigma factor activity in Streptomyces coelicolor

SCO4677 is one of a large number of similar genes in Streptomyces coelicolor that encode proteins with an HATPase_c domain resembling that of anti-sigma factors such as SpoIIAB of Bacillus subtilis. However, SCO4677 is not located close to genes likely to encode a cognate sigma or anti-anti-sigma factor. SCO4677 was found to regulate antibiotic production and morphological differentiation, both of which were significantly enhanced by the deletion of SCO4677. Through protein-protein interaction screening of candidate sigma factor partners using the yeast two-hybrid system, SCO4677 protein was found to interact with the developmentally specific sigma(F), suggesting that it is an antagonistic regulator of sigma(F). Two other proteins, encoded by SCO0781 and SCO0869, were found to interact with the SCO4677 anti-sigma(F) during a subsequent global yeast two-hybrid screen, and the SCO0869-SCO4677 protein-protein interaction was confirmed by coimmunoprecipitation. The SCO0781 and SCO0869 proteins resemble well-known anti-anti-sigma factors such as SpoIIAA of B. subtilis. It appears that streptomycetes may possess an extraordinary abundance of anti-sigma factors, some of which may influence diverse processes through interactions with multiple partners: a novel feature for such regulatory proteins.

Redox control in actinobacteria

As most actinobacteria are obligate aerobes, they have to cope with endogenously generated reactive oxygen species, and actinobacterial pathogens have to resist oxidative attack by phagocytes. Actinobacteria also have to survive long periods under low oxygen tension; for example, Mycobacterium tuberculosis can persist in the host for years under apparently hypoxic conditions in a latent, non-replicative state. Here we focus on the regulatory switches that control actinobacterial responses to peroxide stress, disulfide stress and low oxygen tension. Other unique aspects of their redox biology will be highlighted, including the use of the pseudodisaccharide mycothiol as their major low-molecular-weight thiol buffer, and the [4Fe-4S]-containing WhiB-like proteins, which play diverse, important roles in actinobacterial biology, but whose biochemical role is still controversial.

Secreted-protein response to sigmaU activity in Streptomyces coelicolor

The filamentous bacterium Streptomyces coelicolor forms an aerial mycelium as a prerequisite to sporulation, which occurs in the aerial hyphae. Uncontrolled activity of the extracytoplasmic function sigma factor sigmaU blocks the process of aerial mycelium formation in this organism. Using a green fluorescent protein transcriptional reporter, we have demonstrated that sigU transcription is autoregulated. We have defined a sigmaU-dependent promoter sequence and used this to identify 22 likely sigmaU regulon members in the S. coelicolor genome. Since many of these genes encode probable secreted proteins, we characterized the extracellular proteome of a mutant with high sigmaU activity caused by disruption of rsuA, the presumed cognate anti-sigma factor of sigmaU. This mutant secreted a much greater quantity and diversity of proteins than the wild-type strain. Peptide mass fingerprinting was used to identify 79 proteins from the rsuA mutant culture supernatant. The most abundant species, SCO2217, SCO0930, and SCO2207, corresponded to secreted proteins or lipoproteins of unknown functions whose genes are in the proposed sigmaU regulon. Several unique proteases were also detected in the extracellular proteome of the mutant, and the levels of the protease inhibitor SCO0762 were much reduced compared to those of the wild type. Consequently, extracellular protease activity was elevated about fourfold in the rsuA mutant. The functions of the proteins secreted as a result of sigmaU activity may be important for combating cell envelope stress and modulating morphological differentiation in S. coelicolor.

Streptomyces coelicolor genes ftsL and divIC play a role in cell division but are dispensable for colony formation

We have characterized homologues of the bacterial cell division genes ftsL and divIC in the gram-positive mycelial bacterium Streptomyces coelicolor A3(2). We show by deletion-insertion mutations that ftsL and divIC are dispensable for growth and viability in S. coelicolor. When mutant strains were grown on a conventional rich medium (R2YE, containing high sucrose), inactivation of either ftsL or divIC resulted in the formation of aerial hyphae with partially constricted division sites but no clear separation of prespore compartments. Surprisingly, this phenotype was largely suppressed when strains were grown on minimal medium or sucrose-free R2YE, where division sites in many aerial hyphae had finished constricting and chains of spores were evident. Thus, osmolarity appears to affect the severity of the division defect. Furthermore, double mutant strains deleted for both ftsL and divIC are viable and have medium-dependent phenotypes similar to that of the single mutant strains, suggesting that functions performed by FtsL and DivIC are not absolutely required for septation during growth and sporulation. Alternatively, another division protein may partially compensate for the loss of both FtsL and DivIC on minimal medium or sucrose-free R2YE. Finally, based on transmission electron microscopy observations, we propose that FtsL and DivIC are involved in coordinating symmetrical annular ingrowth of the invaginating septum.

A novel compartment, the 'subapical stem' of the aerial hyphae, is the location of a sigN-dependent, developmentally distinct transcription in Streptomyces coelicolor

Streptomyces coelicolor has nine SigB-like RNA polymerase sigma factors, several of them implicated in morphological differentiation and/or responses to different stresses. One of the nine, SigN, is the focus of this article. A constructed sigN null mutant was delayed in development and exhibited a bald phenotype when grown on minimal medium containing glucose as carbon source. One of two distinct sigN promoters, sigNP1, was active only during growth on solid medium, when its activation coincided with aerial hyphae formation. Transcription from sigNP1 was readily detected in several whi mutants (interrupted in morphogenesis of aerial mycelium into spores), but was absent from all bld mutants tested, suggesting that sigNP1 activity was restricted to the aerial hyphae. It also depended on sigN, thus sigN was autoregulated. Mutational and transcription studies revealed no functional significance to the location of sigN next to sigF, encoding another SigB-like sigma factor. We identified another potential SigN target, nepA, encoding a putative small secreted protein. Transcription of nepA originated from a single, aerial hyphae-specific and sigN-dependent promoter. While in vitro run-off transcription using purified SigN on the Bacillus subtilis ctc promoter confirmed that SigN is an RNA polymerase sigma factor, SigN failed to initiate transcription from sigNP1 and from the nepA promoter in vitro. Additional in vivo data indicated that further nepA upstream sequences, which are likely to bind a potential activator, are required for successful transcription. Using a nepA-egfp transcriptional fusion we located nepA transcription to a novel compartment, the 'subapical stem' of the aerial hyphae. We suggest that this newly recognized compartment defines an interface between the aerial and vegetative parts of the Streptomyces colony and might also be involved in communication between these two compartments.

Role of σH paralogs in intracellular melanin formation and spore development in Streptomyces griseus

Streptomyces griseus possesses multiple stress-response sigma factors including sigma(H). Previously, we have suggested that sigma(H) and related sigma factors are involved in the developmental control of S. griseus. Herein, we studied the role of two sigma(H) paralogs--sigma(F) and sigma(N)--which are encoded in tandem coding sequences of sigF-sigN in S. griseus [sigma(N) has been described as sigma(L) previously (Gene 320:127, 2003)]. A sigF mutant produced decreased levels of intracellular melanin and formed irregular spores. A triple mutant for sigHNF exhibited defective melanin production. While sigN was transcribed by three tandem promoters during the early to late growth phases, sigF was transcribed in the late developmental phase by a single promoter. The activity of the promoter preceding the rpp operon (Prpp), which is responsible for the intracellular melanin biosynthesis, was decreased in the sigF mutant and abolished in the sigHNF, adpA and A-factor biosynthesis mutants. The in vitro transcription assay demonstrated that Esigma(F) transcribed the rpp promoter. Both Esigma(F) and Esigma(N) transcribed a sigma(H)-dependent promoter that preceded the sigH operon, and their activities were repressed by the addition of RshA, an anti-sigma(H) protein. Overall, the results suggest that the three sigma factors have similar functions and that they are required for spore development and pigmentation. The transcription of the rpp operon is regulated both by the stress-response sigma factors and the A-factor regulatory cascade.

Distinctive topologies of partner-switching signaling networks correlate with their physiological roles

Regulatory networks controlling bacterial gene expression often evolve from common origins and share homologous proteins and similar network motifs. However, when functioning in different physiological contexts, these motifs may be re-arranged with different topologies that significantly affect network performance. Here we analyze two related signaling networks in the bacterium Bacillus subtilis in order to assess the consequences of their different topologies, with the aim of formulating design principles applicable to other systems. These two networks control the activities of the general stress response factor sigma(B) and the first sporulation-specific factor sigma(F). Both networks have at their core a "partner-switching" mechanism, in which an anti-sigma factor forms alternate complexes either with the sigma factor, holding it inactive, or with an anti-anti-sigma factor, thereby freeing sigma. However, clear differences in network structure are apparent: the anti-sigma factor for sigma(F) forms a long-lived, "dead-end" complex with its anti-anti-sigma factor and ADP, whereas the genes encoding sigma(B) and its network partners lie in a sigma(B)-controlled operon, resulting in positive and negative feedback loops. We constructed mathematical models of both networks and examined which features were critical for the performance of each design. The sigma(F) model predicts that the self-enhancing formation of the dead-end complex transforms the network into a largely irreversible hysteretic switch; the simulations reported here also demonstrate that hysteresis and slow turn off kinetics are the only two system properties associated with this complex formation. By contrast, the sigma(B) model predicts that the positive and negative feedback loops produce graded, reversible behavior with high regulatory capacity and fast response time. Our models demonstrate how alterations in network design result in different system properties that correlate with regulatory demands. These design principles agree with the known or suspected roles of similar networks in diverse bacteria.

rag genes: novel components of the RamR regulon that trigger morphological differentiation in Streptomyces coelicolor

The filamentous bacterium, Streptomyces coelicolor, undergoes a complex cycle of growth and development in which morphological differentiation coincides with the activation of the orphan response regulator RamR and the biosynthesis of a morphogenic peptide called SapB. SapB is a lantibiotic-like molecule derived from the product of the ramS gene that promotes formation of aerial hyphae by breaking the aqueous tension on the surface of the substrate mycelium. A ramR-disrupted mutant is delayed in aerial hyphae formation while constitutive overexpression of ramR accelerates aerial hyphae formation in the wild-type strain and restores SapB biosynthesis and aerial hyphae formation in all developmental mutants (bld) tested. Using DNA microarrays to globally identify S. coelicolor genes whose transcription was affected by ramR mutation or overexpression, we discovered a ramR-activated locus of contiguous cotranscribed developmental genes that modulate both aerial hyphae formation and sporulation. The genes of this cluster of ramR-activated genes (rag), which are chromosomally distant from previously known RamR-regulated genes, include: ragA (sco4075) and ragB (sco4074), which encode two subunits of an ABC transporter, ragK (sco4073), a putative histidine kinase, and ragR (sco4072), a ramR paralogue. Promoter mapping and protein-DNA binding experiments indicate that RamR activates ragABKR transcription directly, by binding to three sequence motifs in the ragABKR promoter region. A constructed ragABKR null mutant was able to synthesize SapB and erect aerial hyphae; however, these hyphae were unusually branched, reminiscent of substrate hyphae. Subsequent stages of differentiation, septation and sporogenesis were delayed. The role of ragABKR in aerial hyphae formation was shown both by epistasis (ragR-activated aerial hyphae formation in bld mutants) and extracellular complementation (ragR-induced synthesis of an activity allowing aerial hyphae formation in bld mutants) experiments. In conclusion, the ragABKR locus activates a SapB-independent developmental pathway that is involved in both aerial hyphae formation and sporulation, serving to integrate sequential morphogenic changes.

The evolution of development inStreptomycesanalysed by genome comparisons

There is considerable information about the genetic control of the processes by which mycelial Streptomyces bacteria form spore-bearing aerial hyphae. The recent acquisition of genome sequences for 16 species of actinobacteria, including two streptomycetes, makes it possible to try to reconstruct the evolution of Streptomyces differentiation by a comparative genomic approach, and to place the results in the context of current views on the evolution of bacteria. Most of the developmental genes evaluated are found only in actinobacteria that form sporulating aerial hyphae, with several being peculiar to streptomycetes. Only four (whiA, whiB, whiD, crgA) are generally present in nondifferentiating actinobacteria, and only two (whiA, whiG) are found in other bacteria, where they are widespread. Thus, the evolution of Streptomyces development has probably involved the stepwise acquisition of laterally transferred DNA, each successive acquisition giving rise either to regulatory changes that affect the conditions under which development is initiated, or to changes in cellular structure or morphology.

Cascade of sigma factors in streptomycetes: identification of a new extracytoplasmic function sigma factor sigmaJ that is under the control of the stress-response sigma factor sigmaH in Streptomyces coelicolor A3(2)

By using the previously established Escherichia coli two-plasmid system, we identified a promoter recognized by the Streptomyces coelicolor A3(2) stress-response sigma factor sigmaH. The promoter directed expression of the sigJ gene encoding an extracytoplasmic function (ECF) sigma factor. S1-nuclease mapping using RNA prepared from E. coli containing the two-plasmid system, and S. coelicolor A3(2) from various developmental stages identified an identical transcription start point in both strains, corresponding to the sigJp promoter. The sigJp promoter was induced during sporulation of aerial hyphae. The level of the transcript from sigJp was dramatically reduced in a S. coelicolor A3(2) sigH mutant and unaffected in a sigF mutant. The S. coelicolor A3(2) core RNA polymerase, after complementation with sigmaH, was able to recognize the sigJp promoter in vitro. A sigJ mutation had no obvious effect on growth, stress response, differentiation, and production of antibiotics. The results suggested that the S. coelicolor A3(2) sigJ gene is under the control of stress-response sigmaH, thus indicating a cascade of sigma factors in Streptomyces stress response and development. Considering the expression of sigJ and its direct dependence upon developmentally-regulated sigmaH, we assume that sigmaJ may play a role in the later stages of development of S. coelicolor A3(2).

Ecf, an alternative sigma factor from Neisseria gonorrhoeae, controls expression of msrAB, which encodes methionine sulfoxide reductase

A DNA microarray was used to identify genes transcribed in Neisseria gonorrhoeae using Ecf, an alternative sigma factor. No differences between the transcriptional profiles of strain FA1090 and a mutant where ecf had been inactivated could be detected when both were grown in vitro. We therefore constructed a gonococcal strain in which Ecf can be overexpressed. Some differentially expressed genes are clustered with ecf on the genome and appear to form a single transcriptional unit. Expression of the gene encoding MsrAB, which possesses methionine sulfoxide reductase activity, was also dependent on Ecf, suggesting that the regulon responds to oxidative damage. Western blotting confirmed that the increased level of MsrAB protein is dependent on the presence of Ecf.

Characterization of the alternative sigma factor sigmaG in Streptomyces coelicolor A3(2)

Using the previously established two-plasmid system for the identification of promoters recognized by a particular sigma factor, we identified two positive DNA fragments that were active only after induced sigG, encoding sigma factor sigmaG of Streptomyces coelicolor A3(2). High-resolution S1-nuclease mapping in the Escherichia coli two-plasmid system identified potential promoters, PG45 and PG54, whose sequences were similar to the consensus sequence of Bacillus subtilis promoters recognized by the general stress-response sigma factor sigmaB. However, both putative sigmaG-dependent promoters were not active in S. coelicolor. Sequence analysis of the regions potentially governed by the promoters revealed a gene encoding a hypothetical protein SCO5555 and the rrnE gene encoding rRNA operon. To confirm that sigG encodes sigma factor, the sigmaG protein was overproduced in E. coli and purified. In an in vitro transcription assay, sigmaG, after complementation with S. coelicolor core RNA polymerase, was able to recognize both sigmaG-dependent promoters and initiate transcription.