How molecular competition influences fluxes in gene expression networks

Often, in living cells different molecular species compete for binding to the same molecular target. Typical examples are the competition of genes for the transcription machinery or the competition of mRNAs for the translation machinery. Here we show that such systems have specific regulatory features and how they can be analysed. We derive a theory for molecular competition in parallel reaction networks. Analytical expressions for the response of network fluxes to changes in the total competitor and common target pools indicate the precise conditions for ultrasensitivity and intuitive rules for competitor strength. The calculations are based on measurable concentrations of the competitor-target complexes. We show that kinetic parameters, which are usually tedious to determine, are not required in the calculations. Given their simplicity, the obtained equations are easily applied to networks of any dimension. The new theory is illustrated for competing sigma factors in bacterial transcription and for a genome-wide network of yeast mRNAs competing for ribosomes. We conclude that molecular competition can drastically influence the network fluxes and lead to negative response coefficients and ultrasensitivity. Competitors that bind a large fraction of the target, like bacterial σ⁷⁰, tend to influence competing pathways strongly. The less a competitor is saturated by the target, the more sensitive it is to changes in the concentration of the target, as well as to other competitors. As a consequence, most of the mRNAs in yeast turn out to respond ultrasensitively to changes in ribosome concentration. Finally, applying the theory to a genome-wide dataset we observe that high and low response mRNAs exhibit distinct Gene Ontology profiles.

Role of general stress-response alternative sigma factors σ(S) (RpoS) and σ(B) (SigB) in bacterial heat resistance as a function of treatment medium pH

This investigation aimed to determine the role of general stress-response alternative sigma factors σ(S) (RpoS) and σ(B) (SigB) in heat resistance and the occurrence of sublethal injuries in cell envelopes of stationary-phase Escherichia coli BJ4 and Listeria monocytogenes EGD-e cells, respectively, as a function of treatment medium pH. Given that microbial death followed first-order inactivation kinetics (R(2)>0.95) the traditional D(T) and z values were used to describe the heat inactivation kinetics. Influence of rpoS deletion was constant at every treatment temperature and pH, making a ΔrpoS deletion mutant strain approximately 5.5 times more heat sensitive than its parental strain for every studied condition. Furthermore, the influence of the pH of the treatment medium on the reduction of the heat resistance of E. coli was also constant and independent of the treatment temperature (average z value=4.9°C) in both parental and mutant strains. L. monocytogenes EGD-e z values obtained at pH 7.0 and 5.5 were not significantly different (p>0.05) in either parental or the ∆sigB deletion mutant strains (average z value=4.8°C). Nevertheless, at pH 4.0 the z value was higher (z=8.4°C), indicating that heat resistance of both L. monocytogenes strains was less dependent on temperature at pH 4.0. At both pH 5.5 and 7.0 the influence of sigB deletion was constant and independent of the treatment temperature, decreasing L. monocytogenes heat resistance approximately 2.5 times. In contrast, the absence of sigB did not decrease the heat resistance of L. monocytogenes at pH 4.0. The role of RpoS in protecting cell envelopes was more important in E. coli (4 times) than SigB in L. monocytogenes (1.5 times). Moreover, the role of σ(S) in increasing heat resistance seems more relevant in enhancing the intrinsic resilience of the cytoplasmic membrane, and to a lesser extent, outer membrane resilience. Knowledge of environmental conditions related to the activation of alternative sigma factors σ(S) and σ(B) and their effects on heat resistance would help us to avoid and/or identify situations that increase bacterial stress resistance. Therefore, more efficient food preservation processes might be designed.

Gene expression modulation by heat stress in Acidithiobacillus ferrooxidans LR

During bioleaching, Acidithiobacillus ferrooxidans is subjected to different types of stress, including heat stress, which affect bacterial growth. In this work, real time quantitative PCR was used to analyze the expression of heat shock genes, as well as genes that encode proteins related to several functional categories in A. ferrooxidans. Cells were submitted to long-term growth and heat shock, both at 40°C. The results showed that heat shock affected the expression levels of most genes investigated, whilst long-term growth at 40°C resulted in minor changes in gene expression, except for certain genes related to iron transport, which were strongly down-regulated, suggesting that the iron processing capability of A. ferrooxidans was affected by long-term growth at 40°C. A bioinformatic analysis of the genes' promoter regions indicated a putative transcriptional regulation by the σ(32) factor in 12 of the 31 genes investigated, suggesting the involvement of other regulatory mechanisms in the response of A. ferrooxidans to heat stress.

BosR (BB0647) controls the RpoN-RpoS regulatory pathway and virulence expression in Borrelia burgdorferi by a novel DNA-binding mechanism

In Borrelia burgdorferi (Bb), the Lyme disease spirochete, the alternative σ factor σ⁵⁴ (RpoN) directly activates transcription of another alternative σ factor, σ^S (RpoS) which, in turn, controls the expression of virulence-associated membrane lipoproteins. As is customary in σ⁵⁴-dependent gene control, a putative NtrC-like enhancer-binding protein, Rrp2, is required to activate the RpoN-RpoS pathway. However, recently it was found that rpoS transcription in Bb also requires another regulator, BosR, which was previously designated as a Fur or PerR homolog. Given this unexpected requirement for a second activator to promote σ⁵⁴-dependent gene transcription, and the fact that regulatory mechanisms among similar species of pathogenic bacteria can be strain-specific, we sought to confirm the regulatory role of BosR in a second virulent strain (strain 297) of Bb. Indeed, BosR displayed the same influence over lipoprotein expression and mammalian infectivity for strain Bb 297 that were previously noted for Bb strain B31. We subsequently found that recombinant BosR (rBosR) bound to the rpoS gene at three distinct sites, and that binding occurred despite the absence of consensus Fur or Per boxes. This led to the identification of a novel direct repeat sequence (TAAATTAAAT) critical for rBosR binding in vitro. Mutations in the repeat sequence markedly inhibited or abolished rBosR binding. Taken together, our studies provide new mechanistic insights into how BosR likely acts directly on rpoS as a positive transcriptional activator. Additional novelty is engendered by the facts that, although BosR is a Fur or PerR homolog and it contains zinc (like Fur and PerR), it has other unique features that clearly set it apart from these other regulators. Our findings also have broader implications regarding a previously unappreciated layer of control that can be involved in σ⁵⁴–dependent gene regulation in bacteria.

Lyme disease, caused by the bacterium Borrelia burgdorferi (Bb), remains the most common arthropod-borne illness in the United States. A critical strategy for Bb to maintain its presence in nature is adaptation to its diverse tick and mammalian (mouse) hosts. To accomplish this, Bb encodes a potential gene regulator, BB0647 (BosR). Herein, we confirmed that BosR is essential for Bb to establish mammalian infection. We then found that purified recombinant BosR bound to the promoter DNA (regulatory region) of rpoS, suggesting that BosR directly controls the expression of the rpoS gene. This study has revealed a new mechanism of bacterial gene control. The discovery that BosR governs Bb's virulence may lead to new strategies to interrupt the bacterium's complex life cycle.

[Effect of rpoS mutation on two gene clusters of phenazine in Psedomonas aeruginosa PAO1]

OBJECTIVE

As an opportunistic pathogen, Pseudomonas aeruginosa PAO1 can produce phenazine and its derivatives, which play a critical role in their pathogenesis. In many bacteria, RpoS, the product of rpoS gene, mediates biosynthesis of a set of secondary metabolites.

OBJECTIVE

This study aims to elucidate rpoS gene's function and regulation on two phenazine gene clusters in Pseudomonas aeruginosa PAO1.

METHODS

The rpoS gene and its upstream and downstream fragments were cloned from the chromosome of Pseudomonas aeruginosa. With the insertion of gentamycin resistance cassette (aacC1), the mutant PA-SG has been created by homologous recombination. Translational fusion plasmids phz1'-'lacZ (pMEZ1) and phz2'-'lacZ (pMEZ2) were constructed, and then were introduced into the wild type strain PAO1 and the mutant PA-SG, respectively. Activities of beta-galactosidase in them were determined with Miller method.

RESULTS

In KMB or PPM medium, beta-galactosidase activity of phzl'-'lacZ in the mutant PA-SG is much more than that in the wild type strain. However, beta-galactosidase activity of phz2'-'lacZ in the wild type strain is 2 -3 folds more than that in the mutant PA-SG.

CONCLUSION

With these results, it is suggested that regulation mediated by rpoS gene on two phenazine loci is specific and different.

Role of RpoS in the susceptibility of low salinity-adapted Vibrio vulnificus to environmental stresses

Vibrio vulnificus is an opportunistic pathogen commonly found in oyster and marine environments, which frequently encounters low salinity stress in its natural and food processing environment. In this study, the responses of a V. vulnificus wild-type strain C78140o and its rpoS isogenic mutant AH1 to sublethal low salinity were examined to investigate the role of rpoS in this response. Both strains, adapted in low salinity (0.4% NaCl), were protected against the lethal low salinity (0.1% NaCl), but were not protected against heat (45 degrees C) or acid stress (pH 3.5), and were sensitized against 5% bile. Protection of the adapted cells against the lethal low salinity was not inhibited by the addition of chloramphenicol. Hemolysis was detected only in the adapted C78140o cells and its spent medium, and was inhibited by chloramphenicol. Transcription of the mechanosensitive channels (VVl_1542 and VVl_2579) and an aquaporin gene (VVl_2010) was markedly increased in the wild-type cells adapted in low salinity medium, while transcription of these genes was slightly enhanced or inhibited in AH1 cells. Results of this study support the active role of rpoS in the low salinity adaptation of V. vulnificus by regulating the expression of virulence and low salinity-associated factors, although rpoS is not related to the immediate protection of the adapted cells against lethal low salinity.

RpoS-independent and growth phase-dependent expression of dcuSR operon of Escherichia coli

The dcuSR operon of Escherichia coli encodes a two-component sensor/kinase-response/regulator system. This system regulates gene expression in response to external C 4 -dicarboxylates. During entry into stationary phase Gram-negative bacteria express genes that impart cellular resistance to environmental stresses. In E. coli , 50 or more genes are triggered by sigma factor ( sigma s ) during entry into stationary phase. Multi-copy dcuS-lacZ and chromosomally integrated dcuS-lacZ fusions analysis showed that the expression of dcuSR is positively regulated during growth phase. Many genes that are required for stationary-phase adaptation are controlled by RpoS, a conserved alternative sigma factor, whose expression is, in turn, controlled by many factors. To understand whether the dcuSR is dependent upon RpoS, a RpoS- dcuS-lacZ strain was generated. beta -Galactosidase assay and Western blot analysis reported that the generated RpoS- dcuS-lacZ strain and the wild type showed the same expression during stationary phase. Surprisingly, the growth phase-dependence of the expression of dcuSR is still present in RpoS- dcuS-lacZ strain suggesting that other growth-phase-dependent regulatory mechanisms (might be the DcuSR system or cAMP/CRP), in addition to RpoS, may control post-exponential dcuSR expression.

Role of RpoS in stress tolerance and environmental fitness of the phyllosphere bacterium Pseudomonas fluorescens strain 122

Bacteria living epiphytically on aerial plant surfaces encounter severe and rapidly fluctuating environmental conditions, and their capacity to withstand environmental stress contributes to epiphytic fitness. The stationary phase sigma factor RpoS is a key determinant in stress response of gram-negative bacteria, including Pseudomonas spp. This study focused on the role of RpoS in stress response and epiphytic fitness of Pseudomonas fluorescens strain 122 on aerial plant surfaces. RpoS had a significant role in the response of the phyllosphere bacterium P. fluorescens 122 to stresses imposed by desiccation, UV irradiation, starvation, and an oxidative environment. While significant, the difference in stress response between an rpoS mutant and the parental strain was less for strain 122 than for the rhizosphere bacterium P. fluorescens Pf-5. No consistent influence of RpoS on epiphytic population size of strain 122 on pear or apple flowers or leaves was observed in field trials. These data may indicate that P. fluorescens occupies protected microsites on aerial plant surfaces where the bacteria escape exposure to environmental stress, or that redundant stress-response mechanisms are operating in this bacterium, thereby obscuring the role of RpoS in epiphytic fitness of the bacterium.

The stationary-phase sigma factor sigma(S) is responsible for the resistance of Escherichia coli stationary-phase cells to mazEF-mediated cell death

Escherichia coli mazEF is a toxin-antitoxin gene module that mediates cell death during exponential-phase cellular growth through either reactive oxygen species (ROS)-dependent or ROS-independent pathways. Here, we found that the stationary-phase sigma factor sigma(S) was responsible for the resistance to mazEF-mediated cell death during stationary growth phase. Deletion of rpoS, the gene encoding sigma(S) from the bacterial chromosome, permitted mazEF-mediated cell death during stationary growth phase.

Expression of Mycobacterium tuberculosis pe_pgrs33 is repressed during stationary phase and stress conditions, and its transcription is mediated by sigma factor A

Although recent work shows that the expression of the PE/PE_PGRS protein family occur both in vitro and in vivo under stress conditions, very little is known about their promoter and how they are regulated. In this work, the promoter region of a member of PE_PGRS family, the PE_PGRS33 was identified and the promoter boxes were determined. To date, this is one of the few reports that describe a promoter region of a PE_PGRS member. In addition, the gene promoter functionality was assayed in Mycobacterium smegmatis with the green fluorescent protein reporter gene fused to different lengths of pe_pgrs33 promoter sequences. The GFP was down-regulated in the stationary phase, under nutrient starvation and oxygen depletion, suggesting that, in stress conditions, regulation of the gene could be under control of a repressor molecule. A 5' rapid amplification of cDNA end assay of transcriptional fusions evaluated in M. smegmatis and in Mycobacterium tuberculosis mRNA revealed a transcription start point 75 nt upstream of the ATG codon and a -10 like-SigA box. Furthermore, a transcription run assay confirmed that SigA mediates in vitro transcription of pe_pgrs33. Interestingly, conserved -10 SigA boxes were found in the intergenic region of several PE_PGRS genes. These results suggest that expression of some PE_PGRS genes may be mediated by SigA, and the differences in expression observed in the gene family could be explained by the participation of additional regulatory genetic elements.

The flagellar sigma factor fliA is required for Dickeya dadantii virulence

The genome sequence of the Enterobacteriaceae phytopathogen Dickeya dadantii (formerly Erwinia chrysanthemi) revealed homologs of genes required for a complete flagellar secretion system and one flagellin gene. We found that D. dadantii was able to swim and swarm but that ability to swarm was dependent upon both growth media and temperature. Mutation of the D. dadantii fliA gene was pleiotropic, with the alternate sigma factor required for flagella production and development of disease symptoms but not bacterial growth in Nicotiana benthamiana leaves. The flagellar sigma factor was also required for multiple bacterial phenotypes, including biofilm formation in culture, bacterial adherence to plant tissue, and full expression of pectate lyase activity (but not cellulase or protease activity). Surprisingly, mutation of fliA resulted in the increased expression of avrL (a gene of unknown function in D. dadantii) and two pectate lyase gene homologs, pelX and ABF-0019391. Because FliA is a key contributor to virulence in D. dadantii, it is a new target for disease control.

Characterization of single and double inactivation strains reveals new physiological roles for group 2 sigma factors in the cyanobacterium Synechocystis sp. PCC 6803

Cyanobacteria are eubacteria that perform oxygenic photosynthesis like plants. The initiation of transcription, mediated by the RNA polymerase holoenzyme, is the main determinant of gene regulation in eubacteria. The sigma factor of the RNA polymerase holoenzyme is responsible for the recognition of a promoter sequence. In the cyanobacterium Synechocystis sp. PCC 6803, the primary sigma factor, SigA, is essential for cell viability. The SigB, SigC, SigD, and SigE factors show significant sequence similarity with the SigA factor but are nonessential. In this study, we have used homology modeling to construct a three-dimensional model of Synechocystis RNA polymerase holoenzyme and all group 1 and 2 sigma factors. According to the models, the overall three-dimensional structures of group 1 and 2 sigma factors are similar, the SigB and SigD factors being the most similar ones. In addition, we have constructed a complete set of group 2 sigma factor double inactivation strains, DeltasigBC, DeltasigBD, DeltasigBE, DeltasigCD, DeltasigCE, and DeltasigDE. All double mutants grow well under standard conditions, but differences are observed in stress conditions. The transition from lag phase to exponential growth is slow in the DeltasigBD strain, and all strains lacking the SigD factor were found to be sensitive to bright light. Furthermore, all group 2 sigma factors were found to be involved in acclimation to salt- or sorbitol-induced osmotic stresses.

Group 2 sigma factors in cyanobacteria

Group 1 and group 2 sigma factors are sigma factors of bacterial RNA polymerase responsible for transcription from consensus-type promoters. Thus, these sigma factors form the framework for basic transcriptional regulation in bacteria. Cyanobacteria are known to have various group 2 sigma factors, typically more than 4, but only recently the particular function of each sigma factor is being elucidated. In response to environmental signals such as nutrients, light and temperature, cyanobacteria change their transcriptional profile first by activating specific transcription factors and subsequently by modifying the basic transcriptional machinery, which is often involved in the regulation of group 2 sigma factors. In this article, we give an overview of the composition and evolution of group 2 sigma factors in cyanobacteria and summarize what was presently revealed regarding their function.

Gac two-component system in Pseudomonas syringae pv. tabaci is required for virulence but not for hypersensitive reaction

Pseudomonas syringae pv. tabaci 6605 causes wildfire disease on host tobacco plants. To investigate the regulatory mechanism of the expression of virulence, Gac two-component system-defective mutants, DeltagacA and DeltagacS, and a double mutant, DeltagacADeltagacS, were generated. These mutants produced smaller amounts of N-acyl homoserine lactones required for quorum sensing, had lost swarming motility, and had reduced expression of virulence-related hrp genes and the algT gene required for exopolysaccharide production. The ability of the mutants to cause disease symptoms in their host tobacco plant was remarkably reduced, while they retained the ability to induce hypersensitive reaction (HR) in the nonhost plants. These results indicated that the Gac two-component system of P. syringae pv. tabaci 6605 is indispensable for virulence on the host plant, but not for HR induction in the nonhost plants.

Analysis of the determinants of bba64 (P35) gene expression in Borrelia burgdorferi using a gfp reporter

The bba64 (P35) gene of Borrelia burgdorferi, the agent of Lyme disease, encodes a surface-exposed lipoprotein. The expression of bba64 in vitro is tightly regulated and dependent on several environmental factors. In nature, its expression is induced in the tick vector during feeding and maintained during infection of the vertebrate host. The pattern of expression of bba64 suggests that it imparts a critical function to the pathogen. A previous study has shown that the expression of bba64 is down-regulated in the absence of RpoS, suggesting that the alternative sigma factor may be involved in its expression. A DNA-binding protein has also been shown to specifically recognize a sequence in the 5' regulatory region of the gene. Therefore, the contribution of these putative determinants to the differential expression of bba64 was investigated. The role of RpoS was critically evaluated by genetic complementation of the rpoS mutant using a chromosomally targeted copy of the wild-type gene. The results confirm that RpoS is indeed required for the expression of bba64. The role of the upstream DNA-binding site was examined using bba64 promoter-gfp transcriptional fusions in a shuttle vector. The DNA-binding site was studied by targeting mutations to an inverted repeat sequence (IRS), the most prominent feature within the binding site, as well as by deletion of the entire sequence upstream of the basal promoter. Quantitative assessment of gene expression demonstrated that neither the IRS nor the sequence upstream of the promoter was essential for expression. Moreover, the expression of the reporter (GFP) appeared to remain RpoS-dependent in all cases, based on the co-expression of GFP and OspC in a subpopulation of spirochaetes and the selective expression of GFP in the stationary phase. Collectively, the data indicate that RpoS is the sole determinant of differential bba64 expression in cultured spirochaetes.

The extracytoplasmic stress factor, sigmaE, is required to maintain cell envelope integrity in Escherichia coli

Extracytoplasmic function or ECF sigma factors are the most abundant class of alternative sigma factors in bacteria. Members of the rpoE subclass of ECF sigma factors are implicated in sensing stress in the cell envelope of Gram-negative bacteria and are required for virulence in many pathogens. The best-studied member of this family is rpoE from Escherichia coli, encoding the σ^E protein. σ^E has been well studied for its role in combating extracytoplasmic stress, and the members of its regulon have been largely defined. σ^E is required for viability of E. coli, yet none of the studies to date explain why σ^E is essential in seemingly unstressed cells. In this work we investigate the essential role of σ^E in E. coli by analyzing the phenotypes associated with loss of σ^E activity and isolating suppressors that allow cells to live in the absence of σ^E. We demonstrate that when σ^E is inhibited, cell envelope stress increases and envelope integrity is lost. Many cells lyse and some develop blebs containing cytoplasmic material along their sides. To better understand the connection between transcription by σ^E and cell envelope integrity, we identified two multicopy suppressors of the essentiality of σ^E, ptsN and yhbW. yhbW is a gene of unknown function, while ptsN is a member of the σ^E regulon. Overexpression of ptsN lowers the basal level of multiple envelope stress responses, but not that of a cytoplasmic stress response. Our results are consistent with a model in which overexpression of ptsN reduces stress in the cell envelope, thereby promoting survival in the absence of σ^E.

Effect of gacS and gacA mutations on colony architecture, surface motility, biofilm formation and chemical toxicity in Pseudomonas sp. KL28

GacS and GacA proteins form a two component signal transduction system in bacteria. Here, Tn5 transposon gacS and gacA (Gac) mutants of Pseudomonas sp. KL28, an alkylphenol degrader, were isolated by selecting for smooth colonies of strain KL28. The mutants exhibited reduced ability to migrate on a solid surface. This surface motility does not require the action of flagella unlike the well-studied swarming motility of other Pseudomonas sp. The Gac mutants also showed reduced levels of biofilm and pellicle formation in liquid culture. In addition, compared to the wild type KL28 strain, these mutants were more resistant to high concentrations of m-cresol but were more sensitive to H2O2, which are characteristics that they share with an rpoS mutant. These results indicate that the Gac regulatory cascade in strain KL28 positively controls wrinkling morphology, biofilm formation, surface translocation and H2O2 resistance, which are important traits for its capacity to survive in particular niches.

A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria

A transcriptional response to singlet oxygen in Rhodobacter sphaeroides is controlled by the group IV sigma factor sigma(E) and its cognate anti-sigma ChrR. Crystal structures of the sigma(E)/ChrR complex reveal a modular, two-domain architecture for ChrR. The ChrR N-terminal anti-sigma domain (ASD) binds a Zn(2+) ion, contacts sigma(E), and is sufficient to inhibit sigma(E)-dependent transcription. The ChrR C-terminal domain adopts a cupin fold, can coordinate an additional Zn(2+), and is required for the transcriptional response to singlet oxygen. Structure-based sequence analyses predict that the ASD defines a common structural fold among predicted group IV anti-sigmas. These ASDs are fused to diverse C-terminal domains that are likely involved in responding to specific environmental signals that control the activity of their cognate sigma factor.

agr-Genotyping and transcriptional analysis of biofilm-producing Staphylococcus aureus

We investigated the correlation between biofilm production and the accessory-gene-regulator (agr) in 29 strains isolated from catheter-associated infections compared to a control group (30 isolates). All strains were tested for their ability to produce biofilm in a static system, and their agr genotype was determined. ScaI-restriction fragment length polymorphism for agr-typing showed that strong biofilm-producing strains belong to agr-type II. We found two new agr-variants, and sequence analysis of the three PCR products revealed the insertion of IS256 within the agr-locus. Biofilm production was assessed and correlated with agr functionality, with the expression of the ica-operon and of two transcriptional regulators, sarA and rsbU. Our data show that agr-II strains produce large amounts of biofilm, possess a defective agr-system show early transcription of icaA and are defective in haemolysin activity, icaR transcription, and in the expression of the sigma(B) activator rsbU. Strains with agrIII are medium biofilm producers, have an inactive agr-system, but express icaAR and rsbU in the late- and postexponential growth phases. In agrI-IV- and -IA-variants, medium or weak biofilm production was found. In these strains, the agr-locus was fully functional, rsbU-icaR and icaA were found in the late- and/or postexponential phases. Biofilm production was not affected by sarA.

gerT, a newly discovered germination gene under the control of the sporulation transcription factor sigmaK in Bacillus subtilis

We report the identification of a gene, herein designated gerT (formerly yozR), that is involved in germination by spores of Bacillus subtilis. The gerT gene is induced late in sporulation under the positive control of the transcription factor sigma(K) and under the negative control of the DNA-binding protein GerE. The gerT gene product (GerT) is a component of the spore coat, and its incorporation into the coat takes place in two stages. GerT initially assembles into foci, which then spread around the developing spore in a process that is dependent on the morphogenetic protein CotE. Mutant spores lacking GerT respond poorly to multiple germinants and are impaired at an early stage of germination.

Essential internal promoter in the spoIIIA locus of Bacillus subtilis

The Bacillus subtilis spoIIIA locus encodes eight proteins, SpoIIIAA to SpoIIIAH, which are expressed in the mother cell during endospore formation and which are essential for the activation of sigma(G) in the forespore. Complementation studies indicated that this locus may be transcribed from two promoters, one promoter upstream from the first gene and possibly a second unidentified promoter within the locus. Fragments of the spoIIIA locus were expressed at an ectopic site to complement the sporulation-defective phenotype of a spoIIIAH deletion, and we determined that complementation required a fragment of DNA that extended into spoIIIAF. To confirm that there was a promoter located in spoIIIAF, we constructed transcriptional fusions to lacZ and found strong sporulation-induced promoter activity. Primer extension assays were used to determine the transcription start site, and point mutations introduced into the -10 and -35 regions of the promoter reduced its activity. This promoter is transcribed by sigma(E)-RNA polymerase and is repressed by SpoIIID. Therefore, we concluded that the spoIIIA locus is transcribed from two promoters, one at the start of the locus (P1(spoIIIA)) and the other within the locus (P2(spoIIIA)). Based on Campbell integrations and reverse transcription-PCR analysis of the P2(spoIIIA) region, we determined that P2(spoIIIA) is sufficient for transcription of spoIIIAG and spoIIIAH. Inactivation of P2(spoIIIA) blocked spore formation, indicating that P2(spoIIIA) is essential for expression of spoIIIAG and spoIIIAH. The P2(spoIIIA) activity is twice the P1(spoIIIA) activity; therefore, larger amounts of SpoIIIAG and SpoIIIAH than of proteins encoded at the upstream end of the locus may be required.

Regulatory overlap and functional redundancy among Bacillus subtilis extracytoplasmic function sigma factors

Bacillus subtilis encodes seven extracytoplasmic function (ECF) sigma factors that regulate partially overlapping regulons related to cell envelope homeostasis and antibiotic resistance. Here, we investigated their physiological role by constructing a mutant set of single, double, triple, and quadruple ECF sigma factor deletions in the undomesticated B. subtilis strain NCIB3610. This mutant set was subsequently screened for defects in motility, multicellular differentiation, and sensitivity to more than 200 chemicals by using Phenotype MicroArrays. A quadruple mutant strain, harboring deletions of the sigV, sigY, sigZ, and ylaC gene, behaved indistinguishably from the wild-type strain, indicative of either regulatory redundancy or very specific functions of these four ECF sigma factors. In contrast, a triple mutant, inactivated for the sigM, sigW, and sigX genes (but none of the corresponding double mutants), showed a biphasic growth behavior and a complete loss of multicellular differentiation, as judged by both colony formation and the inability to form a pellicle. This triple mutant also displayed a greatly increased sensitivity to detergents and several cell wall antibiotics including beta-lactams, polymyxin B, and d-cycloserine. In several cases, these antibiotic-sensitive phenotypes are significantly enhanced in the triple mutant strain relative to strains lacking only one or two sigma factors.

[Suggested interrelationships of RNA-polymerase sigma S subunit and nitrogen control system in Pseudomonas chlororaphis]

The effect of mutation in rpoS gene encoding sigma S subunit of RNA-polymerase on the capacity of Pseudomonas chlororaphis 449 to assimilate nitrogen was investigated. It has been shown that mutant cells with knocked-out rpoS gene had significantly lower capacity to utilize the nitrogen sources such as alanine, proline, histidine, arginine, urea, and ammonium and glutamine synthetase was downregulated in their cell free extracts. Both defects were abolished by glutamine supplementation to the medium. It is suggested that in Pseudomonas chlororaphis the association of the nitrogen control system and the system of gene expression is regulated by RNA-polymerase sigma S subunit, which can be responsible for cell adaptation at nitrogen supply limitation.

sigmaB and the sigmaB-dependent arlRS and yabJ-spoVG loci affect capsule formation in Staphylococcus aureus

The alternative transcription factor sigma(B) of Staphylococcus aureus affects the transcription of the cap gene cluster, required for the synthesis of capsular polysaccharide (CP), although this operon is lacking an apparent sigma(B)-dependent promoter. Regulation of cap expression and CP production in S. aureus strain Newman was shown here to be influenced by sigma(B), the two-component signal transduction regulatory system ArlRS, and the yabJ-spoVG locus to different extents. Inactivation of arlR or deletion of the sigB operon strongly suppressed capA (CP synthesis enzyme A) transcription. Deletion of spoVG had a polar effect on yabJ-spoVG transcription and resulted in a two- to threefold decrease in capA transcription. Interestingly, immunofluorescence showed that CP production was strongly impaired in all three mutants, signaling that the yabJ-spoVG inactivation, despite its only partial effect on capA transcription, abolished capsule formation. trans-Complementation of the DeltaspoVG mutant with yabJ-spoVG under the control of its native promoter restored CP-5 production and capA expression to levels seen in the wild type. Northern analyses revealed a strong impact of sigma(B) on arlRS and yabJ-spoVG transcription. We hypothesize that ArlR and products of the yabJ-spoVG locus may serve as effectors that modulate sigma(B) control over sigma(B)-dependent genes lacking an apparent sigma(B) promoter.