Altered phosphorylation of Bacillus subtilis DegU caused by single amino acid changes in DegS

PRO-Simat: Protein network simulation and design tool

PRO-Simat is a simulation tool for analysing protein interaction networks, their dynamic change and pathway engineering. It provides GO enrichment, KEGG pathway analyses, and network visualisation from an integrated database of more than 8 million protein-protein interactions across 32 model organisms and the human proteome. We integrated dynamical network simulation using the Jimena framework, which quickly and efficiently simulates Boolean genetic regulatory networks. It enables simulation outputs with in-depth analysis of the type, strength, duration and pathway of the protein interactions on the website. Furthermore, the user can efficiently edit and analyse the effect of network modifications and engineering experiments. In case studies, applications of PRO-Simat are demonstrated: (i) understanding mutually exclusive differentiation pathways in Bacillus subtilis, (ii) making Vaccinia virus oncolytic by switching on its viral replication mainly in cancer cells and triggering cancer cell apoptosis and (iii) optogenetic control of nucleotide processing protein networks to operate DNA storage. Multilevel communication between components is critical for efficient network switching, as demonstrated by a general census on prokaryotic and eukaryotic networks and comparing design with synthetic networks using PRO-Simat. The tool is available at https://prosimat.heinzelab.de/ as a web-based query server.

SwrA as global modulator of the two-component system DegSU in Bacillus subtilis

The two-component system DegSU of Bacillus subtilis controls more than one hundred genes involved in several different cellular behaviours. Over the last four decades, the degU32^Hy allele, supposedly encoding a constitutively active mutant of the response regulator DegU, was exploited to define the impact of this system on cell physiology. Those studies concluded that phosphorylated DegU (DegU∼P) induced degradative enzyme expression while repressing flagellar motility and competence. Recent experiments, however, demonstrated that flagella expression is enhanced by DegU∼P if SwrA, a protein only encoded by wild strains, is present. Yet, to promote motility, SwrA must interact with DegU∼P produced by a wild-type degU allele, as it cannot correctly cooperate with the mutant DegU32^Hy protein. In this work, the impact of DegSU was reanalysed in the presence or absence of SwrA employing a DegS kinase mutant, degS200^Hy, to force the activation of the TCS. Our results demonstrate that the role of SwrA in B. subtilis physiology is wider than expected and affects several other DegSU targets. SwrA reduces subtilisin, cellulases and xylanases production while, besides motility, it also positively modulates competence for DNA uptake, remarkably relieving the inhibition caused by DegU∼P alone and restoring transformability in degS200^Hy strains.

Nitric Oxide Enters Quorum Sensing via the H-NOX Signaling Pathway in Vibrio parahaemolyticus

Nitric oxide (NO) plays a major role in the regulation of mammalian biological functions. In recent years, NO has also been implicated in bacterial life cycles, including in the regulation of biofilm formation, and the metabolism of the bacterial second messenger signaling molecule cyclic-di-GMP. In a previous study, we reported the discovery of an NO-responsive quorum sensing (QS) circuit in Vibrio harveyi. Here, we characterize the homologous QS pathway in Vibrio parahaemolyticus. Spectroscopic analysis shows V. parahaemolyticus H-NOX is an NO sensory protein that binds NO in 5/6-coordinated mixed manner. Further, we demonstrate that through ligation to H-NOX, NO inhibits the autophosphorylation activity of an H-NOX-associated histidine kinase (HqsK; H-NOX-associated quorum sensing kinase) that transfers phosphate to the Hpt (histidine-containing phosphotransfer protein) protein LuxU. Indeed, among the three Hpt proteins encoded by V. parahaemolyticus, HqsK transfers phosphate only to the QS-associated phosphotransfer protein LuxU. Finally, we show that NO promotes transcription of the master quorum sensing regulatory gene opaR at low cell density.

Proteases HtrA and HtrB for α-amylase secreted from Bacillus subtilis in secretion stress

HtrA and HtrB are two important proteases across species. In biotechnological industries, they are related to degradation of secreted heterologous proteins from bacteria, especially in the case of overproduction of α-amylases in Bacillus subtilis. Induction of HtrA and HtrB synthesis follows the overproduction of α-amylases in B. subtilis. This is different from the order usually observed in B. subtilis, i.e., the production of proteases is prior to the secretion of proteins. This discrepancy suggests three possibilities: (i) HtrA and HtrB are constantly synthesized from the end of the exponential phase, and then are synthesized more abundantly due to secretion stress; (ii) There is a hysteresis mechanism that holds HtrA and HtrB back from their large amount of secretion before the overproduction of α-amylases; (iii) Heterologous amylases could be a stress to B. subtilis leading to a general response to stress. In this review, we analyze the literature to explore these three possibilities. The first possibility is attributed to the regulatory pathway of CssR-CssS. The second possibility is because sigma factor σD plays a role in the overproduction of α-amylases and is subpopulation dependent with the switch between "ON" and "OFF" states that is fundamental for a bistable system and a hysteresis mechanism. Thus, sigma factor σD helps to hold HtrA and HtrB back from massive secretion before the overproduction of α-amylases. The third possibility is that several sigma factors promote the secretion of proteases at the end of the exponential phase of growth under the condition that heterologous amylases are considered as a stress.

A single amino acid mutation in Spo0A results in sporulation deficiency of Paenibacillus polymyxa SC2

Sporulating bacteria such as Bacillus subtilis and Paenibacillus polymyxa exhibit sporulation deficiencies during their lifetime in a laboratory environment. In this study, spontaneous mutants SC2-M1 and SC2-M2, of P. polymyxa SC2 lost the ability to form endospores. A global genetic and transcriptomic analysis of wild-type SC2 and spontaneous mutants was carried out. Genome resequencing analysis revealed 14 variants in the genome of SC2-M1, including three insertions and deletions (indels), 10 single nucleotide variations (SNVs) and one intrachromosomal translocation (ITX). There were nine variants in the genome of SC2-M2, including two indels and seven SNVs. Transcriptomic analysis revealed that 266 and 272 genes showed significant differences in expression in SC2-M1 and SC2-M2, respectively, compared with the wild-type SC2. Besides sporulation-related genes, genes related to exopolysaccharide biosynthesis (eps), antibiotic (fusaricidin) synthesis, motility (flgB) and other functions were also affected in these mutants. In SC2-M2, reversion of spo0A resulted in the complete recovery of sporulation. This is the first global analysis of mutations related to sporulation deficiency in P. polymyxa. Our results demonstrate that a SNV within spo0A caused the sporulation deficiency of SC2-M2 and provide strong evidence that an arginine residue at position 211 is essential for the function of Spo0A.

Homogeneity and heterogeneity in amylase production by Bacillus subtilis under different growth conditions

Background

Bacillus subtilis is an important cell factory for the biotechnological industry due to its ability to secrete commercially relevant proteins in large amounts directly into the growth medium. However, hyper-secretion of proteins, such as α-amylases, leads to induction of the secretion stress-responsive CssR-CssS regulatory system, resulting in up-regulation of the HtrA and HtrB proteases. These proteases degrade misfolded proteins secreted via the Sec pathway, resulting in a loss of product. The aim of this study was to investigate the secretion stress response in B. subtilis 168 cells overproducing the industrially relevant α-amylase AmyM from Geobacillus stearothermophilus, which was expressed from the strong promoter P(amyQ)-M.

Results

Here we show that activity of the htrB promoter as induced by overproduction of AmyM was “noisy”, which is indicative for heterogeneous activation of the secretion stress pathway. Plasmids were constructed to allow real-time analysis of P(amyQ)-M promoter activity and AmyM production by, respectively, transcriptional and out-of-frame translationally coupled fusions with gfpmut3. Our results show the emergence of distinct sub-populations of high- and low-level AmyM-producing cells, reflecting heterogeneity in the activity of P(amyQ)-M. This most likely explains the heterogeneous secretion stress response. Importantly, more homogenous cell populations with regard to P(amyQ)-M activity were observed for the B. subtilis mutant strain 168degUhy32, and the wild-type strain 168 under optimized growth conditions.

Conclusion

Expression heterogeneity of secretory proteins in B. subtilis can be suppressed by degU mutation and optimized growth conditions. Further, the out-of-frame translational fusion of a gene for a secreted target protein and gfp represents a versatile tool for real-time monitoring of protein production and opens novel avenues for Bacillus production strain improvement.

An alternate route to phosphorylating DegU of Bacillus subtilis using acetyl phosphate

Background

Two-component signal transduction pathways allow bacteria to sense and respond to the environment. Typically such pathways comprise a sensor histidine kinase and a response regulator. Phosphorylation of the response regulator commonly results in its activation, allowing the protein to bind to target promoter elements to regulate transcription. Several mechanisms are used to prevent inappropriate phosphorylation of the response regulator, thereby ensuring a specific response. In Bacillus subtilis, the DegS-DegU two-component system controls transcription of target genes in a manner dependent on the level of the phosphorylated response regulator, DegU. Previous work has tentatively indicated that DegU, and DegU H¹²L, a DegU variant which displays enhanced stability of the phosphoryl moiety, can be phosphorylated in the absence of the kinase, DegS.

Results

The data presented here reveal that DegU H¹²L requires aspartic acid 56 (D⁵⁶), the identified DegU phosphorylation site, for its activity. By indirectly measuring the level of DegU ~ P in the cell by assessment of several well recognised DegU regulated processes it was shown that DegU H¹²L retains its activity in the absence of DegS, and that mutation of D⁵⁶ produced an inactive protein. Further experiments designed to raise the level of acetyl phosphate within the cell suggest that DegU can be phosphorylated by acetyl phosphate in the absence of degS. Additionally, the phenotypic and biochemical experiments presented indicate that DegU H¹²L can reliably mimic high levels of phosphorylated DegU.

Conclusions

The ability of acetyl phosphate to modify DegU, and indeed DegU H¹²L, reveal an additional layer of regulation for DegU phosphorylation that will be relevant when the level of DegS is low or in the absence of degS. Given the number of processes that DegU can activate or inhibit, extensive regulation at a number of levels is required to ensure that the system is not inappropriately stimulated. DegS has both kinase and phosphatase activity and our findings demonstrate that the phosphatase activity of DegS is essential to control the level of DegU phosphate. Overall we contribute to our understanding of how the intricate signalling pathway DegS-DegU is regulated in B. subtilis.

The role of SwrA, DegU and P(D3) in fla/che expression in B. subtilis

In B. subtilis swarming and robust swimming motility require the positive trigger of SwrA on fla/che operon expression. Despite having an essential and specific activity, how SwrA executes this task has remained elusive thus far. We demonstrate here that SwrA acts at the main σ^A-dependent fla/che promoter P_A(fla/che) through DegU. Electrophoretic mobility shift assays (EMSA) reveal that SwrA forms a complex with the phosphorylated form of DegU (DegU~P) at P_A(fla/che) while it is unable to do so with either unphosphorylated DegU or the DegU32(Hy) mutant protein. Motility assays show that a highly phosphorylated DegU is not detrimental for flagellar motility provided that SwrA is present; however, DegU~P represses P_A(fla/che) in the absence of SwrA. Overall, our data support a model in which DegU~P is a dual regulator, acting either as a repressor when alone or as a positive regulator of P_A(fla/che) when combined with SwrA. Finally, we demonstrate that the σ^D-dependent P_D3(fla/che) promoter plays an important role in motility, representing a contingent feedback loop necessary to maintain basal motility when swrA is switched to the non-functional swrA^- status.

Mutations suppressing the loss of DegQ function in Bacillus subtilis (natto) poly-γ-glutamate synthesis

The degQ gene of Bacillus subtilis (natto), encoding a small peptide of 46 amino acids, is essential for the synthesis of extracellular poly-gamma-glutamate (γPGA). To elucidate the role of DegQ in γPGA synthesis, we knocked out the degQ gene in Bacillus subtilis (natto) and screened for suppressor mutations that restored γPGA synthesis in the absence of DegQ. Suppressor mutations were found in degS, the receptor kinase gene of the DegS-DegU two-component system. Recombinant DegS-His(6) mutant proteins were expressed in Escherichia coli cells and subjected to an in vitro phosphorylation assay. Compared with the wild type, mutant DegS-His(6) proteins showed higher levels of autophosphorylation (R208Q, M195I, L248F, and D250N), reduced autodephosphorylation (D250N), reduced phosphatase activity toward DegU, or a reduced ability to stimulate the autodephosphorylation activity of DegU (R208Q, D249G, M195I, L248F, and D250N) and stabilized DegU in the phosphorylated form. These mutant DegS proteins mimic the effect of DegQ on wild-type DegSU in vitro. Interestingly, DegQ stabilizes phosphorylated DegS only in the presence of DegU, indicating a complex interaction of these three proteins.

SwrAA activates poly-γ-glutamate synthesis in addition to swarming in Bacillus subtilis

Poly-γ-glutamic acid (γ-PGA) is an extracellular polymer produced by various strains of Bacillus. Ιt was first described as the component of the capsule in Bacillus anthracis, where it plays a relevant role in virulence. γ-PGA is also a distinctive component of ‘natto’, a traditional Japanese food consisting of soybean fermented by Bacillus subtilis (natto). Domesticated B. subtilis strains do not synthesize γ-PGA although they possess the functional biosynthetic pgs operon. In the present work we explore the correlation between the genetic determinants, swrAA and degU, which allow a derivative of the domestic strain JH642 to display a mucoid colony morphology on LB agar plates due to the production of γ-PGA. Full activation of the pgs operon requires the co-presence of SwrAA and the phosphorylated form of DegU (DegU∼P). The presence of either DegU∼P or SwrAA alone has only marginal effects on pgs operon transcription and γ-PGA production. Although SwrAA was identified as necessary for swarming and full swimming motility together with DegU, we show that motility is not involved in γ-PGA production. Activation of γ-PGA synthesis is therefore a motility-independent phenotype in which SwrAA and DegU∼P display a cooperative effect.

A pivotal role for the response regulator DegU in controlling multicellular behaviour

Bacteria control multicellular behavioural responses, including biofilm formation and swarming motility, by integrating environmental cues through a complex regulatory network. Heterogeneous gene expression within an otherwise isogenic cell population that allows for differentiation of cell fate is an intriguing phenomenon that adds to the complexity of multicellular behaviour. This review focuses on recent data about how DegU, a pleiotropic response regulator, co-ordinates multicellular behaviour in Bacillus subtilis. We review studies that challenge the conventional understanding of the molecular mechanisms underpinning the DegU regulatory system and others that describe novel targets of DegU during activation of biofilm formation by B. subtilis. We also discuss a novel role for DegU in regulating multicellular processes in the food-borne pathogen Listeria monocytogenes.

Involvement of nitrogen regulation in Bacillus subtilis degU expression

Bacillus subtilis DegS-DegU belongs to a bacterial two-component system that controls many processes, including the production of exocellular proteases and competence development. It was found that when the glutamine synthetase gene glnA, which is involved in nitrogen regulation, was disrupted, the expression of the response regulator degU gene was increased. Deletion analysis and 5'-end mapping of the degU transcripts showed that the increase was caused by induction of a promoter (P2) located before the degU gene. Disruption of tnrA, a global regulator of nitrogen regulation, eliminated the P2 promoter induction by the glnA mutation. The fact that the P2 promoter is under nitrogen regulation was demonstrated by an increase in P2 expression with nitrogen-limited growth. It was also found by primer extension analysis that degU was transcribed by another promoter, P3, that is located downstream of P2. Efficient expression of P3 was dependent on phosphorylated DegU, as inactivation of the sensor kinase gene, degS, resulted in the loss of degU expression, although less efficient stimulation of degU expression was also observed with an enhanced level of DegU in a degS-deficient mutant. The promoter located upstream of the degSU operon, designated the P1 promoter here, was insensitive to glnA and degU mutations. These results suggest that degU expression is controlled by the three promoters under different growth conditions.

Gradual activation of the response regulator DegU controls serial expression of genes for flagellum formation and biofilm formation inBacillus subtilis

In natural environments, bacteria fluctuate between growth as motile cells and growth as sessile, biofilm-forming cells. However, what controls the transition between these two-growth modes in Bacillus subtilis is not well understood yet. The degU mutation prevents both flagellum formation and biofilm formation, suggesting that one of the transition mechanisms may underlie regulation of the DegU activity. The expression profiles of DegU-regulated genes differed; flagellar genes and several unknown genes were expressed during the exponential phase, whereas other genes were induced in the stationary phase. The degS mutation did not affect transcription of the flgB-sigD operon, but reduced transcription of sigma(D)-dependent flagellar genes, degU and other DegU-regulated genes. In addition, the degQ mutation did not affect transcription of flagellar genes but reduce transcription of other DegU-regulated genes. Purified DegQ protein stimulated phosphotransfer from phospho-DegS to DegU in vitro. Moreover, DegU binds the promoter region of flgB with a high affinity, whereas DegU binds to the promoter regions of other DegU-regulated genes with a low affinity and in a DegS-dependent manner. Taken together, we propose that a gradual increase in DegU and phospho-DegU levels induces a transition from growth as motile cells to growth as sessile, biofilm-forming cells.

Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein

The large majority of histidine kinases (HKs) are multifunctional enzymes having autokinase, phosphotransfer and phosphatase activities, and most of these are transmembrane sensor proteins. Sensor HKs possess conserved cytoplasmic phosphorylation and ATP-binding kinase domains. The different enzymatic activities require participation by one or both of these domains, implying the need for different conformational states. The catalytic domains are linked to the membrane through a coiled-coil segment that sometimes includes other domains. We describe here the first crystal structure of the complete cytoplasmic region of a sensor HK, one from the thermophile Thermotoga maritima in complex with ADPbetaN at 1.9 A resolution. The structure reveals previously unidentified functions for several conserved residues and reveals the relative disposition of domains in a state seemingly poised for phosphotransfer. The structure thereby inspires hypotheses for the mechanisms of autophosphorylation, phosphotransfer and response-regulator dephosphorylation, and for signal transduction through the coiled-coil segment. Mutational tests support the functional relevance of interdomain contacts.

DegU-P represses expression of the motility fla-che operon in Bacillus subtilis

Bacillus subtilis implements several adaptive strategies to cope with nutrient limitation experienced at the end of exponential growth. The DegS-DegU two-component system is part of the network involved in the regulation of postexponential responses, such as competence development, the production of exoenzymes, and motility. The degU32(Hy) mutation extends the half-life of the phosphorylated form of DegU (DegU-P); this in turn increases the production of alkaline protease, levan-sucrase, and other exoenzymes and inhibits motility and the production of flagella. The expression of the flagellum-specific sigma factor SigD, of the flagellin gene hag, and of the fla-che operon is strongly reduced in a degU32(Hy) genetic background. To investigate the mechanism of action of DegU-P on motility, we isolated mutants of degU32(Hy) that completely suppressed the motility deficiency. The mutations were genetically mapped and characterized by PCR and sequencing. Most of the mutations were found to delete a transcriptional termination signal upstream of the main flagellar operon, fla-che, thus allowing transcriptional readthrough from the cod operon. Two additional mutations improved the sigmaA-dependent promoter sequence of the fla-che operon. Using an electrophoretic mobility shift assay, we have demonstrated that purified DegU binds specifically to the PA promoter region of the fla-che operon. The data suggest that DegU represses transcription of the fla-che operon, and they indicate a central role of the operon in regulating the synthesis and assembly of flagella.

The bacterial condensin/cohesin-like protein complex acts in DNA repair and regulation of gene expression

Structural maintenance of chromosome (SMC) and the SMC-interacting kleisin protein families have key functions in the chromosome organization of most organisms. Here, we report that the Bacillus subtilis kleisin, ScpA, can form a ternary complex with the SMC and ScpB proteins in a yeast tri-hybrid assay, supporting the notion of a bacterial cohesin/condensin-like complex. Furthermore, ScpA interacts in two-hybrid assays with the AddAB complex, essential for recombinational repair, with DegS, a two-component sensor kinase, as well as with other potential transcription regulators. Point mutations in scpA allowing growth under conditions not permissive for the spcA null and not affecting chromosome condensation were isolated. Among these mutations, some affected DNA repair and gene regulation, thus separating ScpA functions in these two pathways from its functions in chromosome condensation and segregation. Some separation-of-function mutations in scpA caused a deficiency in the repair of mitomycin C DNA lesions that was suppressed by increasing the intracellular dosage of the interacting AddAB complex. Another mutation in scpA deregulated the expression of genes encoding degradative enzymes that are known to be controlled by the interacting DegS kinase. We propose that the SMC-ScpA-ScpB complex could: (i) recruit the AddAB helicase/nuclease to act in post-replicative repair; and (ii) form a complex with the DegS sensor kinase that inhibits its kinase activity. Moreover, our results indicate that the role of cohesin and condensin complexes in DNA repair and gene regulation is evolutionary conserved.

Involvement of stringent factor RelA in expression of the alkaline protease gene aprE in Bacillus subtilis

Expression of Bacillus subtilis aprE, encoding an extracellular alkaline protease, is positively regulated by phosphorylated DegU, the regulator of a two-component regulatory system, DegS-DegU. We found that the expression of an aprE'-'lacZ fusion was greatly reduced in a disruption mutant with a mutation of relA, which encodes the stringent factor RelA. The level of DegU in the relA mutant was similar to that in the wild-type cell. A relA degU double mutation did not result in a further decrease of the aprE'-'lacZ level found in a degU single mutant. The expression of the aprE'-'lacZ fusion in the relA mutant was stimulated by multicopy degR or the degU32(Hy) and degS200(Hy) mutations that cause the stabilization of phosphorylated DegU. Furthermore, the expression of sacB'-'lacZ, which is also dependent on phosphorylated DegU, was stimulated by the relA mutation, and this stimulation was not seen in the relA degU double mutant. These results show that RelA (or its product guanosine-3',5'-bisdiphosphate [pp Gpp]) does not affect the phosphorylation of DegU and suggest that it participates in the expression of aprE and sacB through the regulation of DegU-dependent transcription.

Complexation precedes phosphorylation for two-component regulatory system FixL/FixJ of Sinorhizobium meliloti

The FixL/FixJ two-component regulatory system of Sinorhizobium meliloti controls the expression of nitrogen fixation genes in response to O2. When phosphorylated, the transcription factor FixJ binds to the nifA and fixK promoters in S. meliloti and induces expression of the corresponding genes, both of which encode key transcription activators. Phosphorylation of FixJ has been proposed to occur via the following cascade. The sensor kinase FixL reacts with ATP independently of FixJ, transferring a phosphoryl group to one of its own histidine residues. Dissociation of O2 from a heme-binding PAS domain in FixL greatly accelerates the rate of this autophosphorylation. The phosphoryl group is rapidly transferred from phospho-FixL to an aspartate residue on FixJ. The resulting phospho-FixJ is short-lived, due to a FixL-catalyzed hydrolysis of the aspartyl phosphate. Here, we show that phosphorylation of FixLJ, i.e. the complex of FixL with FixJ, is at least tenfold faster than the phosphorylation of FixL without FixJ. We further show that a phospho-FixJ phosphatase, thought to reside in FixL, is absent from this complex. These results indicate that FixLJ reacts with ATP as a unit and much more efficiently than FixL alone, and that autophosphorylation and phosphoryl transfer do not occur independently, in sequence, but rather in a closely coupled processive reaction. These findings highlight the possible influence of synergistic interactions of the regulatory components in two-component-system signal transduction.

Decay of activated Bacillus subtilis pho response regulator, PhoP approximately P, involves the PhoR approximately P intermediate

PhoR of Bacillus subtilis is a histidine sensor-kinase belonging to the family of two-component signal transduction systems. PhoR is responsible for processing the phosphate-starvation signal and providing phosphate input to regulate the level of phosphorylated response regulator, PhoP, which activates/represses Pho regulon gene transcription. The catalytic domain of PhoR is sufficient for the low-phosphate inducible expression of Pho regulon genes since removing the N-terminal membrane-associated domain did not alter the kinetics of Pho induction, albeit the total level of induction was decreased (1). In this study we showed that the complete B. subtilis PhoR protein produced in Escherichia coli can be reverse phosphorylated by PhoP-phosphate. We also used a C-terminal fragment of the PhoR protein, PhoR, to demonstrate that the phosphoryl group on phospho-PhoP was transferred back to PhoR in the reverse phosphorylation reaction or released as inorganic phosphate to the reaction mixture. The reverse phosphorylation of the PhoR protein likely occurs at the same histidine residue (His360) that is utilized for the autokinase reaction by the same protein. In the presence of ADP, the phosphoryl group is further transferred to ADP to form ATP. While the autokinase reaction, the forward phosphotransfer reaction from PhoR approximately P to PhoP, and the release of inorganic phosphate from PhoP approximately P in the presence of PhoR require Mg(2+), the reverse phosphotransfer from PhoP approximately P to PhoR does not. These results indicate that the energy levels of the phosphoryl groups on PhoP and PhoR are very similar. The reversible autokinase reaction and/or the reversible phosphotransfer reaction between PhoR approximately P and PhoP may have a role in PhoP approximately P decay thus influencing the PhoP approximately P concentration in the cell.

Signal decay through a reverse phosphorelay in the Arc two-component signal transduction system

Escherichia coli senses and signals anoxic or low redox conditions in its growth environment by the Arc two-component system. Under those conditions, the tripartite sensor kinase ArcB undergoes autophosphorylation at the expense of ATP and subsequently transphosphorylates its cognate response regulator ArcA through a His --> Asp --> His --> Asp phosphorelay pathway. In this study we used various combinations of wild-type and mutant ArcB domains to analyze in vitro the pathway for signal decay. The results indicate that ArcA-P dephosphorylation does not occur by direct hydrolysis but by transfer of the phosphoryl group to the secondary transmitter and subsequently to the receiver domain of ArcB. This reverse phosphorelay involves both the conserved His-717 of the secondary transmitter domain and the conserved Asp-576 of the receiver domain of ArcB but not the conserved His-292 of its primary transmitter domain. This novel pathway for signal decay may generally apply to signal transduction systems with tripartite sensor kinases.

Transcription of Bacillus subtilis degR is sigma D dependent and suppressed by multicopy proB through sigma D

Production of Bacillus subtilis exoproteases is positively regulated by the DegS-DegU two-component regulatory system and other regulatory factors including DegR and ProB. It was shown that the expression of degR was virtually abolished in a sigD mutant and that the transcriptional initiation site in vivo is preceded by a sequence very similar to the consensus sequence of sigma D-recognized promoters. Alteration of the -10 sequence of the putative promoter greatly reduced the expression of degR. These results show that degR expression is driven by the alternative sigma factor, sigma D. It was found that degR expression was suppressed by multiple copies of proB on plasmid pLC1 and that this suppression was exerted at the transcriptional level through a target in the vicinity of the degR promoter. Furthermore, it was shown that the expression of another sigma D-directed gene, hag, was suppressed by pLC1. Suppression by pLC1 diminished when the sequence of the -10 element of the degR promoter was changed to a sigma A-like promoter sequence. pLC1, however, did not suppress sigD expression. On the basis of these results, we conclude that multicopy proB on pLC1 inhibits transcription from sigma D-driven promoters by affecting some posttranscriptional process of sigma D.

Cloning and sequencing the degS-degU operon from an alkalophilic Bacillus brevis

The sacU region from an alkalophilic Bacillus brevis was cloned and sequenced. The two open reading frames of the degS-degU operon encode polypeptides that gave calculated molecular masses of 43.8 kDa and 27.0 kDa, respectively. Sequence comparisons at the amino acid level to the B. subtilis degS-degU genes showed 74% and 84% similarity, respectively. On a multicopy vector the B. brevis degS-degU genes were found to cause hypersecretion of several extracellular enzymes in a B. subtilis rec- strain as well as in a B. subtilis sacU(HY) strain.

Multiple copies of the proB gene enhance degS-dependent extracellular protease production in Bacillus subtilis

Bacillus subtilis secretes extracellular proteases whose production is positively regulated by a two-component regulatory system, DegS-DegU, and other regulatory factors including DegR. To identify an additional regulatory gene(s) for exoprotease production, we performed a shotgun cloning in the cell carrying multiple copies of degR and found a transformant producing large amounts of the exoproteases. The plasmid in this transformant, pLC1, showed a synergistic effect with multiple copies of degR on the production of the extracellular proteases, and it required degS for its enhancing effect. The DNA region responsible for the enhancement contained the proB gene, as shown by restriction analyses and sequence determination. The proB gene encoding gamma-glutamyl kinase was followed by the proA gene encoding glutamyl-gamma-semialdehyde dehydrogenase at an interval of 39 nucleotides, suggesting that the genes constitute an operon. pLC1 contained the complete proB gene and a part of proA lacking the proA C-terminal region. It was also found that proB on the chromosome showed a synergistic effect with multiple copies of degR. We consider on the basis of these results that the metabolic intermediate, gamma-glutamyl phosphate, would transmit a signal to DegS, resulting in a higher level of phosphorylated DegU. Possible involvement of DegR in this process is discussed.

Stabilization of the phosphorylated form of Bacillus Subtilis DegU caused by degU9 mutation

A Bacillus subtilis response regulator, DegU9, carrying an amino acid alteration caused by the degU9(Hy) mutation was partially purified and phosphorylation and dephosphorylation of the protein was studied. The extent of phosphorylation was not as high as the level attained with wild-type DegU, but the DegU9-phosphate once formed was more stable that the wild-type DegU-phosphate. An in vivo study with a degU9 mutant showed that degS was necessary for the overproduction of exoproteases. These results suggest that phosphorylation is necessary for the mutant DegU9 to exert its effect and that the higher stability of phosphorylated DegU9 is responsible for the overproduction phenotype.

Mutants of the two-component regulatory protein FixJ of Rhizobium meliloti that have increased activity at the nifA promoter

FixL and FixJ belong to a two-component regulatory system in Rhizobium meliloti that induces the expression of numerous nitrogen-fixation genes during symbiosis with alfalfa. FixJ is a positive activator required for transcription of the regulatory genes nifA and fixK, while FixL is an oxygen-binding hemoprotein capable of regulating the phosphorylation status of both itself and FixJ, in response to oxygen availability. In this study, we isolated four FixJ mutants that display increased activity at the nifA promoter (PnifA) in Escherichia coli. All four mutants possess amino acid changes in a domain of FixJ that is conserved in other response regulator proteins, and all exhibit increased activity at PnifA in R. meliloti that is dependent on the presence of FixL. One of the mutant proteins, while less efficient at accepting phosphate from a truncated derivative of FixL (FixL*), nevertheless has a phosphorylated form that is more stable than the phosphorylated form of wild-type (wt) FixJ and is more resistant to the phosphatase activity of FixL*. The wt FixJ-phosphate was found to have a half-life of approximately 4 h, which makes it an unusually long-lived response regulator protein. The exceptional stability of wt FixJ-phosphate and the altered phosphorylation properties observed for the mutant are discussed in relation to signal transduction in the FixLJ system.

ATP-dependent protein kinases in bacteria

Protein phosphorylation has been shown to occur in over fifty different bacterial species and, therefore, seems to be a universal device among prokaryotes. Most of the protein kinases responsible for this modification of proteins share the common property of using adenosine triphosphate as phosphoryl donor. However, they differ from one another in a number of structural and functional aspects. Namely, they exhibit a varying acceptor amino acid specificity and can be classified, on this basis, in three main groups: protein-histidine kinases, protein-serine/threonine kinases and protein-tyrosine kinases.

Stabilization of phosphorylated Bacillus subtilis DegU by DegR

The production of Bacillus subtilis extracellular proteases is under positive and negative regulation. The functional role of degR, one of the positive regulators, was studied in relation to the degS and degU gene products, which belong to the bacterial two-component regulatory system. Studies with a translational fusion between the Escherichia coli lacZ and the Bacillus subtilis subtilisin (aprE) genes indicated that the stimulatory site of DegR lay upstream of position -140, with the region upstream of position -200 being the major target. It was also found that degS and degU were epistatic to degR. These results suggested some relationship among the degR, degS, and degU gene products. The DegR protein was purified to homogeneity, and its in vitro effect on the phosphorylation reaction involving DegS and DegU was studied. For this purpose, a soluble-extract system in which the formation and dephosphorylation of DegU-phosphate could be examined was devised. The addition of DegR to the soluble-extract system enhanced the formation of DegU-phosphate. The enhancing effect was found to be due to the protection of DegU-phosphate from dephosphorylation. From these results, it was concluded that the positive effect of DegR on the production of the extracellular proteases is brought about by the stabilization of DegU-phosphate, which in turn may result in the stimulation of transcription of the exoprotease genes.

A degU-containing SP beta prophage complements superactivator mutations affecting the Bacillus subtilis degSU operon

The Bacillus subtilis degSU two-gene operon encodes a two-component regulatory system which positively controls expression of a variety of genes encoding degradative enzymes. Point superactivator mutations in either degS or degU increase the production of these enzymes. A specialized transducing SP beta phage which partially complements several of these mutations was isolated from a phage library of the B. subtilis chromosome. This phage was shown to contain the degU (wild-type) gene. This unexpected co-dominance is discussed.