ALT: a new factor involved in the synthesis of RNA by Escherichia coli

Mutations in the Global Transcription Factor CRP/CAP: Insights from Experimental Evolution and Deep Sequencing

The Escherichia coli cyclic AMP receptor protein (CRP or catabolite activator protein, CAP) provides a textbook example of bacterial transcriptional regulation and is one of the best studied transcription factors in biology. For almost five decades a large number of mutants, evolved in vivo or engineered in vitro, have shed light on the molecular structure and mechanism of CRP. Here, we review previous work, providing an overview of studies describing the isolation of CRP mutants. Furthermore, we present new data on deep sequencing of different bacterial populations that have evolved under selective pressure that strongly favors mutations in the crp locus. Our new approach identifies more than 100 new CRP mutations and paves the way for a deeper understanding of this fascinating bacterial master regulator.

Bacterial sigma factors: a historical, structural, and genomic perspective

Transcription initiation is the crucial focal point of gene expression in prokaryotes. The key players in this process, sigma factors (σs), associate with the catalytic core RNA polymerase to guide it through the essential steps of initiation: promoter recognition and opening, and synthesis of the first few nucleotides of the transcript. Here we recount the key advances in σ biology, from their discovery 45 years ago to the most recent progress in understanding their structure and function at the atomic level. Recent data provide important structural insights into the mechanisms whereby σs initiate promoter opening. We discuss both the housekeeping σs, which govern transcription of the majority of cellular genes, and the alternative σs, which direct RNA polymerase to specialized operons in response to environmental and physiological cues. The review concludes with a genome-scale view of the extracytoplasmic function σs, the most abundant group of alternative σs.

Insensitivity of D-amino acid dehydrogenase synthesis to catabolic repression in dadR mutants of Salmonella typhimurium

It has been found that synthesis of D-amino acid dehydrogenase in Salmonella typhimurium is stimulated by cyclic AMP and crp gene product. This indicates that catabolic control of the dehydrogenase resembles other bacterial systems of catabolic repression. We have isolated S. typhimurium mutants, dadR, which are resistant to L-methionine-interference with D-histidine utilization and are able to utilize D-tryptophan as a precursor of L-tryptophan. Mapping data indicate that the dadR locus is closely linked to dadA coding for the structure of D-amino acid dehydrogenase. The synthesis of the dehydrogenase in dadR mutants is completely insensitive to the repression by glucose, but remains inducible by L-alanine. We conclude thereof that dadR mutants have changes in the promoter region which increase the expression of the dadA gene in the presence of glucose metabolism. A likely possibility that induction of the dad operon by alanine might be under positive control is discussed.

Amino acid contacts between sigma 70 domain 4 and the transcription activators RhaS and RhaR

The RhaS and RhaR proteins are transcription activators that respond to the availability of L-rhamnose and activate transcription of the operons in the Escherichia coli L-rhamnose catabolic regulon. RhaR activates transcription of rhaSR, and RhaS activates transcription of the operon that encodes the L-rhamnose catabolic enzymes, rhaBAD, as well as the operon that encodes the L-rhamnose transport protein, rhaT. RhaS is 30% identical to RhaR at the amino acid level, and both are members of the AraC/XylS family of transcription activators. The RhaS and RhaR binding sites overlap the -35 hexamers of the promoters they regulate, suggesting they may contact the sigma70 subunit of RNA polymerase as part of their mechanisms of transcription activation. In support of this hypothesis, our lab previously identified an interaction between RhaS residue D241 and sigma70 residue R599. In the present study, we first identified two positively charged amino acids in sigma70, K593 and R599, and three negatively charged amino acids in RhaR, D276, E284, and D285, that were important for RhaR-mediated transcription activation of the rhaSR operon. Using a genetic loss-of-contact approach we have obtained evidence for a specific contact between RhaR D276 and sigma70 R599. Finally, previous results from our lab separately showed that RhaS D250A and sigma70 K593A were defective at the rhaBAD promoter. Our genetic loss-of-contact analysis of these residues indicates that they identify a second site of contact between RhaS and sigma70.

Bacterial two-hybrid analysis of interactions between region 4 of the sigma(70) subunit of RNA polymerase and the transcriptional regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa

A number of transcriptional regulators mediate their effects through direct contact with the sigma(70) subunit of Escherichia coli RNA polymerase (RNAP). In particular, several regulators have been shown to contact a C-terminal portion of sigma(70) that harbors conserved region 4. This region of sigma contains a putative helix-turn-helix DNA-binding motif that contacts the -35 element of sigma(70)-dependent promoters directly. Here we report the use of a recently developed bacterial two-hybrid system to study the interaction between the putative anti-sigma factor Rsd and the sigma(70) subunit of E. coli RNAP. Using this system, we found that Rsd can interact with an 86-amino-acid C-terminal fragment of sigma(70) and also that amino acid substitution R596H, within region 4 of sigma(70), weakens this interaction. We demonstrated the specificity of this effect by showing that substitution R596H does not weaken the interaction between sigma and two other regulators shown previously to contact region 4 of sigma(70). We also demonstrated that AlgQ, a homolog of Rsd that positively regulates virulence gene expression in Pseudomonas aeruginosa, can contact the C-terminal region of the sigma(70) subunit of RNAP from this organism. We found that amino acid substitution R600H in sigma(70) from P. aeruginosa, corresponding to the R596H substitution in E. coli sigma(70), specifically weakens the interaction between AlgQ and sigma(70). Taken together, our findings suggest that Rsd and AlgQ contact similar surfaces of RNAP present in region 4 of sigma(70) and probably regulate gene expression through this contact.

Genetic evidence that transcription activation by RhaS involves specific amino acid contacts with sigma 70

RhaS activates transcription of the Escherichia coli rhaBAD and rhaT operons in response to L-rhamnose and is a member of the AraC/XylS family of transcription activators. We wished to determine whether sigma(70) might be an activation target for RhaS. We found that sigma(70) K593 and R599 appear to be important for RhaS activation at both rhaBAD and rhaT, but only at truncated promoters lacking the binding site for the second activator, CRP. To determine whether these positively charged sigma(70) residues might contact RhaS, we constructed alanine substitutions at negatively charged residues in the C-terminal domain of RhaS. Substitutions at four RhaS residues, E181A, D182A, D186A, and D241A, were defective at both truncated promoters. Finally, we assayed combinations of the RhaS and sigma(70) substitutions and found that RhaS D241 and sigma(70) R599 met the criteria for interacting residues at both promoters. Molecular modeling suggests that sigma(70) R599 is located in very close proximity to RhaS D241; hence, this work provides the first evidence for a specific residue within an AraC/XylS family protein that may contact sigma(70). More than 50% of AraC/XylS family members have Asp or Glu at the position of RhaS D241, suggesting that this interaction with sigma(70) may be conserved.

Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase sigma70 subunit

The sigma subunit of RNA polymerase orchestrates basal transcription by first binding to core RNA polymerase and then recognizing promoters. Using a series of 16 alanine-substitution mutations, we show that residues in a narrow region of Escherichia coli sigma70 (590 to 603) are involved in transcription activation by a mutationally altered CRP derivative, FNR and AraC. Homology modeling of region 4 of sigma70 to the closely related NarL or 434 Cro proteins, suggests that the five basic residues implicated in activation are either in the C terminus of a long recognition helix that includes residues recognizing the -35 hexamer region of the promoter, or in the subsequent loop, and are ideally positioned to permit interaction with activators. The only substitution that has a significant effect on activator-independent transcription is at R603, indicating that this residue of sigma70 may play a distinct role in transcription initiation.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

A structure/function analysis of Escherichia coli RNA polymerase

Control of RNA polymerase is a common means of regulating gene expression. A detailed picture of both the structure and how the structural details of RNA polymerase encode function is a key to understanding the molecular strategies used to regulate RNA polymerase. We review here data which ascribes functions to some regions of the primary sequence of the subunits (alpha, beta beta' sigma) which make up E. coli RNA polymerase. We review both genetic and biochemical data which place regions of the primary sequence that are distant from one another in close proximity in the tertiary structure. Finally we discuss the implications of these findings on the quaternary structure of RNA polymerase.

Evidence for a ppGpp-binding site on Escherichia coli RNA polymerase: proximity relationship with the rifampicin-binding domain

On amino acid starvation, Escherichia coli cells exhibit an adaptive facility termed the stringent response. This is characterized by the production of high levels of a regulatory nucleotide, ppGpp, and concomitant curtailment in rRNA synthesis. Various studies reported earlier indicated that RNA polymerase is the site of action of ppGpp although a direct demonstration of the interaction of ppGpp with E. coli RNA polymerase is still lacking. Here we report the labelling of ppGpp with a fluorescent probe, 1-aminonapthalene-5-sulphonate (AmNS), at the terminal phosphates. AmNS-ppGpp responded much like a ppGpp molecule in an in vitro total transcription assay at selective promoters. Fluorescence titration of the tryptophan emission of RNA polymerase by AmNS-ppGpp indicated a unique binding site in the absence of template DNA. Competition experiments showed that unlabelled ppGpp binds to the enzyme at the same site. Sigma factor seems to have no effect on this binding. The titration profile is also characterized by a single slope in the Scatchard analysis. The presence of GTP or GDP does not influence the binding of AmNS-ppGpp with RNA polymerase. Forster's distance measurement was carried out which placed AmNS-ppGpp 27 A away from the rifampicin-binding domain of RNA polymerase.

Amino acid substitutions in the -35 recognition motif of sigma 70 that result in defects in phage lambda repressor-stimulated transcription

The phage lambda repressor activates transcription of its own gene from the promoter PRM. Previous work has suggested that this activation involves a protein-protein interaction between DNA-bound repressor and RNA polymerase. To identify the subunit of RNA polymerase that participates in this putative interaction, we searched for polymerase mutants that responded poorly to repressor. We report here the isolation of three sigma mutants that caused defects in repressor-stimulated, but not basal, transcription from PRM. These mutants bear amino acid substitutions in a putative helix-turn-helix motif that sigma uses to recognize the promoter -35 region. We suggest that lambda repressor interacts directly with this helix-turn-helix motif in facilitating the formation of a productive initiating complex.

Target of the transcriptional activation function of phage lambda cI protein

Activation of transcription initiation by the cI protein of phage lambda is thought to be mediated by a direct interaction between cl and RNA polymerase at the PRM promoter. Two negatively charged amino acid residues in the DNA binding domain of cI play a key role in activation, suggesting that these residues contact RNA polymerase. The subunit of RNA polymerase involved was identified by selecting polymerase mutants that restored the activation function of a mutant form of cI protein. Although previous studies suggest that several activators interact with the alpha subunit of RNA polymerase, the results here suggest that cI interacts with the sigma subunit. An arginine to histidine change near the carboxyl terminus of sigma specifically suppresses an aspartic acid to asparagine change in the activation region of cI. This finding supports the direct-contact model and suggests that a cluster of positively charged residues near the carboxyl terminus of sigma is the target of the negatively charged activation region of cI.

Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase

We have systematically assayed the in vivo promoter recognition properties of 13 mutations in rpoD, the gene that encodes the sigma 70 subunit of Escherichia coli RNA polymerase holoenzyme, using transcriptional fusions to 37 mutant and wild-type promoters. We found three classes of rpoD mutations: (1) mutations that suggest contacts between amino acid side-chains of sigma 70 and specific bases in the promoter; (2) mutations that appear to affect either sequence independent contacts to promoter DNA or isomerization of the polymerase; and (3) mutations that have little or no effect on promoter recognition. Our results lead us to suggest that a sequence near the C terminus of sigma 70, which is similar to the helix-turn-helix DNA binding motif of phage and bacterial DNA binding proteins, is responsible for recognition of the -35 region, and that a sequence internal to sigma 70, in a region which is highly conserved among sigma factors, recognizes the -10 region of the promoter. rpoD mutations that lie in the recognition helix of the proposed helix-turn-helix motif affect interactions with specific bases in the -35 region, while mutations in the upstream helix, which is thought to contact the phosphate backbone, have sequence-independent effect on promoter recognition.

Mutations in rpoD, the gene encoding the sigma 70 subunit of Escherichia coli RNA polymerase, that increase expression of the lac operon in the absence of CAP-cAMP

We have isolated a new class of mutations in rpoD, the gene encoding the sigma 70 subunit of Escherichia coli RNA polymerase, that alter the transcription initiation properties of RNA polymerase holoenzyme. The rpoD(Lac) mutations increase expression of the lac operon in the absence of CAP-cAMP, allowing a strain lacking adenyl cyclase to grow on lactose. Four of the six alleles isolated have three- to fivefold increases in the amount of lac mRNA and beta-galactosidase per cell. We show that these four mutations increase transcription initiation from the same promoter used by wild-type RNA polymerase. The mutations were mapped and sequenced. One mutation occurs in the codon for amino acid 389 of the sigma 70 polypeptide. The remaining five mutations are clustered, affecting residues 570, 571 and 575. These five mutations are within or near a proposed helix-turn-helix motif in the C terminus of sigma 70.

Mutations in rpoD that increase expression of genes in the mal regulon of Escherichia coli K-12

The sigma subunits of eubacterial RNA polymerases determine the site selectivity of initiation of transcription at promoters. Mutations in rpoD, the gene that encodes sigma 70, the major sigma factor in Escherichia coli, should be useful in determining the molecular details of the process of transcription initiation. However, such mutations are likely to be deleterious or lethal, since sigma70 is an essential gene product. We designed a system for the rapid isolation and fine structure mapping of mutations in rpoD, which allows selection of mutations that would otherwise be deleterious to the cell. We used this system to isolate a new class of mutations in rpoD, mutations that relieve the requirement for CAP-cAMP for initiation at promoters in the mal regulon. These mutations, which we designate rpoD(Mal) mutations, occur in two clusters in the rpoD gene within regions previously suggested by amino acid sequence comparisons to be important for sigma structure or function. We cannot distinguish whether the rpoD(Mal) mutations affect mal expression by altering interaction between RNA polymerase and mal promoters or between RNA polymerase and the accessory transcription factor MalT. However, the effects of the mutations on activator-independent transcription from the lac promoter (4 rpoD(Mal) mutations decrease CAP-independent expression of the lac promoter in vivo) suggest that the regions of sigma identified by our mutations may be directly involved in promoter recognition.

Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are homologous proteins

We show, using dot matrix comparisons and statistical analysis of sequence alignments, that seven sequenced sigma factors, E. coli sigma-70 and sigma-32, B. subtilis sigma-43 and sigma-29, phage SP01 gene products 28 and 34, and phage T4 gene product 55, comprise a homologous family of proteins. Sigma-70, sigma-32, and sigma-43 each have two copies of a sequence similar to the helix-turn-helix DNA binding motif seen in CRP, and lambda repressor and cro proteins. B. subtilis sigma-29, SP01 gp28, and SP01 gp34 have at least one copy similar to this sequence. We propose that a second sequence, conserved in all seven proteins is the core RNA polymerase binding site. A third region, present only in sigma-70 and sigma-43, may also be involved in interaction with core. Available mutational evidence supports our model for sigma factor structure.

RNA polymerase mutant able to express in vivo and in vitro the lactose operon in the absence of the cAMP-CRP complex

By genetic analysis, we have localized a new mutation, isolated from rho-crp background, responsible for a carbohydrate-positive phenotype. The mutation maps in the rpoB gene coding for the beta-subunit of Escherichia coli RNA polymerase. Using reverse transcriptase analysis of transcripts obtained in vivo and transcription assays in vitro, we have shown that this altered RNA polymerase can efficiently initiate the transcription of the lactose operon in the absence of the cAMP-CRP complex both in vivo and in vitro.

Mutations in the sigma subunit of E. coli RNA polymerase which affect positive control of transcription

The sigma subunits of bacterial RNA polymerases are required for the selective initiation of transcription. We have isolated and characterized mutations in rpoD, the gene which encodes the major form of sigma in E. coli, which affect the selectivity of transcription. These mutations increase the expression of araBAD up to 12-fold in the absence of CAP-cAMP. Expression of lac is unaffected, while expression of malT-activated operons is decreased. We determined the DNA sequence of 17 independently isolated mutations, and found that they consist of three different changes in a single CGC arginine codon at position 596 in the sigma polypeptide.

Regulation of cyclic AMP synthesis in Escherichia coli K-12: effects of the rpoD800 sigma mutation, glucose, and chloramphenicol

An immediate 12-fold inhibition in the rate of beta-galactosidase synthesis occurs in Escherichia coli cells containing the mutant sigma allele rpoD800 after a shift to 42 degrees C. In the present study we characterize the nature of the inhibition. The severe inhibition of beta-galactosidase synthesis was partly relieved by cyclic AMP (cAMP). We inferred that the inhibition might be mediated by a decreased intracellular concentration of cAMP. Consistent with this inference, the rate of cAMP accumulation in mutant cells after a temperature upshift was depressed relative to that in wild-type cells. Glucose and chloramphenicol, two agents known to inhibit differentially beta-galactosidase mRNA synthesis, caused a similar inhibition in the rate of cAMP accumulation. Thus, three diverse stimuli, glucose, chloramphenicol, and a temperature-sensitive sigma mutation, appear to affect beta-galactosidase synthesis by regulating the synthesis of cAMP.

Promoter selectivity of Escherichia coli RNA polymerase. II: Altered promoter selection by mutant holoenzymes

Using the in vitro mixed transcription system (Kajitani and Ishihama (1983a, 1983b), we examined selective transcription of truncated DNA templates carrying lac(UV5), rrnE or rpsA promoters by RNA polymerase holoenzymes from pairs of wild-type parents and mutants with a mutation in one or more RNA polymerase subunit genes. The promoter selectivity of RNA polymerases from two sigma-subunit mutants carrying either rpoD2 or rpoD285 differed markedly from that of the respective wild-type enzymes. Both the parental RNA polymerases, however, exhibited abnormal promoter selectivity compared with holoenzymes from various wild-type E. coli strains. On the other hand, all the RNA polymerases from rpoB and/or rpoC mutants and the respective wild-type parents were similar, if not identical, in promoter selection at low temperature. At high temperature, however, RNA polymerases from mutants carrying rpoB2B7 and rpoC4, affecting the beta and beta' subunits, respectively, showed decreased transcription from the high-affinity slow-transcribable promoter rrnEp2 whereas the rpoC92 and rpoB906 X rpoC907 mutant enzymes both lost transcription activity from the strong promoter lacP(UV5). Taking all these observations together we conclude that not only the sigma subunit but also the beta and beta' subunits are involved in the recognition of promoters.

Regulation of the F conjugation genes studied by hybridization and tra-lacZ fusion

Hybridization experiments and tra-lacZ fusions were used to obtain further insight into the complex series of control systems that affect F conjugation. We confirmed that the regular IncF FinOP control system represses transcription of traJ, and found that the traJ product is required for transcription of traM as well as of the traY-Z operon. The chromosomal sfrA gene product may be required to prevent premature termination of traJ transcription, while the sfrB gene product prevents premature termination at two sites within the traY-Z operon. The FinQ inhibition system determined by several IncI plasmids caused termination at three different sites in the operon, and that of JR66a at one further site. JR66a and R485 strongly inhibit F transfer, but have weak, or no (respectively) effects on transcription: they may inhibit function of one or more transfer gene products.

Influence of the rho-15 temperature-sensitive (ts) mutation on the expression of the deo-operon in Escherichia coli

In the rho-15 temperature-sensitive (ts) mutant deo-operon enzymes show no sensitivity to catabolite repression and are not derepressed under the influence of a constitutive regulatory mutation, cytR. These data suggest that intact Rho-protein along with CRP protein is necessary for a catabolite sensitive deo-operon promoter cytP to work. In addition, there are data suggesting that Rho-factor and CRP-protein interact with each other in regulation of the deo-operon. Thus, in studies of the effect of the rho-15 (ts) and crp mutations, maximum deo-enzyme levels have been found in the double rho-15 (ts) crp mutant, and therefore intact Rho-protein in the crp genome or intact CRP-protein on the rho-15 (ts) background seems to be an obstacle for the deoP promoter in the deo-operon. In rho-15 (ts) a relative increase has been observed in the enzyme activity for a distal purine nucleoside phosphorylase gene with respect to a proximal thymidine phosphorylase gene. However in crp, the rho-15 (ts) mutation has no effect on the polarity gradient, that is on the background of impaired CRP protein Rho-factor does not seem to work as a transcription terminator within the operon.

Mecillinam susceptibility of Escherichia coli K-12 mutants deficient in the adenosine 3',5'-monophosphate system

The mecillinam resistance of Escherichia coli K-12 mutants deficient in the enzyme responsible for the synthesis of adenosine 3',5'-monophosphate, adenylate cyclase, has been investigated. The results suggest that resistance to this antibiotic may be a consequence of the slow growth rate of these mutants rather than an intrinsic property of their genetic lesion.

Catabolite repression in Escherichia coli mutants lacking cyclic AMP receptor protein

Pleiotropic carbohydrate-positive pseudorevertants have been isolated from a specific class of rho-crp double mutants of Escherichia coli carrying both defective transcription termination protein, rho, and cyclic AMP receptor protein. The modulation of catabolite repression of beta-galactosidase, amylomaltase, and tryptophanase has been studied in the pseudorevertants. It has been found that these mutants exhibit catabolite repression. Because catabolite-sensitive operons can be expressed in the absence of functional cyclic AMP receptor protein, this would suggest on the one hand that the cyclic AMP-receptor protein complex is not the exclusive mediator of catabolite repression and on the other hand that rho might be involved in the regulation of catabolite-sensitive operons.

Functional heterogeneity of Escherichia coli ribonucleic acid polymerase holoenzyme

On zone sedimentation Escherichia coli RNA polymerase holoenzyme exhibits functional heterogeneity with respect to template preference, regulation by ppGpp, and affinity for fMet-tRNA. The template preference of a subpopulation of RNA polymerase molecules correlates with both its sedimentation position and its ability to respond to effectors of polymerase selectivity. Incubation of such functionally distinct populations of enzyme molecules at physiological temperatures results in functional and structural equivalence. We suggest that RNA polymerase normally exists as a mixture of interconvertible forms and that promoter selection can be controlled by varying the number and proportions of forms present.

A new mutation rpoD800, affecting the sigma subunit of E. coli RNA polymerase is allelic to two other sigma mutants

We have characterized a new mutation rpoD800 affecting the sigma gene of E. coli. Upon tranfer to high temperature, a strain with the rpoD800 mutation ceases growth within 30 min. We find that this mutation renders sigma about 10-fold more thermolabile than the wild type sigma at 45 degrees C in vitro. We have compared the temperature profile for inactivation of wild type and mutant sigma and find that the mutant inactivates at a temperature about 9 degrees C lower than does the wild type. The chromosomal locus affected by rpoD800 is shown to be allelic to the locus affected by the spontaneous mutants ts285 and alt-1. All three mutations result in altered sigma and in altered growth at high temperature. We argue that the single locus affected is the structural gene for the sigma subunit of E. coli RNA polymerase.

Lambda transducing bacteriophage carrying deletions of the argCBH-rpoBC region of the Escherichia coli chromosome

Deletions in the rpoBC region have been transferred to phage lambda and characterized in detail by genetic, structural, and functional tests. We thus extend and confirm knowledge of the organization of this part of the chromosome. The new phages are useful tools for studying the genes for the bacterial transcription and translation machinery.

Altered chemical properties in three mutants of E. coli RNA polymerase sigma subunit

We have analyzed some chemical properties of the sigma subunit of RNA polymerase from the sigma mutants: rpoD1 (Gross et al., 1978), rpoD2 (formerly known as alt-1) (Silverstone et al., 1972; Travers et al., 1978), and rpoD800 (Gross et al., 1979). Each of the three mutants is located at about 66 min on the E. coli genetic map and exhibits an alteration in the enzymatic properties of its sigma subunit. The tryptic peptides and isoelectric focusing behavior were analyzed for mutant and wild type sigma. A single, but different altered lysine tryptic peptide was observed for each mutant. No altered arginine tryptic peptides were observed. The rpoD800 mutant sigma showed an altered isoelectric point. These studies provide chemical evidence that the sigma polypeptide in all three mutants is altered and strongly support the conclusion that the mutations are in the structural gene for sigma.

The cyclic 3',5'-adenosine monophosphate receptor protein and regulation of cyclic 3',5'-adenosine monophosphate synthesis in Escherichia coli

Rates of synthesis of cyclic 3',5'-adenosine monophosphate (cAMP) were measured in cultures of Escherichia coli aerating without a carbon source. This technique provides a representative measure of adenylate cyclase activity in the absence of inhibition caused by transport of the carbon source. Adenylate cyclase activity was found to vary more than 20-fold depending on the carbon source that had been available during growth. Synthesis of cAMP in cells aerating in the absence of the carbon source was highest when cells had been grown with glucose or fructose which inhibit adenylate cyclase activity severely. Synthesis of cAMP was much lower when cells had been grown with glycerol or succinate which cause only minimal inhibition of the activity. The variation in cAMP synthesis due to different carbon sources requires a functional cAMP receptor protein (CRP). Crp- mutants synthesize cAMP at comparable rates regardless of the carbon source that afforded growth. A novel mutant of E. coli having a CRP no longer dependent on cAMP has been isolated and characterized. Adenylate cyclase activity in this mutant no longer responds normally to variations in the carbon source.

RNA polymerase mutant with altered sigma factor in Escherichia coli

A structural gene for sigma factor (rpoD) of DNA-dependent RNA polymerase (RNA nucleotidyltransferase; nucleoside-triphosphate: RNA nucleotidyltransferase, E.C. 2.7.7.6) was mapped precisely by a set of F' factors including those already published (Proc. Natl. Acad. Sci. USA. 74, 1831-1835 (1977)). Based on the result that rpoD is located at the dnaG-uxaAC region, a number of mutants containing a temperature-sensitive mutation at or near the uxaA gene were isolated by localized mutagenesis. One of these mutants was found to produce RNA polymerase altered in both thermostability and optimum salt concentration as a result of structural alteration of sigma factor. This mutation, U303, maps at 66 min on the genetic map of E. coli, near the dnaG locus, and affects normal growth of cells.

Involvement of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system in regulation of transcription of catabolic genes

Synthesis of catabolite-sensitive enzymes is repressed in mutants defective in the general proteins (enzyme I and HPr) of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system (ptsI and ptsH mutations). To elucidate the mechanism of this phenomenon we constructed isogenic strains carrying pts mutations as well as different lesions of regulation of the lac operon or mutations affecting adenylate cyclase activity (cya mutation) and synthesis of cyclic AMP-receptor protein (crp mutation) Measurements of the differential rate of beta-galactosidase synthesis in these strains showed that the repressive effect of pts mutations was revealed in lac+, lacI, lacOc and cya bacteria, but it was lost in lacP and crp strains. It was concluded that mutational damage to the general components of the phosphoenolpyruvate-dependent phosphotransferase system diminishes activity of the lac promoter. The results obtained led to the conclusion that pts gene products (apparently phospho approximately HPr) are necessary for the initiation of transcription of catabolite-sensitive operons in E. coli.

A mutation affecting the sigma subunit of RNA polymerase changes transcriptional specificity

The RNA polymerase mutation, alt-1, affects the sigma subunit and alters the in vitro selectivity of RNA polymerase to parallel the in vivo phenotype. We propose that the mutation changes the distribution of functionally distinct polymerase isomers.

Mutations affecting catabolite repression of the L-arabinose regulon in Escherichia coli B/r

Expression of the L-arabinose regulon in Escherichia coli B/r requires, among other things, cyclic adenosine-3', 5'-monophosphate (cAMP) and the cAMP receptor protein (CRP). Mutants deficient in adenyl cyclase (cya-), the enzyme which synthesizes cAMP, or CRP (crp-) are unable to utilize a variety of carbohydrates, including L-arabinose. Ara+ revertants of a cya-crp- strain were isolated on 0.2% minimal L-arabinose plates, conditions which require the entire ara regulon to be activated in the absence of cAMP and CRP. Evidence from genetic and physiological studies is consistent with placing these mutations in the araC regulatory gene. Deletion mapping with one mutant localized the site within either araO or araC, and complementation tests indicated the mutants acted trans to confer the ability to utilize L-arabinose in a cya-crp- genetic background. Since genetic analysis supports the conclusion, that the mutant sites are in the araC regulatory gene, the mutants were designated araCi, indicating a mutation in the regulatory gene affecting the cAMP-CRP requirement. Physiological analysis of one mutant, araCi1, illustrates the trans-acting nature of the mutation. In a cya-crp- genetic background, araCi1 promoted synthesis of both isomerase, a product of the araBAD operon, and permease, a product of the araE operon. Isomerase and permease levels in araCi1 cya+ crp+ were hyperinducible, and the sensitivity of each to cAMP was altered. Two models are presented that show the possible mutational lesion in the araCi strains.

Metabolism of cyclic adenosine 3',5'-monophosphate and induction of tryptophanase in Escherichia coli

The relationship between cyclic adenosine 3',5'-monophosphate (cyclic AMP) metabolism and the induction of tryptophanase and beta-galactosidase was studied in several strains of Escherichia coli grown with succinate, acetate, glycerol, or glucose as the carbon source. No consistent relationship between the intracellular concentration of cyclic AMP in the several strains cultured and the various carbon sources was discerned. In E. coli K-12-1 the induction of tryptophanase was found to vary in the order: succinate greater than acetate greater than glycerol greater than glucose, and that of beta-galactosidase was found in the order: glycerol greater than acetate greater than succinate greater than glucose. Rate of accumulation of cyclic AMP in the culture filtrate was in the order: succinate greater than acetate greater than glycerol greater than glucose. The addition of glycerol to E. coli K-12-1 grown in acetate caused inhibition of tryptophanase and slight inhibition of accumulation of extracellular cyclic AMP. These same conditions caused beta-galactosidase induction to be stimulated. The addition of exogenous cyclic AMP to cultures grown with four different carbon sources had an effect characteristic for each of the two enzymes studied as well as each individual carbon source. The results suggest that there are control elements distinct from cyclic AMP and its receptor protein which respond to the catabolic situation of the cell.

Comparative studies on induction of sporulation and synthesis of inducible enzymes in Bacillus subtilis

An attempt was made to determine whether sporulation and inducible enzyme synthesis in Bacillus subtilis are controlled by the same mechanism of catabolite repression. By the use of a thymine-requiring strain, it has been shown that, whereas sporulation remained repressed unless chromosome replication proceeded to completion, the induction of the enzymes histidase, sucrase, and alpha-glucosidase proceeded quite normally in the absence of continued deoxyribonucleic acid synthesis. It is concluded that the mechanism for overcoming the repression of sporulation differs qualitatively from that involved in overcoming the repression of inducible enzyme synthesis. Attempts to isolate pleiotropic mutants that would provide additional support for this contention were unsuccessful. A pleiotropic mutant deficient in phosphoenolpyruvate-dependent phosphotransferase activity sporulated quite well, whereas a mutant presumed deficient in glutamate synthetase sporulated poorly under all conditions.