Involvement of DNA gyrase in the transcription of ribosomal RNA

Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis

Malaria parasites have evolved unusual metabolic adaptations that specialize them for growth within heme-rich human erythrocytes. During blood-stage infection, Plasmodium falciparum parasites internalize and digest abundant host hemoglobin within the digestive vacuole. This massive catabolic process generates copious free heme, most of which is biomineralized into inert hemozoin. Parasites also express a divergent heme oxygenase (HO)-like protein (PfHO) that lacks key active-site residues and has lost canonical HO activity. The cellular role of this unusual protein that underpins its retention by parasites has been unknown. To unravel PfHO function, we first determined a 2.8 Å-resolution X-ray structure that revealed a highly α-helical fold indicative of distant HO homology. Localization studies unveiled PfHO targeting to the apicoplast organelle, where it is imported and undergoes N-terminal processing but retains most of the electropositive transit peptide. We observed that conditional knockdown of PfHO was lethal to parasites, which died from defective apicoplast biogenesis and impaired isoprenoid-precursor synthesis. Complementation and molecular-interaction studies revealed an essential role for the electropositive N-terminus of PfHO, which selectively associates with the apicoplast genome and enzymes involved in nucleic acid metabolism and gene expression. PfHO knockdown resulted in a specific deficiency in levels of apicoplast-encoded RNA but not DNA. These studies reveal an essential function for PfHO in apicoplast maintenance and suggest that Plasmodium repurposed the conserved HO scaffold from its canonical heme-degrading function in the ancestral chloroplast to fulfill a critical adaptive role in organelle gene expression.

Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli

Recent studies have shown that RNA polymerase (RNAP) is organized into distinct clusters in Escherichia coli and Bacillus subtilis cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use of membranes, which may offer insights into unique functions and regulations. It has been proposed that the formation of RNAP clusters is driven by active ribosomal RNA (rRNA) transcription and that RNAP clusters function as factories for highly efficient transcription. In this work, we examined these hypotheses by investigating the spatial organization and transcription activity of RNAP in E. coli cells using quantitative superresolution imaging coupled with genetic and biochemical assays. We observed that RNAP formed distinct clusters that were engaged in active rRNA synthesis under a rich medium growth condition. Surprisingly, a large fraction of RNAP clusters persisted in the absence of high rRNA transcription activities or when the housekeeping σ⁷⁰ was sequestered, and was only significantly diminished when all RNA transcription was inhibited globally. In contrast, the cellular distribution of RNAP closely followed the morphology of the underlying nucleoid under all conditions tested irrespective of the corresponding transcription activity, and RNAP redistributed into dispersed, smaller clusters when the supercoiling state of the nucleoid was perturbed. These results suggest that RNAP was organized into active transcription centers under the rich medium growth condition; its spatial arrangement at the cellular level, however, was not dependent on rRNA synthesis activity and was likely organized by the underlying nucleoid.

Development of a Method for the Detection of Verotoxin-Producing Escherichia coli in Food

The growing recognition of the role of non-O157 verotoxigenic Escherichia coli (VTEC) in foodborne illness underscores the importance of developing methods to detect it in the food supply. We describe here the development of a protocol for the detection, isolation, and characterization of VTEC from foods, designed for the serotype-independent enrichment, detection, and isolation of VTEC, in combination with rapid characterization of VTEC O157, O26, O103, O111, and O145. This study examined the inhibitory concentration of six antimicrobial agents used either singly or in combination for the optimal enrichment of a panel of 18 different O serogroups of VTEC in modified tryptic soy broth. Considerable variability in resistance to the different antimicrobials tested was noted among different VTEC strains. The combination enabling growth of strains of all 18 different O serogroups was vancomycin (10 μg/ml) and cefsulodin (3 μg/ml). A similar combination of antimicrobials formulated in agar plates was found beneficial in the recovery of VTEC strains from enrichment broth cultures. The efficacy of these media in the recovery of selected VTEC (O26, O103, O111, O145, and O157) from ground beef and O157 VTEC from lettuce, spinach, and apple cider was demonstrated. The selective enrichment media described herein would appear suitable for incorporation in methods for the recovery and detection of a wide range of VTEC serogroups.

Growth rate regulation in Escherichia coli

Growth rate regulation in bacteria has been an important issue in bacterial physiology for the past 50 years. This review, using Escherichia coli as a paradigm, summarizes the mechanisms for the regulation of rRNA synthesis in the context of systems biology, particularly, in the context of genome-wide competition for limited RNA polymerase (RNAP) in the cell under different growth conditions including nutrient starvation. The specific location of the seven rrn operons in the chromosome and the unique properties of the rrn promoters contribute to growth rate regulation. The length of the rrn transcripts, coupled with gene dosage effects, influence the distribution of RNAP on the chromosome in response to growth rate. Regulation of rRNA synthesis depends on multiple factors that affect the structure of the nucleoid and the allocation of RNAP for global gene expression. The magic spot ppGpp, which acts with DksA synergistically, is a key effector in both the growth rate regulation and the stringent response induced by nutrient starvation, mainly because the ppGpp level changes in response to environmental cues. It regulates rRNA synthesis via a cascade of events including both transcription initiation and elongation, and can be explained by an RNAP redistribution (allocation) model.

Thirty years of Escherichia coli DNA gyrase: from in vivo function to single-molecule mechanism

The level of negative DNA supercoiling of the Escherichia coli chromosome is tightly regulated in the cell and influences many DNA metabolic processes including DNA replication, transcription, repair and recombination. Gyrase is the only type II topoisomerase able to introduce negative supercoils into DNA, a unique ability that arises from the specialized C-terminal DNA wrapping domain of the GyrA subunit. Here, we review the biological roles of gyrase in vivo and its mechanism in vitro.

Analysis of sequence elements important for the synthesis and control of ribosomal RNA in E coli

The regulation of the synthesis of ribosomal RNA is a key problem for the understanding of bacterial growth. Many different regulatory mechanisms involving cis and trans acting components participate in a concerted way to achieve the very efficient, flexible and coordinated production of this class of molecules. We have studied three different sequence regions within a ribosomal RNA transcription unit which are believed to control different stages of ribosomal RNA expression. In the first part of the study the function of AT-rich sequences upstream of the -35 hexamer of rRNA promoter P1 in the activation of rRNA transcription was analyzed. We confirm that a sequence dependent bend upstream of P1 is responsible for the high promoter activity. Experiments employing linker scanning mutations demonstrated that the distance as well as the angular orientation of the bent DNA is crucial for the degree of activation. In addition, the effect of the trans activating protein Fis on the transcription initiation of promoter P1 was investigated. We can show, using the abortive initiation assay, that the predominant effect of Fis is due to an increase in the affinity of RNA polymerase for the promoter (binding constant KB) while the isomerisation rate (kf) from a closed to an open RNA polymerase promoter complex is not altered significantly. We also describe the characterization of sequence determinants important for stringent regulation and growth rate control. Evidence is provided that the discriminator motif GCGC is a necessary but not sufficient element for both types of control. Furthermore we show that not simply a particular DNA primary structure but the higher order conformation of the complete promoter region is recognized and triggers the two regulatory mechanisms, both of which are apparently mediated by the effector molecule guanosine tetraphosphate (ppGpp). Finally, we have carried out a systematic mutational analysis of the rrnB leader region preceding the structural gene for 16S RNA. We could demonstrate that highly conserved sequence elements within the rrnB leader, which were believed to be involved in transcription antitermination have post-transcriptional functions. We present evidence that these sequence elements direct the biogenesis of active ribosomal particles.

The effect of nalidixic acid on expression from related E. coli promoters

The effect of the DNA gyrase inhibitor, nalidixic acid, on expression from E. coli promoters was studied using the pKO-1, galactokinase expression vector system. Expression from a series of related hybrid promoters, tet promoter variants and the trp promoter flanked by oligonucleotide blocks was measured after incubation with nalidixic acid. Expression from the pBR322 tet promoter and tet promoter mutants within the -10 region was reduced after the drug treatment. The lacUV5, trp, and tettrp promoters were essentially unaffected while the trplac and the trptet promoters were stimulated. Studies of the trp promoter flanked by upstream or downstream oligonucleotide blocks revealed similar responses to the trp promoter parent control plasmids.

Effect of DNA gyrase inactivation on RNA synthesis in Escherichia coli

The average chain growth rates of rRNA and of total RNA were not affected by a thermal inactivation of DNA gyrase in a temperature-sensitive gyrB mutant of Escherichia coli. The fact that total RNA synthesis decreased under these conditions suggests that transcription is primarily affected at the step of chain initiation. The fraction of rRNA in total pulse-labeled RNA was not altered by inactivation of the enzyme, indicating that the latter is not required to actively maintain a high rate of synthesis of this RNA species.

Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmids

The tandem P1, P2 promoter region of the rrnA ribosomal operon has been fused to the t1, t2 terminator region of the rrnB operon in pBR322 plasmid derivatives. This deletes most internal RNA structural elements ordinarily processed out of ribosomal operon transcripts. In vivo as well as in vitro transcripts arising from both promoters terminate predominantly in the t1 terminator region about 40 base pairs beyond the mature rrnB 5S RNA gene. Stringent control of the P1 and P2 promoted transcripts has been assessed in vivo. In these plasmid fusions, the upstream (P1) promoter activity was subject to stringent control, while the downstream (P2) promoter activity was inhibited by amino acid starvation in both stringent and relaxed hosts. A plasmid with an additional deletion of the P2 region also showed stringent regulation of the P1 promoter.

Functional interrelationship between two tandem E. coli ribosomal RNA promoters

The Escherichia coli chromosome carries seven cistrons encoding ribosomal RNA sequences. In all cases studied, in vitro and in vivo, it has been established that transcription is initiated from two tandem promoters. The expression of the rRNA cistrons is regulated in response to growth rate as well as to aminoacyl tRNA availability. In the present study, a plasmid (pPS1) carrying the promoter region of the rrnA cistron fused to the terminator region of rrnB has been used for in vitro transcription experiments. The presence of the terminators (T1 and T2) together with the fact that supercoiled DNA is found to be a highly efficient template, provide an ideal in vitro system in which to study the functional interrelationship between the two tandem promoters of E. coli rRNA cistrons. The results suggest that the rate of rRNA synthesis in E. coli cells growing in various conditions, as reflected by the availability of RNA polymerase, is primarily dependent on the properties of the two tandem rRNA promoters.

[Molecular biology of the germination of Bacillus spores]

The review deals with recent results and problems of gene expression during germination of Bacillus spores. Three problems were selected: 1. The activation of metabolism as a prerequisite for the synthesis of nucleic acids and proteins. 2. The activation of nucleic acid and protein synthesis during germination. 3. The gene expression programme of germinating spores. Using the highly sensitive two-dimensional polyacrylamide gel analysis three major classes of proteins were distinguished, depending on the time of onset and duration of their syntheses: a) proteins made throughout germination (main class), b) proteins whose synthesis started only after a lag phase and then continued throughout germination, and c) proteins which are synthesized only during the early phases of germination. The programme of protein synthesis is an indicator for the control of gene expression during germination. The regulation of expression of these major gene groups during spore outgrowth is discussed.

Novel pleiotropic effect of rifampicin resistance mutation in a Micromonospora sp

Rifampicin-resistant mutants have been isolated from aMicromonosporasp. In one of these, rifampicin failed to inhibit [3H]UTP incorporation in osmotically shocked cells; consequently, resistance was probably not due to the alteration of rifampicin permeability. Parallel to the rifampicin resistance there was a substantial increase in the novobiocin sensitivity of the mutants. Rifampicin-sensitive revertants exhibited their original novobiocin sensitivity. At the same time there was no increase in their sensitivity towards coumermycin A1, an agent of related structure and activity. The possible mechanism for this pleiotropy is discussed.

Nucleotide sequence of the rrnG ribosomal RNA promoter region of Escherichia coli

The primary structure of the promoter region for a ribosomal RNA transcription unit (rrnG) of Escherichia coli K12 has been determined. The sequence was obtained from 1 1.5 kbp EcoRI fragment derived from the hybrid plasmid pLC23-30. This fragment contains 455 bp preceding P1 of the rrnG promoter region and 674 bp of the rrnG 16S RNA gene. The sequence before the rrnG promoter region contains an open reading frame (ORF-BG) followed by a possible hairpin structure that resembles other known transcription terminators. The sequence of the rrnG promoter region is similar but not identical to that of rrnA and rrnB. Several minor differences between the sequences of the 16S RNA genes of rrnG and rrnB were also noted. In addition, sequences were found that could generate special structures involving the promoter regions of rrn loci. Such structures are described and their possible involvement in the regulation of ribosomal RNA synthesis is discussed.

[Effect of nalidixic acid on the activation of RNA synthesis in outgrowing spores of Bacillus subtilis]

Outgrowth of B. subtilis spores depends on the action of DNA gyrase (comp. Matsuda and Kameyama 1980). Application of nalidixic acid (100 micrograms/ml) to dormant spores of Bacillus subtilis prevents the outgrowth. Application of nalidixic acid (100 micrograms/ml) during the early outgrowth phase (after a 20 min germination period) does not prevent, but only delay spore outgrowth. Germination of spores is not influenced. Nalidixic acid is an effective inhibitor of RNA synthesis in outgrowing spores, whereas vegetative cells are more resistant. Spores can grow out inspite of a remarkably reduced intensity of RNA synthesis. Nalidixic acid particularly inhibits the synthesis of stable RNA, probably that of ribosomal RNA. We suggest that DNA gyrase-catalyzed alterations in DNA structure are involved in the regulation of the gene expressional program of outgrowing B. subtilis spores.

Differential effects of antibiotics inhibiting gyrase

Both oxolinic acid and coumermycin A1, inhibitors of DNA gyrase, block DNA synthesis in Escherichia coli. At low concentrations of oxolinic acid, the rate of bacterial DNA synthesis first declines rapidly but then gradually increases. This gradual increase in synthesis rate depended on the presence of wild-type recA and lexA genes; mutations in either gene blocked the increase in synthesis rate. In such mutants, oxolinic acid caused a rapid decline, followed by a slow, further decrease in DNA synthesis rate. Coumermycin A1, however, produced a more gradual decline in synthesis rate which is unaffected by defects in the recA or lexA genes. An additional difference between the two drugs was observed in a dnaA mutant, in which initiation of replication is temperature sensitive. Low concentrations of oxolinic acid, but not coumermycin A1, reduced thermal inhibition of DNA synthesis rate.

Single-stranded DNA transcription by yeast RNA polymerase B

Single-stranded DNA is not transcribed randomly by yeast RNA polymerase B. A denatured yeast DNA fragment, containing the gene for yeast alcohol dehydrogenase I, directs the transcription of defined RNA products visualized as discrete RNA . DNA hybrid bands following S1 nuclease treatment and agarose gel electrophoresis. Blocking the 3' end of the template by 3' deoxyadenosine did not change the band pattern but reduced the proportion of RNA covalently bound to the DNA from 20 to 4%. On the other hand, the band pattern was affected by the salt concentration, the nature of the divalent cation and the nucleoside triphosphate concentration. The four major RNA bands, found at low substrate concentration, hybridized to the same region of the template. This observation suggests the potential requirement for DNA destabilization in gene activation.

Enhancement of ribosomal ribonucleic acid synthesis by deoxyribonucleic acid gyrase activity in Escherichia coli

The effect of the deoxyribonucleic acid (DNA) gyrase inhibitors coumermycin A1, novobiocin, and oxolinic acid on ribonucleic acid (RNA) synthesis in Escherichia coli was studied in vivo and in vitro. Preferential inhibition of ribosomal RNA (rRNA) synthesis was observed. No effect of oxolinic acid and coumermycin on rRNA synthesis was seen in mutants having a DNA gyrase which is resistant to these inhibitors. In a temperature-sensitive DNA gyrase mutant rRNA synthesis was decreased at nonpermissive temperatures. Thus, a functional DNA gyrase is required for rRNA synthesis. Purified DNA gyrase had no effect on rRNA synthesis in a purified system. However, DNA gyrase does show preferential stimulation of rRNA synthesis in a system supplemented with other proteins. Apparently, DNA gyrase stimulation of rRNA synthesis requires another protein.

A mutation in the RNA polymerase beta' subunit causing depressed ribosomal RNA synthesis in Escherichia coli

Macromolecular synthesis in an Escherichia coli mutant with a temperature-sensitive beta' subunit of RNA polymerase was analysed. At the non-permissive temperature ribosomal RNA synthesis is strongly reduced while messenger RNA synthesis is affected to only a slightly extent. The overall protein synthesis is only slightly affected. We conclude that the beta' subunit is involved in promoter recognition and plays a role in transcriptional selectivity.

Electron microscopic analysis of transcription of a ribosomal RNA operon of E. coli

Transcription in vitro of the E. coli ribosomal RNA operon, rrnE, was analysed by electron microscopy. The transcription initiation sites of the two rrnE promoters in tandem, P1 and P2, were mapped and the transcription from both sites was compared. The first and the second transcription initiation site are about equally used when all nucleotides are present at 200 microM. Lowering the concentration of the second promoter's start nucleotide CTP to 3 microM reduces the use of the P2 site sharply. At all CTP concentrations used the nascent RNA chains from P1 are in the average longer than those from P2 after a fixed transcription time. Most probably, this difference is caused by a longer average interval before formation of the productive complex with the second promoter.