Insertions of transposon Tn5 into ribosomal protein PNA polymerase operons

Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons

Many bacteria use operons to coregulate genes, but it remains unclear how operons benefit bacteria. We integrated E. coli's 788 polycistronic operons and 1,231 transcription units into an existing whole-cell model and found inconsistencies between the proposed operon structures and the RNA-seq read counts that the model was parameterized from. We resolved these inconsistencies through iterative, model-guided corrections to both datasets, including the correction of RNA-seq counts of short genes that were misreported as zero by existing alignment algorithms. The resulting model suggested two main modes by which operons benefit bacteria. For 86% of low-expression operons, adding operons increased the co-expression probabilities of their constituent proteins, whereas for 92% of high-expression operons, adding operons resulted in more stable expression ratios between the proteins. These simulations underscored the need for further experimental work on how operons reduce noise and synchronize both the expression timing and the quantity of constituent genes. A record of this paper's transparent peer review process is included in the supplemental information.

Monitoring in vivo fitness of rifampicin-resistant Staphylococcus aureus mutants in a mouse biofilm infection model

OBJECTIVES

To investigate in vivo fitness of rifampicin-resistant Staphylococcus aureus mutants in a mouse biofilm model using bioluminescence imaging.

MATERIALS AND METHODS

S. aureus was engineered with a luciferase operon to emit bioluminescence that can be detected in vivo using an IVIS imaging system. Two rifampicin-resistant strains of S. aureus that were previously isolated from animals undergoing rifampicin treatment, S464P (resistant to low concentrations of rifampicin) and H481Y (resistant to high concentrations of rifampicin), were characterized and then compared with their parental strain for in vivo fitness to form biofilm infections in the absence of rifampicin.

RESULTS

The mutant S464P showed better adaptation to in vivo growth than either the parental strain or H481Y without selective pressure. Six days after implanting pre-colonized catheters, bioluminescent signals were seen from 100% of the catheters coated by the mutant S464P. In comparison, only 83% and 61% of the catheters coated by the parental strain and H481Y, respectively, maintained a signal in vivo. Rifampicin treatment of S464P biofilms in vivo resulted in a slight decline, but earlier rebound in bioluminescence from these catheters compared with the parental signal, whereas rifampicin had no affect on bioluminescence in mice infected with mutant H481Y.

CONCLUSIONS

The mutant with low-level rifampicin resistance appears to be better adapted to in vivo growth than the mutant that has high-level rifampicin resistance. Moreover, the former mutant may actually have a slight competitive advantage over the rifampicin-susceptible strain (parental), raising awareness for the occurrence of such strains in clinical environments.

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.

Tn5/IS50 target recognition

This communication reports an analysis of Tn5/IS50 target site selection by using an extensive collection of Tn5 and IS50 insertions in two relatively small regions of DNA (less than 1 kb each). For both regions data were collected resulting from in vitro and in vivo transposition events. Since the data sets are consistent and transposase was the only protein present in vitro, this demonstrates that target selection is a property of only transposase. There appear to be two factors governing target selection. A target consensus sequence, which presumably reflects the target selection of individual pairs of Tn5/IS50 bound transposase protomers, was deduced by analyzing all insertion sites. The consensus Tn5/IS50 target site is A-GNTYWRANC-T. However, we observed that independent insertion sites tend to form groups of closely located insertions (clusters), and insertions very often were spaced in a 5-bp periodic fashion. This suggests that Tn5/IS50 target selection is facilitated by more than two transposase protomers binding to the DNA, and, thus, for a site to be a good target, the overlapping neighboring DNA should be a good target, too. Synthetic target sequences were designed and used to test and confirm this model.

Inhibition of bacteriophage lambda development by the klaA gene of broad-host-range plasmid RK2

The kil-kor regulon of broad-host-range plasmid RK2 is an unusual array of eight co-regulated operons that express at least 21 genes, including the plasmid replication initiator gene. Some of the operons were first identified as kil loci because uncontrolled expression in the absence of certain kor regulatory genes leads to death of the host cells. The functions of kilA, C and E are unknown, although co-regulation with the replication initiator gene suggests that they may have importance in the maintenance or host range of the plasmid. Here we report studies on the function of klaA, the first of three host-lethal genes in the kilA operon. We found that lambda pklaA-1, a lambda phage containing the klaA gene, is unable to form plaques unless the host expresses the KorA and KorB repressors needed to regulate transcription from the klaA promoter. The failure to form plaques depends on the klaA gene product and results from the inability of infected cells to produce viable phage particles. Transcription of early, delayed early and late genes or processing of lambda DNA are not affected by klaA overexpression, while cell lysis, lambda DNA replication and production of functional phage heads are reduced. However, the failure to produce viable phage is best explained by the inability to synthesize lambda tails. The finding that klaA strongly inhibits a specific morphogenetic step in the assembly of lambda phage particles has significance with respect to the function of klaA on plasmid RK2.

The kilA operon of promiscuous plasmid RK2: the use of a transducing phage (lambda pklaA-1) to determine the effects of the lethal klaA gene on Escherichia coli cells

The kil-kor regulon of promiscuous plasmid RK2 includes the replication initiator gene trfA and several potentially host-lethal kil loci (kilA, kilB, kilC, kilE), whose functions may be involved in plasmid maintenance or broad host range. The kilA locus consists of a single operon of three genes (klaA, klaB, klaC), each of which is lethal when expressed from the klaA promoter in the absence of repressors encoded by korA and korB. In this study, we examined the effects of the unregulated klaA gene on the host cell. Bacteriophage lambda was used to construct a transducing phage (lambda pklaA-1) that allows efficient introduction of the klaA gene into Escherichia coli. Cells lacking korA and korB (to allow uncontrolled expression of klaA) and expressing lambda repressor (to prevent phage lytic growth) are killed by lambda pklaA-1. Cell death is dependent on the klaA structural gene, independent of the SOS system of the host, and is prevented by the presence of korA and korB. lambda pklaA-1 was used to synchronously infect cells lacking korA and korB to determine the effects of klaA on the cells over time. The earliest effects, visible at two hours post-infection, are inhibition of growth of the culture, formation of elongated cells, and striking changes in the appearance of the outer membrane. After four to five hours, the viability of the culture declined sharply and macromolecular synthesis ceased. The distinct class of early events is consistent with the hypothesis that the KlaA polypeptide interacts with a specific target in the host cell.

In vivo analysis of overlapping transcription units in the rplKAJLrpoBC ribosomal protein-RNA polymerase gene cluster of Escherichia coli

Transcription of the rplKAJLrpoBC ribosomal protein (rpl) RNA polymerase (rpo) gene cluster is governed by a complex set of signals. To dissect the transcription units active in vivo and to quantify the relative contribution of each, an extensive array of rplKAJLrpoB/lacZ gene fusions were constructed on lambda phage derivatives and introduced in single copy into the chromosomes of lac- cells. Measurements of beta-galactosidase production from fusions containing wild-type and/or mutagenized rplrpo DNA fragments permitted the establishment of high-resolution transcription profiles of the gene cluster. The results show that transcription initiated at the upstream rplKp promoter (located just before rplK) does not terminate before the rplJp promoter (located upstream from rplJ), but instead reads through into the distal genes. In addition, rplJp continues to function efficiently in the presence of readthrough transcription from rplKp. As a result the rplJL genes are transcribed at almost twice the frequency of the upstream rplKA genes. However, the transcription of rpoB, which is situated downstream from the previously identified attenuator (rpoBa), is only marginally increased (20%) when both promoters are present. This suggests that although both transcription units overlap, transcriptional termination at rpoBa is modulated in response to the frequency of initiation from both promoters.

Sequence and transcriptional pattern of the essential Escherichia coli secE-nusG operon

Two genes, secE and nusG, situated between the tufB and ribosomal protein rplKAJL operons in the rif region at 90 min on the Escherichia coli chromosome, have been sequenced and characterized. The secE gene encodes a 127-amino-acid-long polypeptide, which is an integral membrane protein essential for protein export (P. J. Schatz, P. D. Riggs, A. Jacq, M. J. Fath, and J. Beckwith, Genes Dev. 3:1035-1044, 1989). The nusG gene encodes a 181-amino-acid-long polypeptide and is involved in transcription antitermination. The protein product of nusG is essential for bacterial viability. The secE-nusG genes are cotranscribed, with transcripts initiated at the PEG promoter and terminated at the Rho-independent terminator in the region of the rplK promoter. The majority of transcripts are processed at a number of sites in the 5' untranslated leader region by RNase III and are possibly also processed by a second unidentified nuclease. The role of transcript processing in the regulation of secE and nusG has not yet been established. The juxtaposition and coregulation of a protein export factor and a transcriptional factor raise questions concerning a functional connection between the two processes.

Long-range translational coupling in the rplJL-rpoBC operon of Escherichia coli

In Escherichia coli the genes encoding ribosomal proteins L10 and L7/L12, rplJ and rplL, are cotranscribed, and translation of both cistrons is regulated by binding of L10 or a complex of L10 and L7/L12 to a single target in the mRNA leader region. Co-ordinated regulation is assured by some kind of translational coupling, the mechanism of which was investigated here by deletion analysis of plasmids carrying either the intact rplL gene or rplL-lacZ gene fusions. Unless the rplL ribosome binding site was modified by deletion, efficient initiation of translation required translation of a region located more than 500 nucleotides upstream on the transcript within the rplJ cistron. It is proposed that the wild-type rplL ribosome binding site is blocked by long-range RNA base-pairing to this region, when translation of the rplJ sequence is inhibited.

Allele-specific malE mutations that restore interactions between maltose-binding protein and the inner-membrane components of the maltose transport system

Active accumulation of maltose and maltodextrins by Escherichia coli depends on an outer-membrane protein. LamB, a periplasmic maltose-binding protein (MalE, MBP) and three inner-membrane proteins, MalF, MalG and MalK. MalF and MalG are integral transmembrane proteins, while MalK is associated with the inner aspect of the cytoplasmic membrane via an interaction with MalG. Previously we have shown that MBP is essential for movement of maltose across the inner membrane. We have taken advantage of malF and malG mutants in which MBP interacts improperly with the membrane proteins. We describe the properties of malE mutations in which a proper interaction between MBP and defective MalF and MalG proteins has been restored. We found that these malE suppressor mutations are able to restore transport activity in an allele-specific manner. That is, a given malE mutation restores transport activity to different extents in different malF and malG mutants. Since both malF and malG mutations could be suppressed by allele-specific malE suppressors, we propose that, in wild-type bacteria, MBP interacts with sites on both MalF and MalG during active transport. The locations of different malE suppressor mutations indicate specific regions on MBP that are important for interacting with MalF and MalG.

narI region of the Escherichia coli nitrate reductase (nar) operon contains two genes

In previous studies it has been established that in Escherichia coli the three known subunits of anaerobic nitrate reductase are encoded by the narGHI operon. From the nucleotide sequence of the narI region of the operon we conclude that, in addition to the narG and narH genes, the nar operon contains two other open reading frames (ORFs), ORF1 and ORF2, that encode proteins of 26.5 and 25.5 kilodaltons, respectively. Protein fusions to each of the genes in the operon showed that expression of all four genes was similarly regulated. The reading frames of ORF1 and ORF2 were verified, and the N-terminal sequence for the ORF1 fusion protein was determined. The nar operon therefore contains four genes designated and ordered as narGHJI.

In vivo formation of gene fusions in Pseudomonas putida and construction of versatile broad-host-range vectors for direct subcloning of Mu d1 and Mu d2 fusions

The Mu d1 and Mu d2 prophages were integrated into the conjugative broad-host-range plasmid R751. The two plasmids were then transferred into Pseudomonas putida, and derivatives carrying intact Mu prophages were recovered. After induction of Mu at 42 degrees C, both operon and gene fusions were observed on 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside (X-Gal) plates. Broad-host-range vectors were constructed which allow direct cloning of both operon or gene fusions and their analysis in Escherichia coli and P. putida. By using one of these vectors, two operon fusions were isolated from the P. putida chromosome and comparatively analyzed in E. coli and P. putida.

Evidence that Rho and NusA are involved in termination in the rplL-rpoB intercistronic region

The frequency of transcription of the ribosomal protein and RNA polymerase gene segments of the rplKAJL-rpoBC gene cluster was measured for Escherichia coli K-12 strains carrying mutations in the genes for transcriptional termination factors. The results of our study suggest that Rho increases and that both NusA and the product of sfrB decrease termination frequency in the rplL-rpoB intercistronic region.

Transcription products from the rplKAJL-rpoBC gene cluster

Transcripts from the rplKAJL-rpoBC ribosomal protein-RNA polymerase gene cluster have been quantified and their ends mapped using RNA-DNA hybridization, sucrose density-gradient sedimentation, Northern hybridization and S1 nuclease protection. The results indicate that the most abundant transcript is the 2600 nucleotide tetracistronic L11-L1-L10-L12 mRNA initiated at the upstream major PL11 promoter and terminated at the transcription attenuator in the L12-beta intergenic space. Somewhat less abundant 1300 nucleotide L11-L1 and L10-L12 bicistronic transcripts were observed. The 3' ends of the L11-L1 transcripts were heterogeneous; most of the ends were localized to three sites within a 110 base-pair region in the L1-L10 intergenic space. This intergenic space encodes also the major PL10 promoter and the mRNA binding site for the L10 translational control protein. Two 5' ends were observed for L10-L12 bicistronic mRNA, one at the PL10 promoter and the other 150 nucleotides further downstream in a region in which promoter activity has not been detected. It is suggested that this second downstream 5' end is generated by processing of the transcripts initiated at the major PL10 promoter. No transcript initiation in the L10-L12 intergenic space was detected. About 80% of the transcripts reading through the L12 gene were terminated in the vicinity of the transcription attenuator that is responsible for the reduction in the expression of the downstream RNA polymerase genes. Transcripts reading through the attenuator were partially processed by RNase III within a potential hairpin structure in the RNA transcript. Processing appears to produce 3' and 5' transcript end sites separated by about ten nucleotides. No other major 5' ends were observed in the L12-beta intergenic space. These results indicate that the two major promoters, PL11 and PL10, are both utilized to drive the interrelated transcriptional expression of this ribosomal protein-RNA polymerase gene cluster.

Growth rate-dependent regulation of RNA polymerase synthesis in Escherichia coli

The rate of synthesis of the beta and beta' subunits of RNA polymerase relative to the rate of synthesis of total protein was found to remain constant with increasing steady state growth rate. This is in contrast to the relative synthesis rates of ribosomal proteins which are known to increase with growth rate. Yet the ratio of the rate of transcription of the ribosomal protein (rplJL) and RNA polymerase (rpoBC) domains of the rplKAJLrpoBC gene cluster was found to be invariant. Fusions to lacZ were used to relate the rate of transcription of the rplKAJL genes to the rate of synthesis of total protein. No change was seen at growth rates above 0.8 doublings per hour. This indicates that the growth rate-dependent expression of these ribosomal proteins is regulated at the post-transcriptional level. However because both the relative rate of transcription of rpoBC and rate of synthesis of beta and beta' were found to remain invariant over this growth range it suggests the expression of these RNA polymerase subunits is regulated at the transcriptional level.

Isolation and characterization of delta ompB strains of Escherichia coli by a general method based on gene fusions

We isolated a series of delta ompR delta envZ mutants by inducing a strain carrying a lambda prophage in the closely linked gene malP and screening the bacterial survivors for loss of the major outer membrane porins OmpF and OmpC. Characterization of these deletion strains showed that both OmpR and EnvZ were necessary for transcription of ompF and ompC and that neither gene was essential for cell viability. Moreover, the deletion strains did not exhibit the pleiotropic membrane protein deficiency observed with certain envZ mutants. The method described should allow the simple isolation of deletions in any region of the chromosome.

Autogenous posttranscriptional regulation of RNA polymerase beta and beta' subunit synthesis in Escherichia coli

Bacterial strains carrying poorly suppressed amber mutations in the RNA polymerase beta subunit gene (rpoB) exhibit regulatory compensation. This compensation allows these strains to produce an adequate content of RNA polymerase to support a near normal rate of growth despite the poorly suppressed amber mutation. The primary compensatory mechanism permitting the elevated expression functions by permitting a much more efficient (up to threefold) loading of ribosomes at the beta cistron translation initiation site on the mRNA. This result supports the concept that the production of beta and beta' RNA polymerase subunits are autogenously regulated at the level of mRNA translation; this translational mechanism is clearly distinct from the transcriptional mechanism regulating beta and beta' expression described previously (P. P. Dennis, Proc. Natl. Acad. Sci. U.S.A. 74:5416-5420, 1977).

Autoregulation of the DNA replication gene dnaA in E. coli K-12

The dnaA gene in E. coli K-12 is required for the initiation of DNA replication. Although the specific function of the dnaA protein is unknown, it has been suggested that it is a regulator of the frequency of initiation. In this paper we report that the expression of both a dnaA-lacZ translational fusion and a dnaA-trpA-lacZ transcriptional fusion in vivo are sensitive to changes in the level of functional dnaA protein. Overproduction of the dnaA gene product leads to a reduction in expression from both fusions while introduction of dnaA- alleles results in an increased expression. Results from a deletion analysis of the dnaA promoter/regulatory region suggest that both dnaA promoters are regulated by the dnaA gene product and that a site between the two promoters is responsible for the regulation. DNAase protection experiments showed that the dnaA protein binds to DNA in the region of the two dnaA promoters. Our results indicate that the dnaA gene product regulates its own synthesis by inhibiting transcription from both of its promoters.

Heat shock regulatory gene htpR influences rates of protein degradation and expression of the lon gene in Escherichia coli

Upon a shift to high temperature, Escherichia coli increase their rate of protein degradation and also the expression of a set of "heat shock" genes. Nonsense mutants of htpR (also called hin), suppressed by a temperature-sensitive suppressor, show lower expression of heat shock genes at 30 degrees C and fail to respond to a shift to 42 degrees C. These mutants were found to have a lower capacity to degrade abnormal or incomplete proteins than that of wild-type cells. This reduction in proteolysis equals or exceeds that in lon mutants, which encode a defective ATP-dependent protease, protease La, and is particularly large in htpR lon double mutants. The activity of protease La was higher in wild-type cells than in htpR mutants grown at 30 degrees C and increased upon shift to 42 degrees C only in the wild type. To determine whether htpR influences transcription of the lon gene, a lon-lacZ operon fusion was utilized. Introduction of the htpR mutation reduced transcription from the lon promoter at 30 degrees C and 37 degrees C. This defect was corrected by a plasmid (pFN97) carrying the wild-type htpR allele. Induction of the heat shock response with ethanol had little or no effect in htpR mutants but stimulated lon transcription 2-3 fold in wild-type cells and htpR cells carrying pFN97. Thus, lon appears to be a heat shock gene, and increased synthesis of protease La under stressful conditions may help to prevent the accumulation of damaged cellular protein.

Selection of lac gene fusions in vivo: ompR-lacZ fusions that define a functional domain of the ompR gene product

We describe a simple method for selecting Escherichia coli mutants that carry gene fusions between a cloned gene and lacZ. We test this technique with the ompR gene, which codes for a positive regulatory factor in porin synthesis. A number of OmpR-LacZ hybrid proteins are examined, and several unusual phenotypes associated with these protein fusions are described. Evidence is presented to support the two-domain model for ompR proposed previously (Hall and Silhavy, J. Mol. Biol. 151:1-15). In addition, one of the ompR-lacZ fusions exhibits a dominant OmpR- phenotype. The utility of isolating a series of lacZ gene fusions to any target gene is discussed.

Relative activities of the transcriptional regulatory sites in the rplKAJLrpoBC gene cluster of Escherichia coli

The pattern of transcription of the rplKAJLrpoBC gene cluster of Escherichia coli appears to be complex. At least four different promoters and a transcriptional attenuator have been identified. To compare the relative effect of each of the putative promoters and the attenuator on transcription of these genes, we fused these regulatory sites to lacZ. These transcriptional fusions were constructed on lambda transducing phages so a single copy of each could be stably integrated into the chromosome. The level of beta-galactosidase in a lysogen of each phage reflects the activity of the transcriptional regulatory site. We find that the promoters preceding rplK (rplKp) and rplJ (rplJp) are indeed the major promoters of this gene cluster. The minor promoter before rplL (rplLp) is much weaker and contributes little to the transcription of the downstream genes. Under these conditions, we find no evidence of a promoter (rpoBp) in the rplL-rpoB intercistronic region. The attenuator (atn) terminates ca. 70% of the transcripts initiated at the promoters preceding it. Although we cannot rule out that some transcripts from rplKp may read through into rplJLrpoBC, we find that rplJp alone is sufficient for high-level expression of these genes.

Physiological characterization of Escherichia coli rpoB mutants with abnormal control of ribosome synthesis

We have previously reported the isolation of Escherichia coli rpoB mutants in which the control of ribosome synthesis by the nucleotide effector guanosine tetraphosphate (ppGpp) is altered, owing to a 20-fold increased sensitivity of the mutant RNA polymerases to ppGpp. In these mutants, the level of ppGpp during exponential growth is decreased about 10-fold, relative to that of rpoB+ wild-type strains, such that a near normal partitioning of RNA polymerase occurs with respect to stable RNA (rRNA and tRNA) gene activity. Here, the physiological effects of two different rpoB alleles in a relA+ and relA background were analyzed in greater detail by comparison with their isogenic rpoB+ wild-type parents. For a given growth medium, the rpoB mutations were found to affect four parameters which resulted in a reduction of growth rate. The results reinforce a previous conclusion that a key element in control of the bacterial growth rate is a mutual relationship between control of ribosome synthesis by ppGpp and control of relA-independent ppGpp metabolism by the concentration and function of ribosomes.