Use of gene fusions to isolate promoter mutants in the transfer RNA gene tyrT of Escherichia coli

Conjugal DNA Transfer in Sodalis glossinidius, a Maternally Inherited Symbiont of Tsetse Flies

Tsetse flies are the insect vectors of T. brucei, the causative agent of African sleeping sickness—a zoonotic disease that inflicts a substantial economic cost on a broad region of sub-Saharan Africa. Notably, tsetse flies can be infected with the bacterium S. glossinidius to establish an asymptomatic chronic infection. This infection can be inherited by future generations of tsetse flies, allowing S. glossinidius to spread and persist within populations. To this effect, S. glossinidius has been considered a potential expression platform to create flies which reduce T. brucei stasis and lower overall parasite transmission to humans and animals. However, the efficient genetic manipulation of S. glossinidius has remained a technical challenge due to its complex growth requirements and uncharacterized physiology. Here, we exploit a natural mechanism of DNA transfer among bacteria and develop an efficient technique to genetically manipulate S. glossinidius for future studies in reducing trypanosome transmission.

Stable associations between insects and bacterial species are widespread in nature. This is the case for many economically important insects, such as tsetse flies. Tsetse flies are the vectors of Trypanosoma brucei, the etiological agent of African trypanosomiasis—a zoonotic disease that incurs a high socioeconomic cost in regions of endemicity. Populations of tsetse flies are often infected with the bacterium Sodalis glossinidius. Following infection, S. glossinidius establishes a chronic, stable association characterized by vertical (maternal) and horizontal (paternal) modes of transmission. Due to the stable nature of this association, S. glossinidius has been long sought as a means for the implementation of anti-Trypanosoma paratransgenesis in tsetse flies. However, the lack of tools for the genetic modification of S. glossinidius has hindered progress in this area. Here, we establish that S. glossinidius is amenable to DNA uptake by conjugation. We show that conjugation can be used as a DNA delivery method to conduct forward and reverse genetic experiments in this bacterium. This study serves as an important step in the development of genetic tools for S. glossinidius. The methods highlighted here should guide the implementation of genetics for the study of the tsetse-Sodalis association and the evaluation of S. glossinidius-based tsetse fly paratransgenesis strategies.

IMPORTANCE Tsetse flies are the insect vectors of T. brucei, the causative agent of African sleeping sickness—a zoonotic disease that inflicts a substantial economic cost on a broad region of sub-Saharan Africa. Notably, tsetse flies can be infected with the bacterium S. glossinidius to establish an asymptomatic chronic infection. This infection can be inherited by future generations of tsetse flies, allowing S. glossinidius to spread and persist within populations. To this effect, S. glossinidius has been considered a potential expression platform to create flies which reduce T. brucei stasis and lower overall parasite transmission to humans and animals. However, the efficient genetic manipulation of S. glossinidius has remained a technical challenge due to its complex growth requirements and uncharacterized physiology. Here, we exploit a natural mechanism of DNA transfer among bacteria and develop an efficient technique to genetically manipulate S. glossinidius for future studies in reducing trypanosome transmission.

The length of the 5' leader of Escherichia coli tRNA precursors influences bacterial growth

Based on a computational analysis of the 5' regions of tRNA-encoding genes, the average length of the 5' leaders in tRNA precursors in Escherichia coli appears to be 17-18 residues long. An in vivo assay based on tRNA nonsense suppression was developed and used to investigate the function of the 5' leader of the tRNA precursors on tRNA processing and bacterial growth. Our data indicate that the 5' leader influences bacterial growth but is surprisingly not absolutely necessary for growth. These findings are consistent with previous in vitro data where it was demonstrated that the 5' leader plays a role in the interaction with RNase P, the endoribonuclease responsible for removing the 5' leader in the cell. We discuss the plausible role of the 5' leader in processing and tRNA gene expression.

Non-contact positions impose site selectivity on Cre recombinase

A first step in Cre-mediated site-specific DNA recombination is binding to the two 13 bp repeats of the 34 bp site loxP. Several nucleotides within loxP do not directly contact the bound enzyme, yet mutation at two of these base pairs, at positions 11 and 12 in each repeat, results in a 100 000-fold reduction in recombination. To understand better how Cre selects DNA sequences for recombination, we combined DNA shuffling mutagenesis and a forward selection strategy to obtain Cre mutants that recombine at 100% efficiency a mutant loxK2 site carrying these dinucleotide changes. The role of the several mutations found in these Cre isolates was analyzed both in vivo and biochemically with purified enzymes. A single mutation at E262 accounts for most but not all of the enhanced activity at loxK2. Secondary mutations act in one or more of three ways: enhancement of loxK2 binding, accelerated synthesis of Cre in vivo or faster DNA recombination at the alternative spacer region present in loxK2. Systematic analysis of all 20 natural amino acids at position E262 shows that the naturally occurring glutamate residue at this position provides the optimal balance of efficiency of recombination at loxP and maximal discrimination against loxK2.

FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter

We have applied laser UV photo-footprinting to characterise kinetically complexes involving the activator protein FIS, RNA polymerase and the tyrT promoter of Escherichia coli. FIS photo-footprints strongly to three binding sites upstream of the core promoter. The polymerase photo-footprints in the near-consensus -35 hexamer on the non-template strand of DNA in a fashion similar to that of stable complexes involving the lacUV5 promoter. The kinetics of the interactions of polymerase alone with the tyrT promoter differ from those observed previously at the lacUV5 promoter. In the absence of FIS, we observe an upstream polymerase-induced signal at -122 within FIS site III that occurs subsequent to changes in the core promoter region and is strongly dependent on negative supercoiling. These observations support the proposal that the upstream region of the promoter is wrapped around the polymerase. We propose that the wrapped DNA allows the polymerase to overcome, at least in part, the barrier to DNA untwisting imparted by the G+C-rich discriminator. We further suggest that FIS plays a similar role and may facilitate polymerase escape.

Multicopy suppression of cold-sensitive sec mutations in Escherichia coli

Mutations in the secretory (sec) genes in Escherichia coli compromise protein translocation across the inner membrane and often confer conditional-lethal phenotypes. We have found that overproduction of the chaperonins GroES and GroEL from a multicopy plasmid suppresses a wide array of cold-sensitive sec mutations in E. coli. Suppression is accompanied by a stimulation of precursor protein translocation. This multicopy suppression does not bypass the Sec pathway because a deletion of secE is not suppressed under these conditions. Surprisingly, progressive deletion of the groE operon does not completely abolish the ability to suppress, indicating that the multicopy suppression of cold-sensitive sec mutations is not dependent on a functional groE operon. Indeed, overproduction of proteins unrelated to the process of protein export suppresses the secE501 cold-sensitive mutation, suggesting that protein overproduction, in and of itself, can confer mutations which compromise protein synthesis and the observation that low levels of protein synthesis inhibitors can suppress as well. In all cases, the mechanism of suppression is unrelated to the process of protein export. We suggest that the multicopy plasmids also suppress the sec mutations by compromising protein synthesis.

A double counter-selection system for the study of null alleles of essential genes in Escherichia coli

The ability to analyze null alleles of genes can be an important means of studying both a protein's function and its interactions with other proteins involved in a particular process. However, if the gene encodes a protein that is essential to the viability of the cell, such analysis becomes complicated because a complementing copy of the gene must be present in the cell. In order to study the effects caused by the null allele, the complementing copy must be inactivated or lost. We report the development of a system in Escherichia coli which facilitates the manipulation of null alleles of essential genes. It consists of a strain deleted chromosomally for the essential gene and complemented for its function by a wild-type (wt) copy expressed from a plasmid counter-selectable for two markers bracketing the gene. Using this system, we have (i) searched for bypass suppressors of a deletion of the essential secE gene, (ii) ascertained the ability of various mutant secE genes to complement a deletion of the wt copy and (iii) isolated intragenic pseudorevertants of a null missense allele of secE. This methodology should be widely applicable to other cases in which essential genes are to be studied genetically.

The rpoE gene encoding the sigma E (sigma 24) heat shock sigma factor of Escherichia coli

Previous work has established that the transcription factor sigma E (sigma 24) is necessary for maintaining the induction of the heat shock response of Escherichia coli at high temperatures. We have identified the gene encoding sigma E using a genetic screen designed to isolate trans-acting mutations that abolish expression from either htrA or rpoHP3, two promoters recognized uniquely by sigma E-containing RNA polymerase. Such a screen was achieved by transducing strains carrying a single copy of either phtrA-lacZ or rpoHP3-lacZ fusions with mutagenized bacteriophage P1 lysates and screening for Lac- mutant colonies at 22 degrees C. Lac- mutants were subsequently tested for inability to grow at 43 degrees C (Ts- phenotype). Only those Lac- Ts- mutants that were unable to accumulate heat shock proteins at 50 degrees C were retained for further characterization. In a complementary approach, those genes which when cloned on a multicopy plasmid led to higher constitutive expression of the sigma E regulon were characterized and mapped. Both approaches identified the same gene, rpoE, mapping at 55.5 min on the E.coli genetic map and encoding a polypeptide of 191 amino acid residues. The wild-type and a mutant rpoE gene products were over-expressed and purified. It was found that the purified wild-type sigma E protein, when used in in vitro run-off transcription assays in combination with core RNA polymerase, was able to direct transcription from the htrA and rpoHP3 promoters, but not from known sigma 70-dependent promoters. In vivo and in vitro analyses of rpoE transcriptional regulation showed that the rpoE gene is transcribed from two major promoters, one of which is positively regulated by sigma E itself.

Residues essential for the function of SecE, a membrane component of the Escherichia coli secretion apparatus, are located in a conserved cytoplasmic region

Protein export in Escherichia coli is absolutely dependent on two integral membrane proteins, SecY and SecE. Previous deletion mutagenesis of the secE gene showed that only the third of three membrane-spanning segments and a portion of the second cytoplasmic region are necessary for its function in protein export. Here we further define the residues important for SecE function. Alignment of the SecE homologues of various eubacteria reveals that they all contain one membrane-spanning segment, compared with three in E. coli SecE, and that the most conserved region among them lies in their putative cytoplasmic amino termini; little homology exists in their membrane-spanning segments. The SecE homologue of the extreme thermophilic bacterium Thermotoga maritima was cloned and found to complement a deletion of secE in E. coli. Deletion or replacement of the cytoplasmic region of E. coli SecE eliminated SecE function, indicating that this sequence is essential for a functional secretion machinery. Mutant analysis suggests that the most important function of the third membrane-spanning segment is to maintain the proper topological arrangement of the conserved cytoplasmic domain.

Hierarchies of base pair preferences in the P22 ant promoter

Oligonucleotide-directed mutagenesis was used to complete a collection of mutations in the -35 and -10 hexamers of the ant promoter of Salmonella phage P22. The effects of all 36 single-base-pair substitutions on promoter strength in vivo were measured in strains carrying the mutant promoters fused to an ant-lacZ gene on a single-copy prophage. The results of these assays show that certain consensus base pairs are more important than others; in general, the least-critical positions are among the most poorly conserved. Some mutations within the hexamers have smaller effects on promoter strength than certain mutations outside the hexamers in this and other promoters. Several different patterns of base pair preferences are observed. These hierarchies of base pair preferences correlate well (but not perfectly) with the hierarchies defined by the frequency distribution of base pairs at each position among wild-type promoters. The hierarchies observed in the ant promoter also agree well with most of the available information on base pair preferences in other promoters.

Mutational analysis of the histidine operon promoter of Salmonella typhimurium

We isolated a collection of 67 independent, spontaneous Salmonella typhimurium his operon promoter mutants with decreased his expression. The mutants were isolated by selecting for resistance to the toxic lactose analog o-nitrophenyl-beta-D-thiogalactoside in a his-lac fusion strain. The collection included base pair substitutions. small insertions, a deletion, and one large insertion identified as IS30 (IS121), which is resident on the Mu d1 cts(Apr lac) phage used to construct the his-lac fusion. Of the 37 mutations that were sequenced, 14 were unique. Six of the 14 were isolated more than once, with the IS30 insertion occurring 16 times. The mutations were located throughout the his promoter region, with two in the conserved - 35 hexamer sequence, four in the conserved - 10 hexamer sequence (Pribnow box), seven in the spacer between the - 10 and -35 hexamer sequences, and the IS30 insertions just upstream of the -35 hexamer sequence. Four of the five substitution mutations changed a consensus base pair recognized by E sigma 70 RNA polymerase in the -10 or -35 hexamer. Decreased his expression caused by the 14 different his promoter mutations was measured in vivo. Relative to the wild-type promoter, the mutations resulted in as little as a 4-fold decrease to as much as a 357-fold decrease in his expression, with the largest decreases resulting from changes in the most highly conserved features of E sigma 70 promoters.

The cyclization of linear DNA in Escherichia coli by site-specific recombination

The efficiency with which linearized plasmid DNA can transform competent Escherichia coli can be significantly increased by use of the Cre-lox site-specific recombination system of phage P1. Linear plasmid molecules containing directly repeated loxP sites (lox2 plasmids) are cyclized in Cre+ E. coli strains after introduction either by transformation or by mini-Mu transduction. Exonuclease V activity of the RecBC enzyme inhibits efficient cyclization of linearized lox2 plasmids after transformation. By use of E. coli mutants which lack exonuclease V activity, Cre-mediated cyclization results in transformation efficiencies for linearized lox2 plasmids identical to those obtained with covalently closed circular plasmid DNA. Moreover, Cre+ E. coli recBC strains allow the efficient recovery of lox2 plasmids integrated within large linear DNA molecules such as the 150-kb genome of pseudorabies virus.

Mutation that affects pepN translation initiation in Escherichia coli

Mutants altered in their expression of the hybrid pepN-lacZ gene have been selected for resistance to p-nitrophenyl-beta-D-thiogalactopyranoside (a bacteriostatic compound that enters the cells via lac permease). A unique mutation decreasing the level of pepN expression to 9% of that of the wild type has been studied in detail. This mutation controls in cis the expression of the pepN gene. The pepN region from a pepN-lacZ gene fusion has been cloned and sequenced. Comparison of the mutant and wild type sequences indicates that the mutation lies between the Shine-Dalgarno sequence (AGGT) and the initiation codon (AUG). This mutation is a T----C transition which might allow the formation of a stable secondary structure in the region of translation initiation thus decreasing the level of pepN expression.

Conformational change in the DNA associated with an unusual promoter mutation in a tRNA operon of Salmonella

We describe two novel types of mutations which decrease transcription of a tRNA operon in Salmonella typhimurium. One mutation consists of a 3 bp deletion at position -70 from the transcription start site. The second mutation is a single bp insertion between the -10 region and the transcription start site. The region around position -70 shows unusual physical properties. DNA fragments carrying the wild-type version of this region exhibit abnormally low electrophoretic mobility in polyacrylamide gels. This anomalous electrophoretic behavior is corrected if gels are run at high temperature or if the fragments contain the 3 bp deletion at -70. Our results indicate the existence of an unusual DNA conformation, probably involving DNA bending, in the region preceding the tRNA operon promoter. This structure is apparently disrupted by the 3 bp deletion. The transcriptional defect of the -70 mutant suggests a role for the unusual conformation in promoter function.

Point mutations that reduce the expression of malPQ, a positively controlled operon of Escherichia coli

malPQ is one of three operons controlled by the positive regulator gene malT. With the objective of defining DNA sequences essential for malPQ transcription, we looked for cis-dominant mutations that reduced the level of expression of this operon. We first constructed malP-lac fusion strains, selected from one of them a series of mutants resistant to p-nitrophenyl-beta-D-thiogalactopyranoside (a bacteriostatic compound that enters the cells via lac permease), and retained the clones that contained a mutation reducing the expression of the hybrid operon in a cis-dominant fashion. Nineteen such mutations were sequenced, and their effect on an otherwise wild type malPQ operon was studied. Three of them mapped in a transcribed portion of the operon, and are believed to exert their effect at the translation level. The others map upstream from the transcription startpoint (co-ordinate +1) and help define three DNA segments that must play a predominant role in transcription initiation: the Pribnow box (from positions -7 to -12); and two inverted repeats, extending from position -32 to -36, and -59 to -63, respectively, which are proposed to constitute part of the binding site for MalT protein.

RNA polymerase interactions with the upstream region of the E. coli tyrT promoter

The rate of in vivo transcription from the E. coli tRNA and rRNA promoters depends on both cellular growth rate and aminoacid availability. To investigate the molecular mechanisms involved we determined the extent of interaction of RNA polymerase with the promoter of the tyrT stable RNA gene. We show that the enzyme can protect from DNAase I digestion a region of at least 85 bp of the wild-type tyrT promoter and only approximately 62 bp of the lacUV5 mRNA promoter, the protected region extending on the antisense strand to approximately 65 and 42 bp respectively upstream of the transcription startpoint. A mutant tyrT promoter, tyrTp27, is protected more extensively, RNA polymerase interactions extending to at least approximately -130. We propose that these upstream interactions of RNA polymerase perform two functions; activating initiation by polymerase bound at the primary binding site and increasing the concentration of polymerase in the vicinity of the tyrT promoter, thus allowing a high rate of maximal expression and enabling the promoter to be regulated over a wide range of activity.

Fusion of the lac genes to the promoter for the aminopeptidase N gene of Escherichia coli

Strains of Escherichia coli K12 were isolated in which the lac structural genes were fused to the promoter for the aminopeptidasee N structural gene (pepN). Although this enzyme is constitutively produced, the differential rate of synthesis is increased about 4-fold upon phosphate starvation. The pepN-lac fusions were shown to respond to phosphate specific regulatory signals. A plaque forming lambda transducing phage bearing the pepN-lac fusion was isolated. This phage was used to prove genetically the fusion of lac genes to the promoter for the aminopeptidase. These results demonstrate a control at the transcriptional level of aminopeptidase synthesis.

In vitro construction of the tufB-lacZ fusion: analysis of the regulatory mechanism of tufB promoter

To investigate the regulatory mechanism of the tufB operon, we have constructed plasmids in which the lac structural genes have been fused to the regulatory region and the 5'-coding sequence of the tufB gene. The fusion was performed by incorporating the 6.6 kb EcoRI-HpaI fragment of plasmid pTUB1, which carried the tufB gene (Miyajima et al. 1979), into the EcoRI and SmaI sites of pMC1403 lac fusion vector (Casadaban et al. 1980). This gene fusion resulted in the production of a hybrid protein consisting of the N-terminal portion (12 amino acid residues) of EF-TuB and the enzymatically active C-terminal half of beta-galactosidase. Bacteria harboring the recombinant plasmid showed a strong Lac+ phenotype. In such a fusion, the lac gene expression was under the control of the tufB promoter. This was evidenced by the following observations; (i) the tufB-lacZ hybrid protein was synthesized constitutively; (ii) its production augmented in parallel with the increase in growth rate; and (iii) on carbon-source upshift, the hybrid protein was produced at a rate 2.5-fold higher than that of the mass increase. Several derivatives of this recombinant plasmid harboring deletions and/or inversions in the tufB regulatory region have been constructed and their properties are described.

Fusion of Escherichia coli lacZ to the cytochrome c gene of Saccharomyces cerevisiae

Hybrid genes between the Escherichia coli lacZ gene and the iso-1-cytochrome c (CYC1) gene of Saccharomyces cerevisiae were constructed by recombination in vitro. Each of the hybrid genes encodes a chimeric protein with a cytochrome c moiety at the amino terminus and an active beta-galactosidase (beta-D-galactoside galactohydrolase, EC 3.2.1.23) moiety at the carboxy terminus. When these hybrids are introduced into S. cerevisiae on plasmid vectors, they direct synthesis of beta-galactosidase. beta-Galactosidase levels directed by one such plasmid display the pattern of regulation normally seen for cytochrome c (i.e., a reduction of synthesis in cells grown in glucose). This plasmid contains one codon of CYC1 fused to lacZ, and the fused gene is preceded by the 1100 nucleotides that lie upstream from CYC1. An analysis of deletions in the upstream DNA suggests that sequences required for efficient transcription initiation of CYC1 lie within the DNA segment 250--700 base pairs upstream from the start of the CYC1 coding sequence. This region is at least 130 base pairs upstream from the "Hogness box" sequence that precedes the CYC1 coding sequence.

Molecular cloning, correlation of genetic and restriction maps, and determination of the direction of transcription of gnd of Escherichia coli

Expression of the gene gnd of Escherichia coli, which encodes 6-phosphogluconate dehydrogenase, is regulated by growth rate. Using deoxyribonucleic acid from the specialized transducing phage lambda h80 dgnd his as the source of gnd, we cloned restriction fragments carrying the complete gene and portions of it on the plasmid vector pBR322. A hybrid plasmid carrying a 3.7-megadalton HindIII restriction fragment from the phage was prepared and found to be gnd+. Through restriction mapping of this fragment and subcloning segments of it, we prepared a gnd+ hybrid plasmid which carried only 1.85 megadaltons of E. coli deoxyribonucleic acid. A cleavage site for the restriction endonuclease PstI was located on the genetic map of gnd by cloning adjacent EcoRI-PstI restriction fragments and crossing the resulting hybrid plasmids with previously mapped gnd deletion and bacteriophage Mu insertion mutants. A maxicell experiment was used to determine the direction of transcription of gnd, to identify which EcoRI-PstI fragment contains the gnd promote, and to localize th beginning of the structural gene to a region about 850 +/- 150 base pairs from the PstI cleavage site. A fine-structure restriction map surrounding the PstI cleavage site was prepared for endonucleases KpnI, HincII, HaeIII, HpaII, and TaqI.

Bacteriophage lambda vehicle for the direct cloning of Escherichia coli promoter DNA sequences: feedback regulation of the rplJL-rpoBC operon

A derivative of bacteriophage lambda, lambda 21, has been constructed and used for the cloning of Escherichia coli DNA fragments carrying promoters. Phage lambda 21 lacks the lac promoter operator and can accept DNA fragments up to 9.8 kilobases in size at a unique HindIII restriction endonuclease site adjacent to lacZ. Recombinant phage that carry promoters are readily identified by their expression of lacZ. Lysogens of these phages in strains harboring a deletion of the chromosomal lac operon are capable of growth on lactose as sole carbon source and can be used to study some of the regulatory signals that act upon the cloned promoter. In principle, lambda 21 can be used to clone any promoter DNA sequence with HindIII termini. PJ, the primary promoter for the rplJL-rpoBC operon, and P beta, a weak promoter for rpoBC, have been cloned in lambda 21. Transcription of lacZ from PJ was found to be subjected to feedback control by ribosomal protein L10 and to a lesser extent by ribosomal protein L7/L12. This suggests a possible L10-binding site near PJ that regulates transcription from that promoter. Lysogens of the phage that carries P beta responded to two regulatory signals: a rho-sensitive termination site preceding rpoBC and induction of beta-galactosidase synthesis by rifampicin. This suggests that P beta is a bona fide promoter for rpoBC.

Mapping of insertion mutations in gnd of Escherichia coli with deletions defining the ends of the gene

A genetic map was prepared for gnd, the gene of Escherichia coli which encodes the metabolically regulated 6-phosphogluconate dehydrogenase. Direct selection methods were used for the isolation of mutants with deletions that define the respective ends of gnd. These selections depended on the availability of a defective lysogen in which gnd was present on a lambda h80 dgnd his prophage located at the att phi 80 region of the chromosome. Mutants with deletions entering gnd from the his-distal end were selected as Gnd- TonB- mutants. Mutants with his-proximal gnd deletions were selected as Gnd-, temperature-resistant mutants of a specially prepared stable lysogen. Gnd- mutants were also isolated after mutagenesis with bacteriophage Mu cts61, and genetic tests were used to determine which mutants carry a Mu cts61 prophage in gnd. The deletion mutations were mapped against each other and against the insertion mutations through the use of F' merodiploid strains. The insertion mutations mapped at seven distinct sites in gnd; three mapped under the deletions defining the his-proximal portion of the gene and three mapped with the his-distal deletions.