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Novel escherichia coli strain allows efficient recombinant protein production using lactose as inducer.

An important characteristic of promoters used in recombinant protein production in Escherichi coli is their inducibility in a simple and cost-effective manner. The IPTG inducible promoters lac, tac, and trc are powerful and widely used for basic research. However, the use of IPTG in large-scale production is undesirable due to its high cost and toxicity. The promoters mentioned above can also be induced by the addition of lactose, which has the double role of inducer and carbon and energy source. Nevertheless, the use of this sugar in industrial processes has several drawbacks, which result in low volumetric yields and difficulties in process control. We have genetically engineered a BL21 strain to allow the efficient use of lactose as inducer in fed-batch cultures. Two modifications were introduced, the exchange of the wild-type lac operator by a constitutive one (lacO(c)) and the replacement of the gal alleles to recover the Gal(+) phenotype. The constitutive expression of the lac operon overcame the negative effects that the Lac nongenetic heterogeneity of wild-type E. coli introduces when lactose is used as inducer. The gal(+) genotype allowed the complete use of the lactose as carbon and energy source. The relevance of these two modifications in the efficient utilization of lactose as inducer was demonstrated in fed-batch cultures of the novel recombinant strain MP101 harboring expression vectors containing the calf prochymosin gene or the pccB gene, which encodes for the carboxyltransferase component of a propionyl-CoA carboxylase complex from Streptomyces coelicolor. Similar levels of recombinant protein production (up to 16 g/L) were obtained by using either lactose or IPTG as inducers, which confirmed the success of the genetics modifications introduced.

Bacterial Proteins↗

A novel genetic system to isolate a dominant negative effector on DNA-binding activity of Oct-2.

Recent studies have revealed that interactions between transcription factors play an important role in regulation of gene expression in eukaryotic cells. To isolate cDNA clones that dominantly inhibit the DNA-binding activity of Oct-2, chosen as a representative factor, we have developed a novel screening system. This employs an Escherichia coli tester strain carrying a modified lac operon as a reporter gene, with the lac operator sequence replaced by an octamer sequence. Oct-2 expressed in this tester strain represses the expression of the reporter gene and changes the phenotype of the cell from Lac+to Lac-. Introduction of a cDNA expression library prepared from a human T-cell line into the Oct-2-harboring tester strain allowed selection of three Lac+clones out of 1 x 10(5) transformants. One of them, hT86, encoding a putative zinc finger protein was found to derepress beta-galactosidase activity in the Oct-2-harboring tester strain at the transcriptional level. In gel mobility shift assays, hT86 attenuated the intensity of the retarded band composed of the octamer probe and Oct-2, suggesting a dominant negative effect on the DNA-binding activity of Oct-2. The strategy described here provides a new approach for studying protein-protein interactions that govern the complex regulation of gene expression.

Amino Acid Sequence↗

Transcription of the glutamyl-tRNA reductase (hemA) gene in Salmonella typhimurium and Escherichia coli: role of the hemA P1 promoter and the arcA gene product.

In Salmonella typhimurium and Escherichia coli, the hemA gene encodes the enzyme glutamyl-tRNA reductase, which catalyzes the first committed step in the heme biosynthetic pathway. It has recently been reported that a lac operon fusion to the hemA promoter of E. coli is induced 20-fold after starvation for heme. Induction was dependent on the transcriptional regulator ArcA, with a second transcriptional regulator, FNR, playing a negative role specifically under anaerobic conditions (S. Darie and R. P. Gunsalus, J. Bacteriol. 176:5270-5276, 1994). We have investigated the generality of this effect by examining the response to heme starvation of a number of lac operon fusions to the hemA promoters of both E. coli and S. typhimurium. We confirmed that such fusions are induced during starvation of a hemA auxotroph, but the level of induction observed was maximally sixfold and for S. typhimurium fusions it was only two- to fourfold. Sequences required for high-level expression of hemA lie within 129 bp upstream of the major (P1) promoter transcriptional start site. Mutants defective in the P1 promoter had greatly reduced hemA-lac expression both in the presence and in the absence of ALA. Mutations in arcA had no effect on hemA-lac expression in E. coli during normal growth, although the increase in expression during starvation for ALA was half that seen in an arcA+ strain. Overexpression of the arcA gene had no effect on hemA-lac expression. Primer extension analysis showed that RNA 5' ends mapping to the hemA P1 and P2 promoters were not expressed at significantly higher levels in induced cultures. These results differ from those previously reported.

Aldehyde Oxidoreductases↗

The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes.

By equilibrium competition experiments, the dissociation constant (K(RD)) of lac repressor for E. coli DNA carrying a deletion of the lac operon was measured at a variety of salt concentrations. These data are used in the consideration of several aspects of protein-DNA interaction: Quantitative estimates of specificity are made. Specificity changes only slightly with salt concentration. We calculate that in vivo, 98 percent or more of repressor is bound to DNA predominately at sites other than the lac operator. Inducers shift repressor from operator to nonoperator DNA, but do not free it from DNA. The general affinity of repressor for E. coli DNA is sufficient to support a model where repressor slides along DNA for significant distances. The effective dissociation constant of repressor for operator (K(eff)) is very sensitive to the total DNA concentration. We propose that "junk" DNA in eucaryotes functions to maintain total DNA at an optimum concentration. We consider the lac operon in the nucleus of a lymphocyte, point out that severe difficulties would be encountered, and suggest possible solutions.

Cell Nucleus↗

Intermediates in the degradation of mRNA from the lactose operon of Escherichia coli.

We have analyzed the processing of mRNA from the lac operon in an Escherichia coli strain carrying the lac on a multicopy plasmid. Messenger RNA was analyzed by hybridization and nuclease protection of pulse-labeled RNA and precursor-product relationships were determined by quantitating radioactivity in primary and processed transcripts at various times after induction of the lac promoter or inhibition of transcription with rifampicin. Our results support the existence of two types of processed transcripts with endpoints in the lacZ-lacY intercistronic region. One of these carries lacZ sequences and has a 3' endpoint about 30 bases downstream of this gene. The other carries lacY sequences and has a 5' end in the translation termination region of the lacZ gene. Finally, we have found evidence that transcription is continued at least 268 bases beyond the last gene (lacA) and that this 3' non-translated region is shortened by post-transcriptional processing.

Base Sequence↗

Molecular cloning of the uhp region and evidence for a positive activator for expression of the hexose phosphate transport system of Escherichia coli.

The uhp locus of Escherichia coli contains genes for the sugar phosphate transport system (uhpT) and the regulatory system which allows its induction by external glucose 6-phosphate (uhpRA). The uhp region was cloned onto high-copy-number plasmids, both from Uhp(+) plasmids of the Clarke-Carbon collection and from genetically characterized specialized transducing phages carrying uhpT-lac operon fusions. Two Clarke-Carbon plasmids and their Uhp(+) subclones in pBR322 shared restriction sites defining the uhp region, but exhibited different regulation of Uhp expression and dependence on chromosomal uhp genotype. Plasmid pLC17-47 and derivatives conferred constitutive glucose 6-phosphate uptake activity in all strains, even those with complete deletions of uhp. These plasmids also rendered constitutive the expression of a chromosomal uhpT-lac operon fusion. Plasmid pLC40-33 conferred inducible Uhp expression, which required the presence of the uhpA(+) gene on the chromosome. The induced transport levels in all strains carrying these plasmids were not appreciably amplified over haploid levels. Similar behavior was seen with the cloned operon fusions. A fusion-bearing plasmid that carried an intact regulatory system (uhpR(+)A(+)) exhibited trans-dominant constitutive expression of beta-galactosidase, regardless of the chromosomal uhp genotype. In contrast, the cloned fusion carrying only uhpR(+) gave glucose 6-phosphate-inducible production of beta-galactosidase that was dependent on the presence of chromosomal uhpA(+). Expression of both fusions in the haploid state was inducible. From these results, it was concluded that the uhpA product is necessary for uhpT transcription and that elevated dosage of uhpA results in at least partially constitutive expression of uhpT. A tentative model for uhp regulation is presented.

Biological Transport↗

Method for isolation of Escherichia coli mutants with defects in the proton-translocating sector of the membrane adenosine triphosphatase complex.

A technique for selecting mutants of Escherichia coli in which the proton-translocating sector of the adenosine triphosphatase (ATPase) complex has been inactivated is reported. The procedure uses a strain of E. coli (NR-70) lacking the extrinsic (F1) sector of the ATPase complex and which in consequently permeable to protons (B. P. Rosen, J. Bacteriol. 116:1124--1129, 1973). After growing strain NR-70 under noninducing conditions for the lac operon, cells were mutagenized and plated on minimal medium containing low concentrations of lactose. Several mutants of strain NR-70 were isolated as large colonies on these plates, apparently because they could concentrate lactose more efficiently. A description of one of the mutants, strain KW-1, is reported here. The most distinguishing difference in growth properties of the two strains was that, when transferred to medium containing low concentrations of lactose, strain KW-1 induced the lac operon with a shorter lag time than strain NR-70. The mutation in strain KW-1 leading to more rapid growth on lactose was cotransducible with the asn and unc loci, at 83 min on the E. coli genetic map. Intact cells of strain KW-1 actively transported L-proline as well as did wild-type cells, whereas cells of strain NR-70 were markedly deficient in L-proline transport. The improvement in the transport capacity of strain KW-1 correlated with a marked decrease in proton permeability relative to that of strain NR-70. Based on an acid-base pulse technique that measured the proton conductance of the membranes of intact cells, strain NR-70 was at least 10 times more permeable to protons than was the wild type, whereas strain KW-1 was only 2 times more permeable. The transport properties and proton conductance were also compared with membrane vesicles prepared by osmotic shock. With either D-lactate or ascorbate-N-methylphenazonium methosulfate as respiratory substrates, vesicles of strain KW-1 transported L-proline much more rapidly than did vesicles of strain NR-70, but still at rates less rapid than those of the wild type. The passive proton conductance of the membrane vesicles was quantitated by measuring the rate of H+ influx into vesicles in response to a valinomycin-generated K+ diffusion potential. The proton permeability of vesicles of strain KW-1 was reduced 1.5-fold relative to vesicles of strain NR-70, but these vesicles were still four times more permeable to protons than was the wild type. Vesicles of strain KW-1 corresponded to wild-type vesicles treated with 0.5 micrometer carbonylcyanide m-chlorophenylhydrazone (CCCP) and vesicles of strain NR-70 corresponded to wild-type vesicles treated with 1.4 micrometer CCCP. Treatment of wild-type vesicles with these concentrations of CCCP caused decreases in transport comparable to those observed in the mutants. Strain KW-1 lacked ATPase activity. Cross-reacting material to F1-ATPase was not found in strain KW-1 by double immunodiffusion analysis.

Adenosine Triphosphatases↗

[Features of functioning of the promoter of microcin C51 promoter under various conditions of Escherichia coli cell growth].

The level of transcription from the promoter of the microcin C51 operon (Pmcc) depends on the growth phase of Escherichia coli cells: transcription proceeds with low efficiency at the exponential phase of growth and with higher efficiency when growth of cells is delayed during entry into the stationary phase. The functioning of Pmcc was studied in cells grown in different media by a single-copy construct, which contained the cloned promoter region of the microcin C51 operon and the promoterless lac operon. A decrease in the rate of cell growth caused by changes in the sole carbon source in minimal medium correlated with an increase in the level of transcription from the Pmcc promoter at the exponential phase of growth; the expression of Pmcc-lac during cell entry into the stationary phase was higher under unfavorable medium conditions. The use of composite rich media impaired this feature. The addition of l-leucine (100 micrograms/ml) to the medium decreased the expression of Pmcc-lac in wild-type cells carrying the delta lrp mutation. A further increase in leucine concentration and the presence of other amino acids in the medium enhanced transcription that started from Pmcc during cell entry into the stationary growth phase. The capacity of the Pmcc promoter and of the wild-type lacZ gene promoter was virtually the same upon IPTG induction. A mutation in the ompR gene did not markedly influence transcription started from Pmcc.

Amino Acid Sequence↗

Identification and characterization of starvation-regulated genetic loci in Salmonella typhimurium by using Mu d-directed lacZ operon fusions.

We used the technique of Mu d-directed lac operon fusion formation in an effort to identify loci in Salmonella typhimurium which are transcriptionally regulated by nutrient starvation conditions. We identified lacZ operon fusions in eight genetic loci, all of which exhibited increased transcription when starved for two or more of the following nutrients: nicotinate, phosphate, ammonium, glucose, and sulfate. The loci have been designated stiA to stiH for starvation-inducible loci. Mutations in two sti loci (stiC and stiD) significantly decreased cell viability during prolonged periods of nicotinate starvation, stiA and stiD are linked and map at 30 min. The stiC, stiE, stiG, and stiH loci mapped at approximately 77, 43, 88, and 56 min, respectively, on the S. typhimurium linkage map.

Ammonia↗

Phosphoenolpyruvate:sugar phosphotransferase system-mediated regulation of carbohydrate metabolism in Salmonella typhimurium.

The crr mutation was shown to affect the phosphoenolpyruvate:sugar phosphotransferase system-mediated transient repression of the lac operon, intracellular cAMP levels, and sensitivity to inducer exclusion. Our results indicate that the presumed crr gene product, factor IIIGlc, plays a direct role in the regulation of inducer exclusion. We propose a mechanism in which inducer exclusion depends on both the level and state of phosphorylation of factor IIIGlc and the level of an inducer exclusion-sensitive transport system. The results of studies on the sensitivity to inducer exclusion of glycerol and maltose in cultures induced for short periods of time on these substrates (resulting in varying degrees of activity of the respective transport systems) support this model of inducer exclusion. Previously, the crp*-771 mutation has been shown to result in an altered cAMP receptor protein, which has a changed affinity for cAMP, and to affect the sensitivity for inducer exclusion of glycerol. Changes in other functions of the altered cAMP receptor protein were indicated by our results; these changes were in the roles of this protein in (i) the cAMP-dependent initiation of transcription of the lac operon and (ii) the regulation of intracellular cAMP levels and the export of cAMP. We propose that the crp*-771 mutation has an indirect effect in relieving inducer exclusion in repressed or hypersensitive strains, in which the crp*-771 mutation allows the synthesis of inducer exclusion-sensitive transport systems to higher levels than the levels found in strains containing wild-type cAMP receptor protein.

Carbohydrate Metabolism↗

Isolation and characterization of new copy mutants of plasmid R1, and identification of a polypeptide involved in copy number control.

Site-specific deletions and insertions in the replication region of plasmid R1 have generated a new class of copy mutants that are present in the cell with 10-15-fold increased copy number. All mutations described inactivate a copy number control gene which is distinct from another cop inc gene that was identified previously (Molin and Nordström 1980). Insertion of the lac operon lacking the normal lac promoter has been used to determine the direction of transcription of this cop gene. The mutants may all be complemented by wild-type plasmid derivatives and are thus recessive. In incompatibility tests with wild-type R1 plasmids, these mutants are indistinguishable from the wild-type plasmid. It therefore seems that this cop function does not play an important role for the incompatibility function. A polypeptide, molecular weight 11,000, has been identified as being the product of this cop gene.

Bacterial Proteins↗

Stationary phase deletions in Escherichia coli. II. Mutations which stimulate stationary phase deletions in plasmid pMC874.

Deletions in the plasmid pMC874 take place in resting cells incubating on McConkey's or minimal lactose agar and are time rather than generation dependent. These deletions join the km(r) promoter to a promoterless lac operon giving rise to Lac(+) papillae on McConkey's lactose agar, and can occur in the absence of sequence homologies such as direct or inverted repeats. Using this as a selective screen we isolated 31 mutants designated dli (for deletion increase), which enhanced to different extents the frequency of this unusual class of deletions. Six of these were characterized by phenotypic tests and their ability to stimulate other deletion events such as the excision of Tn10 from various chromosomal sites and the loss of cloned fragments between two EcoR1 sites in the gene for chloramphenicol resistance (cat) of plasmid pBR325. Two of them showed contrasting phenotypes and were studied further: one (dli1) stimulated Lac(+) deletions in pMC874 in resting cells but not Tn10 excision from chromosomal locations in log phase cells, and the other one (dli2) did exactly the reverse, i.e. it enhanced Tn10 excision but not Lac(+) deletion incidence. Mapping and complementation tests showed that dli1 is a null mutation in recC and was renamed recC2251. This is strong evidence that resting phase deletions in pMC874 are stimulated by the absence of a functional RecBCD enzyme. The dli2 mutation was identified by mapping and phenotypic tests as a mutation in uvrD, the gene for helicase II, and it was tentatively designated uvrD(-)dli2. These results show that (1) pMC874 is an excellent system to select mutants for genetic functions involved in the generation of resting phase deletions, and (2) there are at least two major deletion pathways in E. coli, one active in resting and the other in actively dividing cells.

Agar↗

Self-organisation and orderly processes by individual protein complexes in the bacterial cell.

In the bacterial cell, individual multimeric proteins and multiprotein assemblies perform and control orderly processes. Individual motor enzyme complexes accomplish highly complex functions, such as nucleic acid and protein syntheses, with impressive efficiency and fidelity. Lac operon repression by the lac repressor is effectively controlled via a single molecular switch. There are only few copies of, for example, DNA polymerase holoenzyme and lac repressor and few specific target molecules/sites, with which these protein complexes interact, present in a single E. coli cell. These interactive processes take place in submicron-sized spaces characterised by extreme crowding (volume exclusion) of macromolecules and small molecules, heterogeneity and non-ideality. Recent evidence reinforces the fundamental difference of the cytoplasmic as compared with in vitro ("test tube") reaction conditions. This is reflected in the breakdown of the applicability of "bulk phase" thermodynamic, macroscopic chemical kinetic and diffusion laws to interactions of individual macromolecules and target sites in a single cell. Stochastic kinetic models and stochastic simulations enable the statistical description and analysis of biochemical reactions and binding processes which involve small numbers of reactants. New unifying concepts and models are required for the quantitative understanding of the microscopic self-organisation of multi-protein complexes and the dynamic order at the single-protein assembly and single-switch level in the living cell.

Bacteria↗

A comprehensive library of fluorescent transcriptional reporters for Escherichia coli.

E. coli is widely used for systems biology research; there exists a need, however, for tools that can be used to accurately and comprehensively measure expression dynamics in individual living cells. To address this we present a library of transcriptional fusions of gfp to each of about 2,000 different promoters in E. coli K12, covering the great majority of the promoters in the organism. Each promoter fusion is expressed from a low-copy plasmid. We demonstrate that this library can be used to obtain highly accurate dynamic measurements of promoter activity on a genomic scale, in a glucose-lactose diauxic shift experiment. The library allowed detection of about 80 previously uncharacterized transcription units in E. coli, including putative internal promoters within previously known operons, such as the lac operon. This library can serve as a tool for accurate, high-resolution analysis of transcription networks in living E. coli cells.

Escherichia coli↗

Synthesis of simian virus 40 t antigen in Escherichia coli.

Plasmids are constructed by using recombination in vitro according to Roberts, T.M., Kacich, R. & Ptashne, M. (1979) Proc. Natl. Acad. Sci. USA 76, 760-764 in which the t antigen gene of simian virus 40 is fused to a promoter of the Escherichia coli lac operon. In the fusions, transcription commences at the lac promoter, and, in some of the fusions, translation begins at the ATG initiator codon of the t gene. This translation is directed most efficiently by those plasmids in which the lac sequences abut the t gene such that a hybrid ribosome binding is encoded. In this case, the Shine-Dalgarno sequence is of lac origin but the ATG derives from the t gene. translation from this initiator codon is greatly decreased if the lac sequences are separated from the ATG by 17 base pairs and is abolished if the AT of this triplet is deleted. Cells bearing the productive fusions synthesize a 20,000-dalton protein with t antigenic determinants. This protein has an isoelectric point(s) indistinguishable from that of t antigen isolated from simian virus 40-transformed cells. Moreover, a partial sequence of the amino-terminal region of the bacterial product is that predicted for authentic t antigen. We conclude that these bacteria are for authentic t antigen. We conclude that these bacteria are producing a protein, the sequence of which is identical to that of authentic t antigen unfused to other polypeptides.

Amino Acid Sequence↗

Spontaneous and cisplatin-induced recombination in Escherichia coli.

To measure cisplatin (cis-diaminodichloroplatinum(II))-induced recombination, we have used a qualitative intrachromosomal assay utilizing duplicate inactive lac operons containing non-overlapping deletions and selection for Lac+ recombinants. The two operons are separated by one Mb and conversion of one of them yields the Lac+ phenotype. Lac+ formation for both spontaneous and cisplatin-induced recombination requires the products of the recA, recBC, ruvA, ruvB, ruvC, priA and polA genes. Inactivation of the recF, recO, recR and recJ genes decreased cisplatin-induced, but not spontaneous, recombination. The dependence on PriA and RecBC suggests that recombination is induced following stalling or collapse of replication forks at DNA lesions to form double strand breaks. The lack of recombination induction by trans-DDP suggests that the recombinogenic lesions for cisplatin are purine-purine intrastrand crosslinks.

Cell Survival↗

Transcriptional regulation and evolution of lactose genes in the galactose-lactose operon of Lactococcus lactis NCDO2054.

The genetics of lactose utilization within the slow-lactose-fermenting Lactococcus lactis strain NCDO2054 was studied with respect to the organization, expression, and evolution of the lac genes. Initially the beta-galactosidase gene (lacZ) was cloned by complementation of an Escherichia coli mutant on a 7-kb HpaI fragment. Nucleotide sequence analysis of the complete fragment revealed part of a gal-lac operon, and the genes were characterized by inactivation and complementation analyses and in vitro enzyme activity measurements. The gene order is galK-galT-lacA-lacZ-galE; the gal genes encode enzymes of the Leloir pathway for galactose metabolism, and lacA encodes a galactoside acetyltransferase. The galT and galE genes of L. lactis LM0230 (a lactose plasmid-cured derivative of the fast-lactose-fermenting L. lactis C2) were highly similar at the nucleotide sequence level to their counterparts in strain NCDO2054 and, furthermore, had the same gene order except for the presence of the intervening lacA-lacZ strain NCDO2054. Analysis of mRNA for the gal and lac genes revealed an unusual transcriptional organization for the operon, with a surprisingly large number of transcriptional units. The regulation of the lac genes was further investigated by using fusions consisting of putative promoter fragments and the promoterless beta-glucuronidase gene (gusA) from E. coli, which identified three lactose-inducible intergenic promoters in the gal-lac operon. The greater similarity of the lacA and lacZ genes to homologs in gram-negative organisms than to those of gram-positive bacteria, in contrast to the homologies of the gal genes, suggests that the genes within the gal operon of L. lactis NCDO2054 have been recently acquired. Thus, the lacA-lacZ genes appear to have engaged the promoters of the gal operon in order to direct and control their expression.

Amino Acid Sequence↗