beta-Galactosidase chimeras: primary structure of a lac repressor-beta-galactosidase protein

Stress-Induced Mutagenesis

Early research on the origins and mechanisms of mutation led to the establishment of the dogma that, in the absence of external forces, spontaneous mutation rates are constant. However, recent results from a variety of experimental systems suggest that mutation rates can increase in response to selective pressures. This chapter summarizes data demonstrating that,under stressful conditions, Escherichia coli and Salmonella can increase the likelihood of beneficial mutations by modulating their potential for genetic change.Several experimental systems used to study stress-induced mutagenesis are discussed, with special emphasison the Foster-Cairns system for "adaptive mutation" in E. coli and Salmonella. Examples from other model systems are given to illustrate that stress-induced mutagenesis is a natural and general phenomenon that is not confined to enteric bacteria. Finally, some of the controversy in the field of stress-induced mutagenesis is summarized and discussed, and a perspective on the current state of the field is provided.

Stress-induced mutagenesis in bacteria

Bacteria spend their lives buffeted by changing environmental conditions. To adapt to and survive these stresses, bacteria have global response systems that result in sweeping changes in gene expression and cellular metabolism. These responses are controlled by master regulators, which include: alternative sigma factors, such as RpoS and RpoH; small molecule effectors, such as ppGpp; gene repressors such as LexA; and, inorganic molecules, such as polyphosphate. The response pathways extensively overlap and are induced to various extents by the same environmental stresses. These stresses include nutritional deprivation, DNA damage, temperature shift, and exposure to antibiotics. All of these global stress responses include functions that can increase genetic variability. In particular, up-regulation and activation of error-prone DNA polymerases, down-regulation of error-correcting enzymes, and movement of mobile genetic elements are common features of several stress responses. The result is that under a variety of stressful conditions, bacteria are induced for genetic change. This transient mutator state may be important for adaptive evolution.

Double illegitimate recombination events integrate DNA segments through two different mechanisms during natural transformation of Acinetobacter baylyi

Acquisition of foreign DNA by horizontal gene transfer is seen as a major source of genetic diversity in prokaryotes. However, strongly divergent DNA is not genomically integrated by homologous recombination and would depend on illegitimate recombination (IR) events which are rare. We show that, by two mechanisms, during natural transformation of Acinetobacter baylyi two IR events can integrate DNA segments. One mechanism is double illegitimate recombination (DIR) acting in the absence of any homology (frequency: 7 x 10(-13) per cell). It occurs about 10(10)-fold less frequent than homologous transformation. The other mechanism is homology-facilitated double illegitimate recombination (HFDIR) being about 440-fold more frequent (3 x 10(-10) per cell) than DIR. HFDIR depends on a homologous sequence located between the IR sites and on recA(+). In HFDIR two IR events act on the same donor DNA molecule as shown by the joint inheritance of molecular DNA tags. While the IR events in HFDIR occurred at microhomologies, in DIR microhomologies were not used. The HFDIR phenomenon indicates that a temporal recA-dependent association of donor DNA at a homology in recipient DNA may facilitate two IR events on the 5' and 3' heterologous parts of the transforming DNA molecule.

The Escherichia coli histone-like protein HU has a role in stationary phase adaptive mutation

Stationary phase adaptive mutation in Escherichia coli is thought to be a mechanism by which mutation rates are increased during stressful conditions, increasing the possibility that fitness-enhancing mutations arise. Here we present data showing that the histone-like protein, HU, has a role in the molecular pathway by which adaptive Lac(+) mutants arise in E. coli strain FC40. Adaptive Lac(+) mutations are largely but not entirely due to error-prone DNA polymerase IV (Pol IV). Mutations in either of the HU subunits, HUalpha or HUbeta, decrease adaptive mutation to Lac(+) by both Pol IV-dependent and Pol IV-independent pathways. Additionally, HU mutations inhibit growth-dependent mutations without a reduction in the level of Pol IV. These effects of HU mutations on adaptive mutation and on growth-dependent mutations reveal novel functions for HU in mutagenesis.

Fast sequence evolution of Hox and Hox-derived genes in the genus Drosophila

Background

It is expected that genes that are expressed early in development and have a complex expression pattern are under strong purifying selection and thus evolve slowly. Hox genes fulfill these criteria and thus, should have a low evolutionary rate. However, some observations point to a completely different scenario. Hox genes are usually highly conserved inside the homeobox, but very variable outside it.

Results

We have measured the rates of nucleotide divergence and indel fixation of three Hox genes, labial (lab), proboscipedia (pb) and abdominal-A (abd-A), and compared them with those of three genes derived by duplication from Hox3, bicoid (bcd), zerknüllt (zen) and zerknüllt-related (zen2), and 15 non-Hox genes in sets of orthologous sequences of three species of the genus Drosophila. These rates were compared to test the hypothesis that Hox genes evolve slowly. Our results show that the evolutionary rate of Hox genes is higher than that of non-Hox genes when both amino acid differences and indels are taken into account: 43.39% of the amino acid sequence is altered in Hox genes, versus 30.97% in non-Hox genes and 64.73% in Hox-derived genes. Microsatellites scattered along the coding sequence of Hox genes explain partially, but not fully, their fast sequence evolution.

Conclusion

These results show that Hox genes have a higher evolutionary dynamics than other developmental genes, and emphasize the need to take into account indels in addition to nucleotide substitutions in order to accurately estimate evolutionary rates.

Different foreign genes incidentally integrated into the same locus of the Streptococcus suis genome

Some strains of Streptococcus suis possess a type II restriction-modification (RM) system, whose genes are thought to be inserted into the genome between purH and purD from a foreign source by illegitimate recombination. In this study, we characterized the purHD locus of the S. suis genomes of 28 serotype reference strains by DNA sequencing. Four strains contained the RM genes in the locus, as described before, whereas 11 strains possessed other genetic regions of seven classes. The genetic regions contained a single gene or multiple genes that were either unknown or similar to hypothetical genes of other bacteria. The mutually exclusive localization of the genetic regions with the atypical G+C contents indicated that these regions were also acquired from foreign sources. No transposable element or long-repeat sequence was found in the neighboring regions. An alignment of the nucleotide sequences, including the RM gene regions, suggested that the foreign regions were integrated by illegitimate recombination via short stretches of nucleotide identity. By using a thermosensitive suicide plasmid, the RM genes were experimentally introduced into an S. suis strain that did not contain any foreign genes in that locus. Integration of the plasmid into the S. suis genome did not occur in the purHD locus but occurred at various chromosomal loci, where there were 2 to 10 bp of nucleotide identity between the chromosome and the plasmid. These results suggest that various foreign genes described here were incidentally integrated into the same locus of the S. suis genome.

Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination

The active uptake of extracellular DNA and its genomic integration is termed natural transformation and constitutes a major horizontal gene-transfer mechanism in prokaryotes. Chromosomal DNA transferred within a species can be integrated effectively by homologous recombination, whereas foreign DNA with low or no sequence homology would rely on illegitimate recombination events, which are rare. By using the nptII(+) gene (kanamycin resistance) as selectable marker, we found that the integration of foreign DNA into the genome of the Gram-negative Acinetobacter sp. BD413 during transformation indeed was at least 10(9)-fold lower than that of homologous DNA. However, integration of foreign DNA increased at least 10(5)-fold when it was linked on one side to a piece of DNA homologous to the recipient genome. Analysis of foreign DNA integration sites revealed short stretches of sequence identity (3-8 bp) between donor and recipient DNA, indicating illegitimate recombination events. These findings suggest that homologous DNA served as a recombinational anchor facilitating illegitimate recombination acting on the same molecule. Homologous stretches down to 183 nucleotides served as anchors. Transformation with heteroduplex DNA having different nucleotide sequence tags in the strands indicated that strands entered the cytoplasm 3' to 5' and that strands with either polarity were integrated by homologous recombination. The process led to the genomic integration of thousands of foreign nucleotides and often was accompanied by deletion of a roughly corresponding length of recipient DNA. Homology-facilitated illegitimate recombination would explain the introgression of DNA in prokaryotic genomes without the help of mobile genetic elements.

Comparative studies on discrete and concatemeric DNA-sepharose columns for purification of transcription factors

Concatemers, tandem copies of DNA elements ligated together, are widely used for the DNA affinity chromatography of transcription factors. Purification of different transcription factors using discrete, concatemeric and T18:A18 tailed DNA affinity columns was studied. Columns having a discrete DNA sequence bound by cytidylic-adenylic-adenylic-thymidylic oligonucleotide (CAAT) enhancer binding protein (C/EBP) yields significantly more green fluorescent protein-C/EBP (GFP-C/EBP) fusion protein than a concatemeric DNA column made from five tandem repeats of the same DNA sequence. For lac repressor protein, the concatemeric and T18:A18 tailed columns show greater retention times than a discrete, untailed DNA affinity column. It was observed that the T18:A18 tailed column gives better resolution than either the discrete or concatemeric columns, of mixtures containing both lac repressor and GFP-C/EBP. Discrete concatemeric and T18:A18 tail columns all bound the Sp1 transcription factor and showed similar retention. The T18:A18 tailed column gives higher yield for Sp1 than the other columns. Our study shows concatemeric columns do not have any distinct advantage for the three different transcription factors we studied including Sp1, the original justification for the concatemeric approach.

Biphasic expression of rnrB in Dictyostelium discoideum suggests a direct relationship between cell cycle control and cell differentiation

Cell differentiation in Dictyostelium is strongly affected by the cell cycle. Cell cycle control is well-understood in other systems, but this has had almost no impact on the study of Dictyostelium cell differentiation, in part because the cell cycle in Dictyostelium is unusual, lacking a G1 phase. Here we describe the cell-cycle regulated expression of rnrB, which codes for the small subunit of ribonucleotide reductase and is a marker of late G1 in many systems. There appear to be two expression peaks, one in mid-G2 and the other near the G2/M transition. Using Xgal/anti-BrdU double staining, we show that cells in asynchronously growing cultures express in both phases, with a gap between them during which the gene is transcriptionally silent. Cold-synchronized cells show exclusively G2/M expression, while mid-G2 expression is seen in high-density synchronized cells and can also be inferred in cells undergoing synchronization by either method. rnrB expression occurs in other systems shortly after cells pass a point (the "restriction point" or "start") at which they commit to complete their current cell cycle. We demonstrate a similar commitment point in Dictyostelium and show that this occurs shortly before the mid-G2 rnrB expression peak. The Dictyostelium cell cycle thus appears to include a well-defined though inconspicuous event, between early and mid-G2, with some features which are normally associated with the G1/S transition. Others have described a switch from stalk to spore differentiation preference at about this time. Since Dictyostelium cells switch back from spore to stalk preference approximately at the G2/M rnrB expression maximum, cell differentiation as well as rnrB expression may be regulated directly by fundamental cell cycle control processes.

Comparative studies on chemically and enzymatically coupled DNA-Sepharose columns for purification of a lac repressor chimeric fusion protein

The length of a DNA sequence attached to an affinity chromatography column affects column retention of transcription factors. Even when unrelated sequences such as a poly(A):poly(T) tail are included in a DNA sequence, transcription factors such as the lac repressor are bound more tightly by the column. The position of the additional sequences is also important. To compare coupling procedures, an identical DNA sequence was covalently attached to Sepharose by chemical coupling or produced enzymatically by template driven enzymatic primer extension. These two types of supports, containing the O1 operator sequence bound by lac repressor, were packed into identical columns and compared by purification of a lac repressor-beta-galactosidase fusion protein. We found that the purity and yield of proteins eluted from the two columns were similar. Overall, the results suggest that there is no significant advantage to either type of support for the purification of some proteins. The study revealed a potentially important effect of the length of DNA sequences on column selectivity.

Heparin elution of transcription factors from DNA-Sepharose columns

A novel method using heparin for eluting transcription factors from DNA-Sepharose columns was characterized. CAAT enhancer binding protein (C/EBP) or lac repressor fusion proteins were both eluted with heparin from columns containing specific DNA sequences coupled to cyanogen bromide activated Sepharose. The amount of the lac repressor chimera which eluted from the column was shown to increase with increases in the mobile phase heparin concentration. The elution of the protein was also shown to be dependent on the amount of DNA coupled to the column and more protein eluted from columns containing lesser amounts of DNA. These data suggest that heparin and DNA compete for binding to the protein; this competition causes elution. Comparison of heparin- and salt-eluted protein demonstrated the heparin-eluted fraction was significantly purer and comparable to that obtained by elution with isopropyl beta-D-thiogalactopyranoside, a lactose analog. Heparin elution represents an important new tool in the purification of transcription factors and other DNA-binding proteins by DNA affinity chromatography.

Mechanisms of mutation in nondividing cells. Insights from the study of adaptive mutation in Escherichia coli

When populations of cells are subjected to nonlethal selection, mutations arise in the absence of cell division, a phenomenon that has been called "adaptive mutation." In a strain of Escherichia coli that cannot metabolize lactose (Lac-) but that reverts to lactose utilization (Lac+) when lactose is its sole energy and carbon source, the mutational process consists of two components. (1) A highly efficient, recombination-dependent mechanism giving rise to mutations on the F' episome that carries the Lac- allele; and (2) a less efficient, unknown mechanism giving rise to mutations elsewhere in the genome. Both selected and nonselected mutations arise in the Lac- population, but nonselected mutations are enriched in Lac+ mutants, suggesting that some Lac+ cells have passed though a transient period of increased mutation. These results have several evolutionary implications. (1) DNA synthesis initiated by recombination could be an important source of spontaneous mutation, particularly in cells that are not undergoing genomic replication. (2) The highly active mutational mechanism on the episome could be important in the horizontal transfer of variant alleles among species that carry and exchange conjugal plasmids. (3) A sub-population of cells in a state of transient mutation could be a source of multiple variant alleles and could provide a mechanism for rapid adaptive evolution under adverse conditions.

The methylthio group (ms2) of N6-(4-hydroxyisopentenyl)-2-methylthioadenosine (ms2io6A) present next to the anticodon contributes to the decoding efficiency of the tRNA

A Salmonella typhimurium LT2 mutant which harbors a mutation (miaB2508::Tn10dCm) that results in a reduction in the activities of the amber suppressors supF30 (tRNA(CUATyr)), supD10 (tRNA(CUASer)), and supJ60 (tRNA(CUALeu)) was isolated. The mutant was deficient in the methylthio group (ms2) of N6-(4-hydroxyisopentenyl)-2-methylthioadenosine (ms2io6A), a modified nucleoside that is normally present next to the anticodon (position 37) in tRNAs that read codons that start with uridine. Consequently, the mutant had i6A37 instead of ms2io6A37 in its tRNA. Only small amounts of io6A37 was found. We suggest that the synthesis of ms2io6A occurs in the following order: A-37-->i6A37-->ms2i6A37-->ms2io6A37. The mutation miaB2508::Tn10dCm was 60% linked to the nag gene (min 15) and 40% linked to the fur gene and is located counterclockwise from both of these genes. The growth rates of the mutant in four growth media did not significantly deviate from those of a wild-type strain. The polypeptide chain elongation rate was also unaffected in the mutant. However, the miaB2508::Tn10dCm mutation rendered the cell more resistant or sensitive, compared with a wild-type cell, to several amino acid analogs, suggesting that this mutation influences the regulation of several amino acid biosynthetic operons. The efficiencies of the aforementioned amber suppressors were decreased to as low as 16%, depending on the suppressor and the codon context monitored, demonstrating that the ms2 group of ms2io6A contributes to the decoding efficiency of tRNA. However, the major impact of the ms2io6 modification in the decoding process comes from the io6 group alone or from the combination of the ms2 and io6 groups, not from the ms2 group alone.

A new mutation in 16S rRNA of Escherichia coli conferring spectinomycin resistance

We report a novel mutation, C1066U in 16S rRNA which was selected for resistance to spectinomycin, an antibiotic which inhibits ribosomal translocation. The minimal inhibitory concentration (MIC) of spectinomycin determined for this mutant (15 micrograms/ml) is greater than with the wild-type plasmid (5 micrograms/ml) but lower than with the well known C1192U mutation (> 80 micrograms/ml). The C1066U mutation also increases the cells sensitivity to fusidic acid, another antibiotic which inhibits translation at the translocation stage, whereas C1192U is unchanged relative to the wild type. We discuss why the acquisition of resistance to one of these drugs is often associated with hypersensitivity to the other.

Thermal denaturation of beta-galactosidase and of two site-specific mutants

The thermal denaturation of wild-type beta-galactosidase and two beta-galactosidases with substitutions at the active site was studied by kinetics, differential scanning calorimetry, electrophoresis, molecular exclusion chromatography, and circular dichroism. From the results, a model is developed for thermal denaturation of beta-galactosidase which includes the reversible dissociation of ligands, reversible formation of an inactive tetramer, irreversible dissociation of the inactive tetramer to inactive monomers, and subsequent aggregation of inactive monomers to dimers and larger aggregates. Under some conditions, partial reversibility of the activity loss could be demonstrated, and several intermediates in the thermal denaturation process were trapped by quenching and observed by electrophoresis and molecular exclusion chromatography. The ligands Mg2+ and phenylethyl thio-beta-D-galactoside increase the stability of beta-galactosidase to heat denaturation by shifting the ligand binding equilibrium according to Le Chatelier's principle, thus decreasing the concentration of the ligand-free tetramer which can proceed to subsequent steps. Circular dichroism results indicated that beta-galactosidase is dominated by beta-sheet with lower amounts of alpha-helix. Large changes in secondary structure begin to occur only after activity has been lost. Single amino acid changes at the active site can have significant effects on thermal stability of beta-galactosidases. Some of the effects result from increased thermal stability of the ligand-free enzyme itself. Other effects result from changes in ligand binding, but the magnitude of the resulting changes in stability is not related to the strength of ligand binding in a simple fashion.

Drosophila Krüppel protein is a transcriptional repressor

Krüppel (Kr), one of the zygotically active Drosophila segmentation genes, is expressed in a restricted domain during the blastoderm stage of embryogenesis and is involved in the control of development of the thoracic and abdominal segments of the fly. Kr encodes a polypeptide containing DNA-binding zinc-finger motifs, disruptions of which yield Kr mutants. We have assayed the transcriptional activities of wild-type Kr protein as well as Lac repressor/Kr fusion proteins in HeLa and CV-1 cells. Wild-type Kr and a Lac-Kr chimaeric protein repressed transcription from reporter promoters in which a consensus Kr binding site derived from sequences within the even-skipped promoter had been inserted in an upstream position. We mapped the repression function of Kr to an alanine-rich amino-terminal region of the protein, as a Lac/Kr fusion protein containing only amino acids 26-110 of Kr repressed transcription from a reporter promoter containing upstream lac operators. This demonstrates that the DNA-binding and repression activities of the Kr protein are distinct. These data are consistent with genetic evidence that Kr represses even-skipped and hunchback expression, and suggest that Kr is a negative regulator of transcription in Drosophila.

Two sequence-specific binding proteins from the promoter region of the c-Ha-ras-I oncogene

The role of sequence-specific binding proteins in transcriptional control in higher eukaryotes is unclear. We have investigated the control region of the c-Ha-ras-I protooncogene containing upstream sequences from the transcriptional initiation point. Two proteins, which bind these sequences, with molecular weights of 20 K and 43 K were found. The possible role in the process of transformation is discussed.

Genetic rearrangements and gene amplification in Escherichia coli: DNA sequences at the junctures of amplified gene fusions

We describe gene fusions that result from genetic duplications of 5-20 kb, which are amplified 50- to 100-fold. Because one end point of the fusion lies within the sequenced lacI gene, the new junctures created by the duplications are readily identified. Using a procedure for dideoxy sequencing of double-stranded DNA, we show that the duplications occur almost exclusively at short sequence repeats (less than 15 bp), sometimes involving broken homologies, in the 30 cases examined. Most of the duplications place the lacI-Z encoded hybrid repressor-beta-galactosidase protein under the control of a downstream promoter, resulting in the production of a more complex hybrid protein with beta-galactosidase activity. In some cases the fusion occurs with the lacY or the lacA gene, which suggests that silent promoters can be uncovered by gene fusion and subsequent amplification. In some ways this system represents a bacterial analog to chromosomal rearrangements of oncogenes in higher cells, since here the expression of a silent gene is the result of a genetic rearrangement that is followed by amplification during selected growth.

Strong inhibitory effect of furanoses and sugar lactones on beta-galactosidase Escherichia coli

Various sugars and their lactones were tested for their inhibition of beta-galactosidase (Escherichia coli). L-Ribose, which in the furanose form has a hydroxyl configuration similar to that of D-galactose at positions equivalent to the 3- and 4-positions of D-galactose, was a very strong inhibitor, and D-lyxose, which in the furanose form also resembles D-galactose, was a much better inhibitor than expected. Structural comparisons prelude the pyranose forms of these sugars from being significant contributors to the inhibition, and inhibition at different temperatures (at which there are different furanose concentrations) strongly supported the conclusion that the furanose form is inhibitory. Studies with sugar derivatives that can only be in the furanose form also supported the conclusion. This is the first report of the inhibitory effect of furanose on beta-galactosidase. Lactones were also inhibitory. Every lactone tested was much more inhibitory than was its parent sugar. D-Galactonolactone was especially good. Experiments indicated that it was D-galactono-1,5-lactone rather than D-galactono-1,4-lactone which was inhibitory. Inhibition of beta-galactosidases from mammalian sources by lactones has been reported previously, but this is the first report of the effect of beta-galactosidase from E. coli. Since furanoses in the envelope form are analogous (in some ways) to half-chair or sofa conformations and since lactones with six-membered rings probably have half-chair or sofa conformations, the results indicate that beta-galactosidase probably destabilizes its substrate into a planar conformation of some type and that the galactose in the transition state may, therefore, also be quite planar.(ABSTRACT TRUNCATED AT 250 WORDS)

Novel method for identifying sequence-specific DNA-binding proteins

We developed a general method for the enrichment and identification of sequence-specific DNA-binding proteins. A well-characterized protein-DNA interaction is used to isolate from crude cellular extracts or fractions thereof proteins which bind to specific DNA sequences; the method is based solely on this binding property of the proteins. The DNA sequence of interest, cloned adjacent to the lac operator DNA segment is incubated with a lac repressor-beta-galactosidase fusion protein which retains full operator and inducer binding properties. The DNA fragment bound to the lac repressor-beta-galactosidase fusion protein is precipitated by the addition of affinity-purified anti-beta-galactosidase immobilized on beads. This forms an affinity matrix for any proteins which might interact specifically with the DNA sequence cloned adjacent to the lac operator. When incubated with cellular extracts in the presence of excess competitor DNA, any protein(s) which specifically binds to the cloned DNA sequence of interest can be cleanly precipitated. When isopropyl-beta-D-thiogalactopyranoside is added, the lac repressor releases the bound DNA, and thus the protein-DNA complex consisting of the specific restriction fragment and any specific binding protein(s) is released, permitting the identification of the protein by standard biochemical techniques. We demonstrate the utility of this method with the lambda repressor, another well-characterized DNA-binding protein, as a model. In addition, with crude preparations of the yeast mitochondrial RNA polymerase, we identified a 70,000-molecular-weight peptide which binds specifically to the promoter region of the yeast mitochondrial 14S rRNA gene.

Nucleotide sequence of Klebsiella pneumoniae lac genes

The nucleotide sequences of the Klebsiella pneumoniae lacI and lacZ genes and part of the lacY gene were determined, and these genes were located and oriented relative to one another. The K. pneumoniae lac operon is divergent in that the lacI and lacZ genes are oriented head to head, and complementary strands are transcribed. Besides base substitutions, the lacZ genes of K. pneumoniae and Escherichia coli have suffered short distance shifts of reading frame caused by additions or deletions or both during evolutionary divergence from a common ancestral gene. Relative to corresponding E. coli sequences, the nucleotide sequences of the lacZ and lacY genes are 61 and 67% conserved, and the lacI genes are 49% conserved. A comparison of both nucleotide and amino acid sequences revealed that the K. pneumoniae and E. coli lacI genes and lac repressor proteins each are related to the galR gene and gal repressor of E. coli to about the same extent. In terms of evolutionary relationships, the divergence of the forerunner of the galR gene from an ancestral lac repressor gene preceded separation and differentiation of the K. pneumoniae and E. coli lac repressor genes.

Novel method for identifying sequence-specific DNA-binding proteins

We developed a general method for the enrichment and identification of sequence-specific DNA-binding proteins. A well-characterized protein-DNA interaction is used to isolate from crude cellular extracts or fractions thereof proteins which bind to specific DNA sequences; the method is based solely on this binding property of the proteins. The DNA sequence of interest, cloned adjacent to the lac operator DNA segment is incubated with a lac repressor-beta-galactosidase fusion protein which retains full operator and inducer binding properties. The DNA fragment bound to the lac repressor-beta-galactosidase fusion protein is precipitated by the addition of affinity-purified anti-beta-galactosidase immobilized on beads. This forms an affinity matrix for any proteins which might interact specifically with the DNA sequence cloned adjacent to the lac operator. When incubated with cellular extracts in the presence of excess competitor DNA, any protein(s) which specifically binds to the cloned DNA sequence of interest can be cleanly precipitated. When isopropyl-beta-D-thiogalactopyranoside is added, the lac repressor releases the bound DNA, and thus the protein-DNA complex consisting of the specific restriction fragment and any specific binding protein(s) is released, permitting the identification of the protein by standard biochemical techniques. We demonstrate the utility of this method with the lambda repressor, another well-characterized DNA-binding protein, as a model. In addition, with crude preparations of the yeast mitochondrial RNA polymerase, we identified a 70,000-molecular-weight peptide which binds specifically to the promoter region of the yeast mitochondrial 14S rRNA gene.

The frequency of transcriptional and translational errors at nonsense codons in the lacZ gene of Escherichia coli

Nonsense alleles in the lacZ gene of E. coli do not completely eliminate enzyme activity as errors during protein synthesis allow some chains to be completed. The relative contributions of transcriptional and translational errors to this leakiness were investigated by two methods: the introduction of rho- alleles into extreme-polar mutants and the kinetics of beta-galactosidase induction. Virtually all the errors appeared to be transcriptional in the case of two extreme-polar and one non-polar mutation. These alleles should prove useful for further in vivo investigations of RNA polymerase accuracy. With two other non-polar alleles, transcriptional mistakes were low and translational ones high. The frequency of RNA polymerase errors was context-dependent and varied for different nonsense codons in the same position and for the same codon in different positions. The reasons why some alleles showed no activity due to translational errors could not be clearly established. However, increasing the rates of ribosomal errors from one such allele with streptomycin raised the contribution of ribosomal errors to activity markedly and non-linearly. Translational mistakes may give rise to active enzyme only if the monomers are formed at a rate sufficient for effective aggregation to the normal tetramer.

In vitro construction and characterization of phoA-lacZ gene fusions in Escherichia coli

Using recombinant DNA techniques, we have constructed phoA-lacZ gene fusions. Two of the fusions encode hybrid proteins containing approximately half of alkaline phosphatase at the amino terminus joined to beta-galactosidase. For the one fusion strain analyzed in detail, it was shown that the hybrid protein is found in the membrane fraction of cells. In its membrane location, the beta-galactosidase activity of the hybrid is not sufficient to support cell growth on lactose. Unexpectedly, fusions containing phoA and lacZ joined in the wrong translational reading frame were also obtained. These fusions direct the phosphate-regulated synthesis of beta-galactosidase, apparently via a translation restart mechanism. Thus, when gene fusions are constructed, the presence of properly regulated beta-galactosidase activity does not necessarily indicate that a hybrid protein is being produced.

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.

Inactivation of beta-Galactosidase by iodination of tyrosine-253

Beta-Galactosidase is rapidly inactivated by iodination catalyzed by lactoperoxidase but is not inactivated in the presence of the substrate analogue, isopropyl beta-D-thiogalactoside (IPTG). Enzyme activity is lost upon the incorporation of 1 mol of iodine per mol of monomer, without dissociation of the tetrameric structure. Tryptic digests of beta-galactosidase iodinated with 125I in the presence and absence of IPTG were separated by high-performance liquid chromatography and were compared. One fraction was found to be more highly labeled in the digest from the inactivated protein. After isolation of the peptide, amino acid analysis indicated it to be Asp-Tyr-Leu-Arg, residues 252-255. Thus, Tyr-253 is the most reactive tyrosine in beta-galactosidase. This suggests that the conformation of this region of the protein may be altered by binding of IPTG to make Tyr-253 less accessible to iodination. Alternatively, Tyr-253 could be an active-site residue.

Construction and characterization of a tufA-lacZ fusion coding for an E. coli EF-Tu-beta-galactosidase chimeric protein

A new phage lambda cloning vector was constructed that has a single EcoRI site upstream from weakly expressed lacI-Z gene isolated by Müller-Hill and Kania (1974). An EcoRI fragment containing the complete tufA gene of E. coli was cloned on the vector and the recombinant phage was crossed into the str operon that has tufA as its last gene. Subsequent selection gave rise to a tufA-lacZ fusion that codes for a chimeric peptide. The fused peptide has a molecular weight of 148,000 and contains 40% of the N-terminal of EF-Tu followed by part of the lac repressor-beta-galactosidase fusion. The specific activity of the fused peptide is about half of the activity of normal beta-galactosidase.

Position of the lacZX90 mutation and hybridization between complete and incomplete beta-galactosidase

The position of the termination codon in lacZX90 was determined by isolation of a lac+ revertant. Lysine was found to replace tyrosine at position 1,012 of beta-galactosidase, indicating that X90 protein lacked the carboxyl-terminal 10 residues. A heat- and urea-sensitive hybrid enzyme was formed in vivo when supC, which supplies tyrosine to the position in the polypeptide corresponding to the nonsense codon, was used to suppress lacZX90. This result shows that suppression that adds back the original amino acid may not lead to the production of the wild-type enzyme if the latter is multimeric, because incomplete chains can be incorporated into the oligomer.

A signal sequence is not sufficient to lead beta-galactosidase out of the cytoplasm

Escherichia coli strains have been constructed in which lacZ, the gene for the cytoplasmic enzyme beta-galactosidase, is fused to lamB, the gene for an outer membrane protein. One such strain produces a beta-galactosidase which remains cytoplasmic even though it possesses the complete signal sequence of the lamB protein precursor at the amino-terminal end.

Mutations which alter the function of the signal sequence of the maltose binding protein of Escherichia coli

The maltose binding protein of Escherichia coli is secreted into the external periplasmic compartment of the cell by virtue of an amino-terminal signal sequence. Using DNA sequencing, we have determined the precise nature of mutations in the signal sequence which prevent the export of the maltose binding protein, causing it to accumulate in the cytoplasm in its precursor form. In most cases, the change of a single hydrophobic or uncharged amino acid to a charged amino acid within the signal sequence is sufficient to block the secretion process.

Positions of early nonsense and deletion mutations in lacZ

The positions of three Escherichia coli lacZ operator-proximal nonsense mutations and one deletion mutation have been determined. The nonsense mutations were suppressed with supF, resulting in the production of active beta-galactosidase by each strain. Amino acid sequencing identified the positions of the tyrosine residues inserted by supF, and thereby established that nonsense mutations lacZ2, lacZ2246, and lacZU131 are at sites corresponding to amino acids 23, 36, and 41 of beta-galactosidase, respectively. The deletion mutant, lacZM112, produced a dimeric beta-galactosidase protein missing amino acid residues 23 through 31 of the native enzyme.

Abstracts of papers presented at the 1980 meetings of the Genetic Society of America. Boulder, Colorado August 18-20, 1980

The transposable tetracycline resistance element, Tn10, can serve as a region of homology to promote rec-dependent deletion, duplication and directed transposition of bacterial genes. Tn10 insertions in regions of the chromosome near the histidine operon (his) have been isolated and characterized in Salmonella typhimurium. When strains are constructed containing two Tn10 insertions flanking the his operon in the same orientation (Tn10-his-Tn10), recombination can occur between Tn10 sequences resulting in the deletion of the intervening his region. The sites of the Tn10 insertions determine the endpoints of the deletion. In crosses designed to construct strains carrying Tn10-his-Tn10, another class of unstable recombinants arises in which the his region exists in tandem duplication, with a Tn10 insertion joining the duplicated copies (his-Tn10-his). The sites of the parental Tn10 insertions mark the endpoints of the duplication. When a strain carrying Tn10-his-Tn10 is used as a donor of his(+) in conjugation or P22-mediated transduction, recombinants can arise in which the his region has been transposed to the site of any Tn10 insertion, far from the normal location of his in the recipient chromosome. In this manner, the his operon has been moved to the site of a pyrB::Tn10 insertion and has been placed on F' plasmids. At these new locations, the his(+) character shows the rec-dependent deletion of his(+) expected for a Tn10-his-Tn10 duplication. These methods should be generally useful for the manipulation of bacterial genes.

Genic heterogeneity within electrophoretic "alleles" and the pattern of variation among loci in Drosophila pseudoobscura

An investigation, similar to our previously reported xanthine dehydrogenase study, was undertaken to examine the extent of hidden genic variation at nine loci (five larval proteins, three esterases and one aldehyde oxidase) by sequential application of various electrophoretic criteria employing pH, gel concentration and buffer variation. Polymorphic loci appear to fall into two distinct groups: weakly polymorphic, including larval protein 6, 7, 8, 10 and 13 and esterase-1 and -6; and highly polymorphic, including esterase-5, Xdh and possibly Ao. Monomorphic loci may belong to a third group different from all polymorphic loci. Bogota, a geographical isolate that is reproductively isolated from the mainland population, was found to be genetically distinct at four of the ten loci examined in detail so far, including Xdh, whereas previously it was found to be genetically distinct at none. These results are discussed in the light of balancing selection, neutral and mutation-selection hypotheses of genic variation in natural populations.

Use of gene fusions to determine a partial signal sequence of alkaline phosphatase

We have isolated strains of Escherichia coli in which an amino-terminal portion of the cytoplasmic enzyme beta-galactosidase is replaced by an amino-terminal portion of the periplasmic enzyme alkaline phosphatase. The synthesis of these hybrid proteins is regulated by inorganic phosphate and they are located in the cytoplasm. One of these proteins was purified, and 14 amino acids of the amino-terminal sequence were determined. The first five amino acids, Met-Lys-Gln-Ser-Thr, appear to represent a portion of the signal sequence of the precursor of alkaline phosphatase, and the remaining sequence corresponds to that of beta-galactosidase, beginning at amino acid residue 20. The approach described here could be used for the analysis of signal sequences of exported proteins and for partial amino acid sequence determination of certain of certain other proteins.

Sites within gene lacZ of Escherichia coli for formation of active hybrid beta-galactosidase molecules

We describe the genetic analysis of 21 Escherichia coli strains in which the amino-terminal sequence of beta-galactosidase has been removed and replaced by an amino-terminal sequence from one or another of the proteins involved in maltose transport. Genetic mapping of the lacZ end of these fused genes indicates that only those fusions in which fewer than 41 amino acids are removed from the amino-terminal sequence of beta-galactosidase result in enzymatically active molecules. Within the region between amino acid 17 and amino acid 41 there are at least four or five sites where enzymatically active hybrid proteins can be formed.

A dimer--dimer binding region in beta-galactosidase

alpha Complementation in beta-galactosidase is the restoration of enzyme activity by addition of the alpha donor CNBr2, from amino acid residues 3--92 of the polypeptide, to inactive M15 protein from the lacZ deletion mutant strain M15. M15 protein lacks residues 11--41 and is a dimer; the active complex, like native beta-galactosidase, is tetrameric [Langley, K. E., & Zabin, I. (1976) Biochemistry 15, 4866--4875]. A dimer--dimer binding region in beta-galactosidase has been identified by proteolytic and immunologic studies of alpha-complementation. Proteolytic experiments were carried out with trypsin. Treatment of native beta-galactosidase with trypsin, followed by reaction of the mixture with cyanogen bromide, yields intact CNBr2 as measured by its ability to complement M15 protein. Active CNBr2 is not obtained when urea-denatured beta-galactosidase is treated in the same way. Therefore the segment corresponding to CNBr2 is apparently buried within the folded protein. Immunologic experiments were carried out with antibodies against CNBr2, tryptic peptide T8 (residues 60--140), and CNBr3 (residues 93--187). Anti-CNBr2 and anti-T8 bind to M15 protein but not to beta-galactosidase, indicating that this area is exposed in the dimer. Anti CNBr2, but not anti-T8 or anti-CNBr3, inhibits the formation of alpha-complemented enzyme. These results indicate that an early part of the sequence, within the segment corresponding to CNBr2, is involved in dimer--dimer interaction.