Effect of DNA superhelicity on transcription termination

Restriction fragments containing either leut (a rho-independent transcription termination site) and/or leut' (a rho-dependent transcription termination site) were cloned into plasmid pOL4. Treatment of plasmid-containing Escherichia coli strains with coumermycin resulted in loss of in vivo plasmid superhelicity 10 min after antibiotic addition. Galactokinase levels specified by these plasmid-containing strains were the same regardless of whether functional DNA gyrase was present. These results suggest that transcription termination is unaffected by the superhelical state of DNA.

Transcription termination sites at the distal end of the leu operon of Salmonella typhimurium

Transcription terminates at two different sites at the distal end of the leucine operon of Salmonella typhimurium. The first of these sites (leut), located 140 base-pairs past the end of leuD, contains a G + C-rich palindrome followed by a run of T residues in the non-coding strand. Termination at leut, both in vitro and in vivo, is independent of rho protein, but is stimulated by the NusA protein. The second termination site (leut'), located 145 base-pairs beyond the first, is rho-dependent both in vitro and in vivo, and is not influenced by NusA protein. The organization of transcription termination sites at the distal end of the leu operon (a rho-independent site followed by a rho-dependent site) is similar to that for the trp operon of Escherichia coli.

The role of the temporal lobe amygdala in ponto-geniculo-occipital activity and sleep organization in cats

Ponto-geniculo-occipital (PGO) spikes propagate to different structures of the limbic system, including the temporal lobe amygdala. There is direct connection between the amygdala and the pontine nuclei involved in the generation of PGO spikes. It has also been shown that both the amount and the pattern of PGO spike discharges are under the influence of several brainstem and forebrain structures. In the present work, PGO activity was analyzed in unrestrained cats submitted to low-intensity amygdaloid electrical stimulation during paradoxical sleep (PS) episodes. General sleep organization as well as number, mean duration and percentage of PS episodes, were assessed in 8-h sleep recordings during amygdaloid stimulation. Amygdaloid stimulation significantly increased PGO number, spike density and, specially, PGO burst density. No significant changes were found in PS episodes or in the slow-wave sleep. It is concluded that the amygdala plays a role in the modulation of PGO activity by means of a facilitatory influence. It is proposed that this influence is probably exerted through a positive feedback mechanism. The independence between PGO generation and PS maintenance mechanisms is emphasized.

Transcription attenuation in Salmonella typhimurium: the significance of rare leucine codons in the leu leader

The leucine operon of Salmonella typhimurium is controlled by a transcription attenuation mechanism. Four adjacent leucine codons within a 160-nucleotide leu leader RNA are thought to play a central role in this mechanism. Three of the four codons are CUA, a rarely used leucine codon within enteric bacteria. To determine whether the nature of the leucine codon affects the regulation of the leucine operon, we used oligonucleotide-directed mutagenesis to first convert one CUA of the leader to CUG and then convert all three CUA codons to CUG. CUG is the most frequently used leucine codon in enteric bacteria. A mutant having (CUA)2CUGCUC in place of (CUA)3CUC has an altered response to leucine limitation, requiring a slightly higher degree of limitation to effect derepression. Changing (CUA)3CUC to (CUG)3CUC has more dramatic effects upon operon expression. First, the basal level of expression is lowered to the point that the mutant grows more slowly than the parent in a minimal medium lacking leucine. Second, the response of the mutant to a leucine limitation is dramatically altered such that even a strong limitation elicits only a modest degree of derepression. If the mutant is grown under conditions of leucyl-tRNA limitation rather than leucine limitation, complete derepression can be achieved, but only at a much higher degree of limitation than for the wild-type operon. These results provide a clear-cut example of codon usage having a dramatic effect upon gene expression.

High A + T content conserved in DNA sequences upstream of leuABCD in Escherichia coli and Salmonella typhimurium

The nucleotide sequence of over 800 base pairs of DNA upstream of leuP was determined for Escherichia coli and Salmonella typhimurium. In both of these enteric bacteria, approximately 500 base pairs of A + T-rich sequences separates leuP from an upstream open reading frame. Although these A + T-rich sequences share little homology, the distribution of A + T base pairs within the region is strikingly conserved. Deletion of the A + T-rich sequences upstream of the E. coli leu operon does not markedly affect the strength of the leu promoter in vivo.

Escherichia coli B/r leuK mutant lacking pseudouridine synthase I activity

Escherichia coli B/r strain EB146 containing mutation leuK16 has elevated levels of enzymes involved in the synthesis of leucine, valine, isoleucine, histidine, and tryptophan (Brown et al., J. Bacteriol. 135:542-550, 1978). We show here that strain EB146 (leuK16) has properties that are similar to those of E. coli and Salmonella typhimurium hisT strains. In tRNA1Leu from both hisT and leuK strains, positions 39 and 41 are uridine residues rather than pseudouridine residues. Furthermore, in tRNA3Leu and tRNA4Leu from a leuK strain, uridine residues at positions 39 and 40, respectively, are unmodified. Pseudouridine synthase I activity is missing in extracts of strain EB146 (leuK16), and extracts of strain EB146 (leuK16) and of a hisT strain do not complement one another in vitro. Four phenotypes of strain EB146 (leuK16), leucine excretion, wrinkled colony morphology, and elevated levels of leu and his enzymes, are complemented by a plasmid having a 1.65-kilobase DNA fragment containing the E. coli K-12 hisT locus. These results indicate that either leuK codes for pseudouridine synthase I (and is thus a hisT locus in reality) or, less likely, it codes for a product that affects the synthesis or activity of pseudouridine synthase I.

Unusual organization of the ilvIH promoter of Escherichia coli

Analysis of plasmids containing ilvIH-galK fusions indicated that the Escherichia coli ilvIH promoter and sequences sufficient to cause leucine repression lie within 363 base pairs (bp) of ilvI. Experiments designed to locate the promoter and regulatory sequences more precisely gave the following results. The positions of the 5' endpoints of both unlabeled and pulse-labeled ilvIH mRNAs transcribed in vivo lie 30 bp upstream of ilvI. By contrast, the major in vitro RNA endpoints lie at positions further upstream. Several mutations which increase the expression of ilvIH lie 40 to 50 bp upstream of ilvI, within a putative promoter termed P1. Deletion of a 50-bp region immediately upstream of ilvI, which includes P1, resulted in the loss of all ilvIH promoter activity. Deletion of sequences more than 200 bp upstream of ilvI reduced ilvIH promoter activity by more than 80%. These results suggest that transcription of the ilvIH operon is initiated from promoter P1 but that sequences more than 200 bp upstream are required for optimal transcription of the operon.

Mutations that convert the four leucine codons of the Salmonella typhimurium leu leader to four threonine codons

In Salmonella typhimurium, expression of the leucine operon is regulated by a transcription attenuation mechanism. According to a current model of attenuation, elevated expression of this operon requires that a ribosome stall at one of four adjacent codons for leucine on a leader RNA. We used oligonucleotide-directed mutagenesis to convert the four leucine codons of the S. typhimurium leu leader to four threonine codons. Analysis of the resulting mutant operon showed that almost all regulation by leucine had been abolished. The mutant operon was, instead, partially derepressed by a limitation for charged threonine tRNA. These results provide direct evidence for the function for the four leucine codons postulated by the attenuator model. An unexpected observation made during these studies was that the wild-type leu operon was partially derepressed by starvation for threonine.

The ilvIH operon of Escherichia coli K-12. Identification of the gene products and recognition of the translational start by polypeptide microsequencing

The ilvI and ilvH gene products were identified physically by electrophoretic analysis of in vivo-labelled polypeptides produced in minicells from plasmids carrying the wild-type ilvIH operon of Escherichia coli K-12 and derivatives of it. An analysis of the distribution of methionine residues in the amino-terminal portion of micro-quantities of the ilvI product eluted from gel showed that the translational start of the ilvI gene is the promoter-proximal one of three putative methionine codons predicted from the DNA sequence.

The nucleotide sequence of a rat myosin light chain 2 gene

A rat myosin light chain 2 gene was characterized by nucleotide sequence and S1 mapping analyses. It contains seven exons separated by six introns. The corresponding mRNA is predicted to be 654 nucleotides long (excluding polyA sequences), with 5'-nontranslated, coding, and 3'-nontranslated lengths of 56, 510, and 88 nucleotides, respectively. The predicted amino acid sequence is identical to that from rabbit except that the rat sequence lacks one of two Gly residues located at positions 12 and 13 in the rabbit sequence. From the nucleotide sequence, nascent rat myosin light chain 2 is predicted to have Met Ala preceding Pro at the N-terminal end.

Phasic activity of the basolateral amygdala, cingulate gyrus, and hippocampus during REM sleep in the cat

We analyzed the electrical activity of the basolateral amygdala (BLA), anterior and posterior regions of the cingulate gyrus (A-CG and P-CG), the dorsal hippocampus (DH), the anterior ventral thalamic nucleus (AVTN), and the sensory motor cortex during the rapid eye movements and ponto-geniculo-occipital (PGO) activity of REM sleep in cats in chronic preparation. Polygraphic recordings and computational perievent averages using the phasic contractions of the lateral rectus muscle (LR) of the eyeball as the triggering signal of the analysis were performed. We observed biphasic potentials (200-300 ms) of variable amplitude, related to the phasic phenomena of REM sleep, in the BLA, A-CG, P-CG, DH, and AVTN. The latencies of the potentials of these regions were always greater than those of the geniculate PGO activities. We propose that the recorded limbic potentials resulted from propagation of PGO activity and that this phenomenon may reflect the limbic structure of the hallucinatory, vegetative, and emotional components of REM sleep.

Promoter mutation causing catabolite repression of the Salmonella typhimurium leucine operon

Two mutations that affect expression of the Salmonella typhimurium leu operon were investigated. leu operon DNA from these mutant strains was cloned, and nucleotide sequences of the leu control regions were determined. leu-500, which eliminates expression of all four leu genes simultaneously, is a point mutation in the -10 region of the leu promoter. leu-2012 is a point mutation within the -35 region of the leu promoter. leu-2012 suppressed leucine auxotrophy caused by leu-500 only when the medium contained a carbon source that does not cause catabolite repression. A cya mutation (adenylate cyclase deficiency) introduced into the leu-500 leu-2012 strain caused leu enzymes to be made only if cAMP was supplied exogenously. A leu-500 leu-2012 strain containing a crp mutation (cAMP receptor protein deficiency), on the other hand, could not make leu enzymes even in the presence of cAMP. In vitro transcription experiments demonstrated that the leu-2012 mutation created a new transcription initiation site. RNA polymerase utilized this site in vitro in the absence of added cAMP receptor protein and cAMP.

Transcription initiation sites of the leucine operons of Salmonella typhimurium and Escherichia coli

Evidence for a transcription attenuation site downstream from the leu promoter was obtained by transcription experiments in vitro. Most transcription initiated in vitro from leuP is terminated prematurely, resulting in the synthesis of a 160 nucleotide leader RNA. We define here the point at which transcription is initiated in vitro and in vivo and demonstrate that the site of premature termination is between the promoter and the first structural gene (leuA). Additional nucleotide sequences are presented that extend the known sequence 200 base-pairs upstream and 300 base-pairs downstream from leuP. The location of the promoter-proximal end of cistron leuA was deduced by comparing nucleotide sequence data with the sequence of the ten amino acids at the N-terminus of alpha-isopropylmalate synthase. To facilitate the isolation of quantities of material for sequencing experiments, the enzyme was isolated from a plasmid-containing strain, CV605, grown under conditions of leucine limitation. Under such conditions, about 20% of the total soluble protein of strain CV605 is alpha-isopropylmalate synthase and another 20% is beta-isopropylmalate dehydrogenase (leuB product).

Molecular structure of ilvIH and its evolutionary relationship to ilvG in Escherichia coli K12

ilvIH of Escherichia coli K12 codes for a valine-sensitive acetohydroxy acid synthase (AHASIII). The DNA sequence of ilvIH was determined. Open reading frames and appropriate translation signals exist for two polypeptides, one containing 565 amino acids (ilvI polypeptide) and the other 160 amino acids (ilvH polypeptide). A graphic matrix analysis shows three clearcut regions of homology between ilvI and ilvG (codes for AHASII). Within these three regions of homology, 50-60% of the amino acid sequences of AHASII and AHASIII are conserved. Inspection of the region between ilvG and ilvE (the K region) revealed that it can potentially code for an 86 amino acid polypeptide. A computer analysis shows small but significant homology between the predicted amino acid sequences of the N-terminal half of the ilvH polypeptide and the putative region K polypeptide. We conclude that ilvIH and ilvG-region K evolved from a common ancestor.

IlvHI locus of Salmonella typhimurium

In Escherichia coli K-12, the ilvHI locus codes for one of two acetohydroxy acid synthase isoenzymes. A region of the Salmonella typhimurium genome adjacent to the leucine operon was cloned on plasmid pBR322, yielding plasmids pCV47 and pCV49 (a shortened version of pCV47). This region contains DNA homologous to the E. coli ilvHI locus, as judged by hybridization experiments. Plasmid pCV47 did not confer isoleucine-valine prototrophy upon either E. coli or S. typhimurium strains lacking acetohydroxy acid synthase activity, suggesting that S. typhimurium lacks a functional ilvHI locus. However, isoleucine-valine prototrophs were readily isolated from such strains after mutagenesis with nitrosoguanidine. In one case we found that the Ilv+ phenotype resulted from an alteration in bacterial DNA on the plasmid (new plasmid designated pCV50). Furthermore, a new acetohydroxy acid synthase activity was observed in Ilv+ revertants; this enzyme was similar to E. coli acetohydroxy acid synthase III in its lack of activity at low pH. This new activity was correlated with the appearance in minicells of a new polypeptide having an approximate molecular weight of 61,000. Strains carrying either pCV49 or pCV50 produced a substantial amount of ilvHI-specific mRNA. These results, together with results from other laboratories, suggest that S. typhimurium has functional ilvB and ilvG genes and a cryptic ilvHI locus. E. coli K-12, on the other hand, has functional ilvB and ilvHI genes and a cryptic ilvG locus.

Transcription attenuation is the major mechanism by which the leu operon of Salmonella typhimurium is controlled

Three mutations, each causing constitutive expression of the Salmonella typhimurium leu operon, were cloned into phage vector lambda gt4 on EcoRI DNA fragments carrying all of that operon except for part of the promoter-distal last gene. Sequence analysis of DNA from these phage demonstrated that each contains a single base change in the leu attenuator. Transcription of mutant DNA in vitro resulted in transcription beyond the usual site of termination. The level of beta-IPM dehydrogenase, the leuB enzyme, was elevated 40-fold in a strain carrying one of these mutations, and starvation of this strain for leucine had little effect on the amount of activity expressed. Using a strain with a wild-type promoter-leader region of the leu operon, the rates of synthesis and degradation of leu leader RNA and readthrough RNA (leu mRNA) were measured by DNA-RNA hybridizations with specific DNA probes. The rate of synthesis of the leu leader was about the same in cells grown with excess or with limiting leucine. On the other hand, the rate of synthesis of leu mRNA was 12-fold higher for cells grown in limiting leucine as opposed to excess leucine. The rate of degradation of these RNA species was the same under both conditions of growth. Thus, the variation in expression of the leu operon observed for cells grown in minimal medium is, for the most part, not caused by control over the frequency of initiation or by the differential stability of these RNA species. Rather, the variation is a direct result of the frequency of transcription termination at an attenuator site. These results taken together suggest that transcription attenuation is the major mechanism by which leucine regulates expression of the leu operon of S. typhimurium for cells growing in a minimal medium.

Nucleotide sequence of dihydrofolate reductase genes from trimethoprim-resistant mutants of Escherichia coli. Evidence that dihydrofolate reductase interacts with another essential gene product

We report the construction of recombinant plasmids containing the dihydrofolate reductase structural gene (fol) from several trimethoprim-resistant mutants of Escherichia coli. Strains carrying some of these plasmids produced approximately 6% of their soluble cell protein as dihydrofolate reductase and are therefore excellent sources of the purified enzyme for inhibitor binding or mechanistic studies. The nucleotide sequence of the fol region from each of the plasmids was determined. A plasmid derived from a Ki mutant which produced a dihydrofolate reductase with lowered affinity for trimethoprim contained a mutation in the structural gene that altered the sequence of the polypeptide in a conserved region which is adjacent to the dihydrofolate binding site. Two other independently-isolated mutants which overproduced dihydrofolate reductase had a mutation in the -35 region of the fol promoter. One of them, strain RS35, was also temperature-sensitive for growth in minimal medium. This phenotype was shown to be the result of an additional mutation in a locus unlinked to fol by P1 transduction. The fol regions from two temperature-independent revertants of strain RS35 were sequenced. One of these had a mutation within the dihydrofolate reductase structural gene which altered some properties of the enzyme. This confirmed some previous enzymological data which suggested that some revertants of strain RS35 had mutations in fol (Sheldon 1977). These results suggest that dihydrofolate reductase interacts physically with some other essential gene product in E. coli.

Amplification and modification of dihydrofolate reductase in Escherichia coli. Nucleotide sequence of fol genes from mutationally altered plasmids

Recombinant plasmids carrying the structural gene for Escherichia coli dihydrofolate reductase (fol) were mutagenized in vitro and in vivo and were used to transform a suitable recipient strain. Twenty-three transformants were isolated that were able to grow in the presence of high levels of the folate analog trimethoprim, and, in each strain, the resistance determinant was shown to be carried on the plasmid. Three of the strains produced dihydrofolate reductase with an increased Ki value for trimethoprim. DNA sequence analysis showed that the plasmids in these strains had mutations in fol which altered a conserved region of the polypeptide that forms part of the dihydrofolate-binding site. Two other strains had approximately 3-fold elevated dihydrofolate reductase levels, apparently resulting from plasmid copy number mutations. The remaining 18 strains had dihydrofolate reductase levels that were 10-30 times higher than those of the starting strain. Surprisingly, three of these strains had no discernible changes either in plasmid copy number or in the nucleotide sequence of the plasmid fol gene. Sequence analysis of the plasmids in 12 more of the strains revealed mutations in the promoter region adjacent to the fol gene. Most of these mutations occurred in the conserved sequences known as the Pribnow box and the -35 region and increased the homology of these sequences with the consensus E. coli promoter sequence. Strains carrying these plasmids produced a significant fraction of their total cell protein as wild type dihydrofolate reductase and should therefore be useful as sources of the purified enzyme.

Amygdaloid kindling during rapid eye movement (REM) sleep in cats

Development of amygdaloid kindling was analyzed during REM sleep and during wakefulness. Daily evolution of electrographic and behavioral changes was significantly delayed in REM kindled rats. The number of kindling trials required to reach the first generalized convulsive seizure was also significantly increased in comparison with awake kindled animals. Changes in sleep organization were measured under REM kindling conditions. A significant increase in total sleep time and in the percentage of light slow-wave sleep was found during the kindling process. No significant sleep changes were observed in REM-established kindling. REM inhibitory influence over epileptogenesis is discussed.

Acetohydroxy acid synthase isoenzymes of Escherichia coli K12 and Salmonella typhimurium

In Escherichia coli K12 and in Salmonella typhimurium the first step common to the biosynthesis of isoleucine, leucine and valine is catalyzed by an intriguing system of isoenzymes. Two of these are normally expressed, while the genetic determinant for a third one is transcribed, but not translated as an active polypeptide. We analyze here the significance of this system in the light of the most recent results.

Kindling in the spinal cord: differential effects on mono- and polysynaptic reflexes and its modifications by atropine and naloxone

We have used the kindling paradigm at the spinal cord level. In spinal, unanaesthetized, paralysed (gallamine 20 mg/kg) cats, the cutaneous afferent (sural) or the muscle afferent (gastrocnemius, tibial and peroneal) nerves were electrically stimulated at 20 min intervals with a 3 sec train (100 Hz, 2 msec pulse duration, 200-400 microA). Kindling was assessed by averaging 16 mono- or polysynaptic ventral root reflex responses produced by constant intensity single shocks. Atropine sulphate (0.5 mg/kg) and naloxone (0.4 mg/kg) effects were measured in the kindled preparation. Kindling induced a progressive increment of the amplitude, ipsilateral propagation and after-discharge frequency. This was greater in polysynaptic responses. When testing monosynaptic responses during the kindling of cutaneous afferents, a cumulative inhibitory effect was observed. In both types of kindled response, atropine had a transient inhibitory effect. Naloxone noticeably augmented the kindled polysynaptic reflexes.

Physical characterization of the ilvHI operon of Escherichia coli K-12

The ilvHI and leu genes of Escherichia coli K-12 are contained on a single 10.9-kilobase EcoRI fragment of deoxyribonucleic acid derived from the leu transducing phage lambda G4. Since the expression of all of these genes is controlled by leucine, we investigated whether they are part of single operon or whether they constitute separate but adjacent operons controlled from a common site. Both cloning and hybridization studies indicated that ilvHI and leu are distinct operons. They are transcribed in opposite directions and are separated by approximately 1,500 base pairs of deoxyribonucleic acid. Hybridization experiments showed that the expression of ilvHI is regulated chiefly at the level of transcription. The size of the ilvHI messenger ribonucleic acid is estimated to be 2,550 bases.