Parent Management Training Augmentation to Address Coercive and Disruptive Behavior in Cognitive-Behavioral Therapy for Pediatric Obsessive-Compulsive Disorder

Coercive and disruptive behaviors commonly interfere with cognitive-behavioral therapy (CBT) trials among youths with obsessive-compulsive disorder (OCD). Although evidence supports parent management training (PMT) for reducing disruptive behavior, no group-based PMT interventions exist for OCD-related disruptive behaviors. We studied feasibility and effectiveness of group-based adjunctive PMT among non-randomized, OCD-affected families receiving family-based group CBT. Linear mixed models estimated treatment effects across OCD-related and parenting outcomes at post-treatment and 1-month follow-up. Treatment response for 37 families receiving CBT + PMT (M_age = 13.90) was compared to 80 families receiving only CBT (M_age = 13.93). CBT + PMT was highly accepted by families. Families who received CBT + PMT had improved disruptive behaviors, parental distress tolerance, and other OCD-related outcomes. OCD-related outcomes did not significantly differ between groups. Results support CBT + PMT as effective treatment for pediatric OCD that may not provide incremental benefits beyond CBT alone. Future research should determine feasible and effective ways to incorporate key PMT components into CBT-based interventions.

Effector function does not contribute to protection from virus challenge by a highly potent HIV broadly neutralizing antibody in nonhuman primates

Protection from immunodeficiency virus challenge in nonhuman primates (NHPs) by a first-generation HIV broadly neutralizing antibody (bnAb) b12 has previously been shown to benefit from interaction between the bnAb and Fcγ receptors (FcγRs) on immune cells. To investigate the mechanism of protection for a more potent second-generation bnAb currently in clinical trials, PGT121, we carried out a series of NHP studies. These studies included treating with PGT121 at a concentration at which only half of the animals were protected to avoid potential masking of FcγR effector function benefits by dominant neutralization and using a new variant that more completely eliminated all rhesus FcγR binding than earlier variants. In contrast to b12, which required FcγR binding for optimal protection, we concluded that PGT121-mediated protection is not augmented by FcγR interaction. Thus, for HIV-passive antibody prophylaxis, these results, together with existing literature, emphasize the importance of neutralization potency for clinical antibodies, with effector function requiring evaluation for individual antibodies.

A case-control study of sleep disturbances in pediatric obsessive-compulsive disorder

BACKGROUND

Sleep disturbances, including delayed sleep phase disorder (DSPD) and disorders of sleep initiation and maintenance (DIMS), have repeatedly been identified in adult obsessive-compulsive disorder (OCD). These disturbances have not been well-characterized objectively in pediatric OCD.

METHODS

Thirty OCD-affected youth (8-18 yrs, 40% male) and 30 age and gender-matched healthy controls (HCs) completed the Sleep Disturbances Scale for Children (SDSC), and one week of continuous actigraphy with concurrent sleep diary documentation. A subsample completed the Children's Sleep Hygiene Scale (CSHS) and Sleep Attitudes and Beliefs Scale (SABS).

RESULTS

Seventy-two percent of OCD participants reported sleep disturbances versus 15% of HC participants (p < 0.001). Convergent actigraphy results suggested DIMS but not DSPD were common.

DISCUSSION

The parents of OCD-affected children seem to be successfully controlling bedtimes, preventing circadian rhythm system disruptions. OCD status does adversely impact, however, the perisleep arousal system. These results have important clinical implications, suggesting sleep problems may be best managed through direct treatment of OCD symptoms. It is recommended that all pediatric OCD patients be screened for sleep disturbances to inform treatment plan development.

Group family-based cognitive behavioral therapy for pediatric obsessive compulsive disorder: Global outcomes and predictors of improvement

This open, uncontrolled study examined the efficacy of a group family-based cognitive behavioral therapy (GF-CBT) protocol in treating pediatric obsessive-compulsive disorder (OCD) and explored predictors of symptom improvement. Eighty-five OCD-affected youth aged 8-18 years (M = 13.9 years, SD = 2.49; 46% male) and their parent(s) participated in a weekly, 12-session GF-CBT program. Data from multiple perspectives were gathered at the beginning and end of treatment, as well as at one-month follow-up. A broad range of assessment measures were utilized to capture clinically-relevant domains and a number of potential predictor variables were explored. Paired t-tests indicated that treatment was associated with significant reductions in clinician- and parent-rated OCD severity (d = 1.47, 1.32), youth and parent-rated functional impairment (d = 0.87, 0.67), coercive/disruptive behaviors (d = 0.75), and family accommodation (d = 1.02), as well as improvements in youth-, mother-, and father-rated family functioning (d = 1.05, 0.50, 0.88). Paired t-tests also indicated that youth remained improved at one-month follow-up. Step-wise regression identified greater homework success as a significant predictor of symptom improvement. This study provides evidence that GF-CBT significantly improves a wide range of domains for youth/families that extends beyond OCD symptom severity and supports homework as a core treatment component.

Prevalence of Acute-Onset Subtypes in Pediatric Obsessive-Compulsive Disorder

BACKGROUND

Pediatric obsessive-compulsive disorder (OCD) is a common, debilitating illness. When childhood OCD symptom onset is described as acute and severe, diagnostic criteria for pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections (PANDAS) and pediatric acute-onset neuropsychiatric syndrome (PANS) should be considered. However, the frequency and differentiating features of these putative syndromes within pediatric OCD remain poorly understood.

OBJECTIVES

To determine the prevalence and characteristics of those meeting PANDAS and/or PANS criteria within pediatric OCD, as determined by parent report and clinician interview.

METHODS

Consecutive youth presenting to a subspecialty pediatric OCD clinic were rigorously assessed through the Anxiety Disorders Interview Schedule for DSM-IV, the Children's Yale-Brown Obsessive-Compulsive Scale, and through self- and parent-report measures, including a medical questionnaire. Strict diagnostic criteria for PANDAS and PANS were applied to determine prevalence rates, and comparative analyses were performed between subgroups.

RESULTS

Among 136 youth with a lifetime OCD diagnosis, 5% (n = 7; 95% adjusted Wald interval: 1%-10%) met proposed criteria for PANDAS and/or PANS, of whom two met PANDAS criteria, four met PANS criteria, and one met criteria for both. Those in the PANDAS/PANS subgroup were more likely to have autoimmune illness, less likely to report symmetry factor symptoms, and had greater OCD-related family impairment during their worst OCD episode.

CONCLUSION

A small yet significant percentage of pediatric OCD outpatients met criteria for PANDAS and/or PANS, justifying routine screening and attention to related characteristics during assessment and management. Longitudinal studies of these putative subtypes are warranted.

The arginine deminase PAD2 is activated by ATP-induced P2X7R signaling in mast cells and modulates the disease course in an inflammatory arthritis model (BA3P.208)

Rheumatoid arthritis is a chronic, systemic inflammatory disease. Citrulline-containing proteins are generated through posttranslational modification of arginine residues in a reaction catalyzed by the Ca2+-dependent peptidyl arginine deiminases or PAD enzymes. Plasma and synovial biopsy specimens from RA patients contain high levels of citrullinated proteins. PAD2 is highly expressed in synovial tissue of RA patients, in close association with citrullinated protein deposits, and its expression correlates with inflammation intensity. The process by which PAD2 is activated and contributes to protein citrullination during RA is unknown. We have identified mast cells as a major source of the PAD2 enzyme. Activation of the P2X7 purinergic receptor by the inflammatory “danger” signal ATP induces PAD2 activity and robust protein citrullination in mast cells. P2X7-mediated activation of PAD2 is sensitive to p38 MAPK and protein kinase C inhibitors, and PAD2 regulates the expression of the TNFR2, Adamts-9, and Rab6b transcripts in mast cells. The PAD2 enzyme and its citrullinated substrate proteins are released from mast cells on activation with ATP. Importantly, mast cells have been shown to play a key role in the development of RA. Our results suggest that P2X7 activation of mast cells may play a role in inflammation by providing PAD2 and PAD2 substrates access to the extracellular space.

Quantitative NAT for pathogen inactivation verification

A novel Quantitative Nucleic Acid Test (Q-NAT) technology has been developed to demonstrate, quantify and verify pathogen inactivation by methods that break pathogen nucleic acids, specifically, gamma irradiation. The Q-NAT technology provides significant advantages in cost, efficiency and broad applicability compared with traditional methods for pathogen inactivation detection and quantification such as cell culture.

Mesenteric panniculitis: case report and literature review

Mesenteric panniculitis is an extremely rare inflammatory condition of the adipose tissue of unknown etiology in which the mesentery is replaced with fibrosis. Knowledge of this rare syndrome should prevent any unwarranted aggressive therapy and help to use the clinical, radiological, and surgical sources to obtain the diagnosis. This paper is a review of symptomatology, pathology, treatment, and outcome of this disorder. A case report is described that presented with obstruction of the sigmoid colon.

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii. The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii, A. fulgidus has fewer restriction-modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.

The complete genome sequence of the gastric pathogen Helicobacter pylori

Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.

A whole genome shotgun gene fusion method for isolation of translation initiation sites in Escherichia coli: identification of Haemophilus influenzae translation initiation sites in E. coli

We have developed a new method for isolating translation initiation sites based on the expression of Haemophilus influenzae Rd gene fusions with the Escherichia coli galactokinase (galK) gene. We cloned random DNA fragments of H. influenzae Rd DNA into a plasmid vector containing the galK coding sequence from which the translation initiation site (the ribosome binding site and translation initiation codon) had been removed. A subset of the cloned DNA fragments contained translation initiation sites that, when fused to the galK gene, produced active galactokinase and complemented the host galK mutation. Molecules expressing galactokinase activity were isolated and characterized by DNA sequence analysis, and the sequences were aligned with the recently completed whole genomic sequence of H. influenzae Rd. Translation initiation sites for known, hypothetical, and new genes were identified. Translation initiation sites internal to the coding sequences of a number of genes were identified, suggesting that internal translation initiation sites are common, especially in large genes. This shotgun method provides functional information on translation initiation sites and helps to define gene coding sequences.

Improved method for the production of M13 phage and single-stranded DNA for DNA sequencing

An improved method is described for the efficient production of M13 phage and M13 single-stranded (ss)DNA in a relatively short time period. Infection of E. coli (F') cells with as few as 5 phage particles can yield 10(12) phage particles/mL in 3 hours if the cells are grown in LB broth or SOB broth supplemented with about 5 mM Mg2+. The method tolerates large variations in the initial multiplicity of infection (5-5000 phage per 5 x 10(7) cells) and still yields about 10(12) phage particles/mL. These amounts are sufficient to purify 10-15 micrograms of ssDNA and to carry out at least 10-15 DNA sequencing reactions.

Mapping domains in proteins: dissection and expression of Escherichia coli adenylyl cyclase

We have used the pRE expression vector containing the Escherichia coli adenylyl cyclase gene (cya) with the unique NdeI restriction site CATATG at the initiation codon in conjunction with a family of self-complimentary oligonucleotides to create amino- and carboxyl-terminal domains in adenylyl cyclase. The three sets of oligonucleotides contain a TAA translation stop codon in all reading frames flanked by the NdeI restriction endonuclease sequence and one or two nucleotides (5' NNCATATGTTAATTAATTAACATATGNN 3'). Ligation of one of these annealed oligonucleotides into a restriction site or creation of 5' TAA/CATATG 3' translation stop/NdeI restriction site along a gene in the pRE expression vector facilitates the premature termination of protein synthesis thus yielding amino-terminal domains. Removal of a fragment of the gene corresponding to the amino-terminal portion by NdeI restriction and ligation brings the 3' end of the gene in frame with the initiator ATG. With this strategy, expression of the carboxyl-terminal domain of a protein is possible which is otherwise not as simple as the expression of the amino-terminal domain. The feasibility of expression of any domain of a protein is demonstrated using the cya gene to create several amino- and carboxyl-terminal domains of adenylyl cyclase.

A molecular chaperone, ClpA, functions like DnaK and DnaJ

The two major molecular chaperone families that mediate ATP-dependent protein folding and refolding are the heat shock proteins Hsp60s (GroEL) and Hsp70s (DnaK). Clp proteins, like chaperones, are highly conserved, present in all organisms, and contain ATP and polypeptide binding sites. We discovered that ClpA, the ATPase component of the ATP-dependent ClpAP protease, is a molecular chaperone. ClpA performs the ATP-dependent chaperone function of DnaK and DnaJ in the in vitro activation of the plasmid P1 RepA replication initiator protein. RepA is activated by the conversion of dimers to monomers. We show that ClpA targets RepA for degradation by ClpP, demonstrating a direct link between the protein unfolding function of chaperones and proteolysis. In another chaperone assay, ClpA protects luciferase from irreversible heat inactivation but is unable to reactivate luciferase.

Escherichia coli cyclic AMP receptor protein mutants provide evidence for ligand contacts important in activation

The three-dimensional model of the Escherichia coli cyclic AMP (cAMP) receptor protein (CRP) shows that several amino acids are involved as chemical contacts for binding cAMP. We have constructed and characterized mutants at four of these positions, E72, R82, S83, and R123. The mutations were made in wild-type crp as well as a cAMP-independent crp, crp*. The activities of the mutant proteins were characterized in vivo for their ability to activate the lac operon. These results provide genetic evidence to support that E72 and R82 are essential and S83 and R123 are important in the activation of CRP by cAMP.

DnaJ, DnaK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization step

We have found that three Escherichia coli heat shock proteins, DnaK (the hsp70 homolog), DnaJ, and GrpE, function in oriP1 DNA replication in vitro solely to activate DNA binding by the replication initiator protein RepA. Activation results from the conversion of P1 or P7 RepA dimers to monomers that bind with high affinity to the origin of replication of plasmid P1. Thus, the essential role of these three heat shock proteins in this replication system is to change the quaternary structure of a single protein, RepA.

Monomerization of RepA dimers by heat shock proteins activates binding to DNA replication origin

DnaK is a major heat shock protein of Escherichia coli and the homolog of hsp70 in eukaryotes. We demonstrate the mechanism by which DnaK and another heat shock protein, DnaJ, render the plasmid P1 initiator RepA 100-fold more active for binding to the P1 origin of replication. Activation is the conversion of RepA dimers into monomers in an ATP-dependent reaction and the monomer form binds with high affinity to oriP1 DNA. Reversible chemical denaturants also convert RepA dimers to monomers and simultaneously activate oriP1 DNA binding. Increasing protein concentration converts monomers to dimers and deactivates RepA. Based on our data and previous work, we present a model for heat shock protein action under normal and stress conditions.

Function of DnaJ and DnaK as chaperones in origin-specific DNA binding by RepA

Heat-shock proteins are normal constituents of cells whose synthesis is increased on exposure to various forms of stress. They are interesting because of their ubiquity and high conservation during evolution. Two families of heat-shock proteins, hsp60s and hsp70s, have been implicated in accelerating protein folding and oligomerization and also in maintaining proteins in an unfolded state, thus facilitating membrane transport. The Escherichia coli hsp70 analogue, DnaK, and two other heat-shock proteins, DnaJ and GrpE, are required for cell viability at high temperatures and are involved in DNA replication of phage lambda and plasmids P1 and F. These three proteins are involved in replication in vitro of P1 DNA along with many host replication proteins and the P1 RepA initiator protein. RepA exists in a stable protein complex with DnaJ containing a dimer each of RepA and DnaJ. We report here that DnaK and DnaJ mediate an alteration in the P1 initiator protein, rendering it much more active for oriP1 DNA binding.

Deletion analysis of the mini-P1 plasmid origin of replication and the role of Escherichia coli DnaA protein

The mini-P1 plasmid origin of replication is contained on a 246 base pair (bp) piece of DNA. At one end there are five 19-bp binding sites for the P1 initiator protein, RepA, and near the other end there are two 9-bp DnaA protein-binding sites. To further define the limits of the origin, we cloned the origin region in M13 and constructed deletions of either end. We sequenced the DNA and tested the replicative form I DNA of the deletion phages for their ability to support RepA-dependent DNA replication in an in vitro system. The origin that is functional in vitro could be reduced to 202 bp. It includes three intact and one incomplete RepA-binding sites at one end and the two DnaA-binding sites at the other end. When the two naturally occurring DnaA-binding sites were replaced with one or two synthetic sites, only the construction containing two sites was active in vitro. We found that the minimal origin that is functional in vivo contains all of the five RepA and the two DnaA-binding sites. Mini-P1 plasmid replication both in vivo and in vitro requires two initiator proteins, the Escherichia coli DnaA protein and the P1 RepA protein. We have found that the ADP form of DnaA is as active as the ATP form of the protein in the in vitro replication of mini-P1. In contrast, only the ATP form is active for in vitro replication of plasmids carrying the E. coli origin (Bramhill, D., and Kornberg, A. (1988) Cell 52, 743-755).

Hyperexpression and purification of Escherichia coli adenylate cyclase using a vector designed for expression of lethal gene products

We describe the construction of a new generation of vectors (pRE) for the hyperexpression of lethal gene products such as adenylate cyclase in Escherichia coli. The pRE vectors are based on the lambda PL promoter and lambda cII ribosome binding site described by Shimatake and Rosenberg (Nature, 292, 128-132, 1981). They have a unique NdeI restriction endonuclease site 3' of the lambda cII ribosome binding site that includes the ATG initiation codon, multilinker cloning sites 3' to the NdeI site, and two lambda transcription terminators 5' and 3' of the lambda PL promoter to eliminate nonspecific transcription and reduce leaky PL transcription, respectively. For hyperexpression of adenylate cyclase, tight control of transcription was necessary since elevation of cAMP levels above the physiological range is lethal to E. coli. Lethality associated with the overproduction of adenylate cyclase was shown to be mediated through the cAMP receptor protein. We used this expression system to overproduce adenylate cyclase 7500 fold, corresponding to 30% of the total cellular protein. Under these conditions the enzyme precipitated with significant loss of activity. Reducing the rate and amount of adenylate cyclase expression to 16% of the total cell protein produced one fourth of the enzyme in a soluble form with high specific activity. The soluble adenylate cyclase was purified to near homogeneity.

A system for on-line detection and resolution of radiolabeled DNA molecules and its application to automated DNA sequence analysis

We describe a system for the real-time detection of radioactively labeled DNA molecules in gel matrix, and we demonstrate the application of this system to DNA sequence analysis. DNA sequencing reactions prepared by the Sanger chain termination method are resolved by electrophoresis on 8% polyacrylamide gels. During electrophoresis the 32P-labeled DNA fragments are detected by solid state detectors positioned 22 cm from the top surface of the gel. This system is able to resolve a DNA sequence of 300 bases or greater. Optimized protocols that allow sequence information to be obtained from single stranded and double-stranded templates are described. A linear relationship exists between the input dpm and the integrated peak values over a 20-fold range indicating that accurate DNA quantitation is also possible using this system.

Arginine substituted for leucine at position 195 produces a cyclic AMP-independent form of the Escherichia coli cyclic AMP receptor protein

Mutant forms (CRP*) of the Escherichia coli cAMP receptor protein (CRP) that activate CRP-dependent promoters in the absence of the normal allosteric effector (cAMP) have been described. A previous report (Harman, J. G., McKenney, K., and Peterkofsky, A. (1986) J. Biol. Chem. 261, 16332-16339) detailed the properties of three CRP* mutant proteins. One protein, 220 CRP, has amino acid substitutions at positions 127 and 170 and low CRP* activity in vivo. A second protein, 222 CRP, has the amino acid substitutions present in 220 CRP and a third substitution (arginine for leucine) at position 195. 222 CRP has high CRP* activity in vivo and high apparent affinity for lacP DNA relative to the 220 CRP in vitro. In this report, we evaluate the effect of a single amino acid substitution at position 195 (leucine to arginine) on CRP activity both in vivo and in vitro. Cells (cya delta crp delta/pJH8crpR195) containing R195 CRP were found to exhibit a CRP* phenotype, expressing a variety of CRP-dependent genes in the absence of added cAMP. R195 CRP exhibited both CRP* activity in vitro and increased apparent affinity for cAMP relative to wild-type CRP. CRP titration experiments performed using an in vitro lac transcription system suggest that the isolated substitution of arginine at position 195 does not confer on CRP the high lacP affinity that distinguishes the 220 and 222 forms of CRP. These findings lead us to the conclusion that the effects of multiple mutations in CRP can be both cumulative and interactive.

Autoregulation of the yeast copper metallothionein gene depends on metal binding

The yeast CUP1 gene product, copper metallothionein, acts to repress the basal transcription of its own structural gene. By creating a series of truncation and amino acid substitutions in CUP1, we show that the ability of the protein to autoregulate is directly correlated to its ability to bind and detoxify copper. These results support a model in which metallothionein controls the level of free intracellular copper available to interact with positive transcription factors. In addition, mutations in chemically equivalent cysteine residues were functionally dissimilar, suggesting that partial sites in the molecule are critical for the formation of the sulfur-metal cluster.

Structural and functional studies of the amino terminus of yeast metallothionein

Purified yeast copper-metallothionein lacks 8 amino-terminal residues that are predicted from the DNA sequence of its gene. The removed sequence is unusual for metallothionein in its high content of hydrophobic and aromatic residues and its similarity to mitochondrial leader sequences. To study the significance of this amino-terminal cleavage, several mutations were introduced into the metallothionein coding gene, CUP1. One mutant, which deletes amino acid residues 2-8, had a minor effect on the ability of the molecule to confer copper resistance to yeast but did not affect CUP1 gene regulation. A second mutation, which changes two amino acids adjacent to the cleavage site, blocked removal of the extension peptide but had no effect on copper detoxification or gene regulation. Immunofluorescence studies showed that both the wild-type and these two mutant proteins are predominantly cytoplasmic with no evidence for mitochondrial localization. The cleavage site mutation allowed isolation and structural characterization of a full length metallothionein polypeptide. The copper content and luminescent properties of this molecule were identical to those of the truncated wild-type protein indicating a homologous cluster structure. Moreover, the amino-terminal peptide was selectively removed by various endopeptidases and an exopeptidase suggesting that it does not participate in the tertiary fold. These results argue that the amino-terminal peptide is not required for either the structural integrity or biological function of yeast metallothionein.

Deletion analysis of the DNA sequence required for the in vitro initiation of replication of bacteriophage lambda

Supercoiled DNA containing the replication origin of bacteriophage lambda can be replicated in vitro. This reaction requires purified lambda O and P replication proteins and a partially purified mixture of Escherichia coli proteins (Tsurimoto, T., and Matsubara, K. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 7639-7643; Wold, M. S., Mallory, J.B., Roberts, J. D., LeBowitz, J. H., and McMacken, R. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 6176-6180). The lambda origin region has four repeats of a 19-base pair sequence to which O protein binds. To the right of these sites on the lambda map is a 40-base pair region that is rich in adenine and thymine, followed by a 28-base pair palindromic sequence. To define more precisely the boundaries of the lambda origin, we cloned a 358-base pair piece of lambda DNA containing the origin region into M13mp8 in both orientations. In vitro replication of RF I DNAs prepared from cells infected with these two M13 ori lambda phage was dependent on lambda O and P proteins and a crude protein fraction from uninfected E. coli; with these conditions there was no replication of M13mp8 RF I DNA. We made deletions from the left and the right ends of the lambda origin DNA and determined the deletion end points by DNA sequencing. We have tested RF I DNAs prepared from cells infected with phage carrying ori lambda deletions for their ability to function as templates for O- and P-dependent replication in vitro. Our results show that lambda DNA between nucleotide positions 39072 and 39160 is required for efficient O- and P-dependent replication. This 89-base pair piece of DNA includes only two of the four 19-base pair O protein-binding sites (the two right-most) and the adjoining adenine- and thymine-rich region to the right of the O-binding sites.

Structure-function analysis of three cAMP-independent forms of the cAMP receptor protein

cAMP receptor protein (CRP)-dependent operon expression in Escherichia coli requires the CRP X cAMP complex form of wild-type CRP. One class of crp mutants (crp*) activates CRP-dependent promoters in strains (cya) incapable of endogenous cAMP synthesis. Of fundamental interest is the difference in regulatory properties exhibited by crp* mutant strains, some of which exhibit glucose-mediated repression of beta-galactosidase synthesis, some of which do not. To gain a better understanding of the mechanisms of cAMP-independent promoter activation and repression we have: determined through cloning and DNA sequence analysis the primary structure of three CRP* forms of CRP; purified the mutant proteins; characterized the effect of these mutations on CRP secondary structure; and studied CRP*-activated lac promoter regulation in a purified in vitro transcription system. The results of this study provide strong evidence that mutations in crp alter the conformation of CRP and result in cAMP-independent activation of CRP-dependent promoters in vitro. In addition, a CRP allele-specific inhibition of CRP* activity by spermidine was observed in vitro that parallels crp* strain-specific sensitivity to glucose-mediated repression of CRP-dependent enzyme synthesis in vivo. This observation provides evidence that catabolite repression in cells lacking cAMP may be mediated through a mechanism that inhibits CRP* activity.

Chromogenic identification of oligonucleotide-directed mutants

We describe a simple plaque color assay for identifying oligonucleotide-directed mutations in cloned DNA fragments. The basis of the method is to: fuse the sequence of interest in-frame to the E.coli lacZ gene to produce a blue plaque phage, mutate the site of interest to a stop codon to generate a white plaque phage, and revert the stop codon and surrounding nucleotides to give a blue plaque phage containing one or more desired amino acid changes. The advantages of this cyclic method are that it produces truncated as well as amino acid substituted protein molecules, it can be repeated to introduce additional mutations, and it eliminates the need for labor intensive screening. Essentially any piece of DNA can be mutated using this method if the fragment has one open reading frame. If there is an open reading frame between the site and the lacZ gene, ATG codons can be inserted at the target site. We have used this method to produce termination and amino acid substitution mutants in the yeast CUP1 gene.

Translational efficiency of the Escherichia coli adenylate cyclase gene: mutating the UUG initiation codon to GUG or AUG results in increased gene expression

Roy et al. [Roy, A., Haziza, C. & Danchin, A. (1983) EMBO J. 2, 791-797] established that translation of Escherichia coli adenylate cyclase initiates at a UUG codon, and they suggested this might decrease the efficiency of translation. We investigated the effect of varying the initiation codon on the expression of the adenylate cyclase (cya) gene. Using oligonucleotide-directed mutagenesis, we changed the UUG initiation codon to GUG and the more common initiator AUG and assayed for cya gene expression in a number of ways. First, the GUG initiation codon, in place of UUG, doubled cya expression when cya was expressed from the dual cya P1/P2 promoters. The corresponding AUG codon construct was nonviable. Second, when the cya gene was placed under the transcriptional control of the thermoinducible phage lambda PL promoter, the relative amounts of cya gene product were 1:2:6 for the UUG, GUG, and AUG initiation codons, respectively. Finally, the cya P2 promoter, Shine-Dalgarno sequence, and the DNA corresponding to the first 86 codons of cya were fused to DNA encoding the E. coli galactokinase gene beginning at the second codon. The relative amounts of the fusion polypeptides, which had galactokinase activity, were 1:2:3 for the UUG, GUG, and AUG initiation codons, respectively. These results demonstrate that the cya UUG initiation codon limits cya expression at the level of translation.

Structure of the galactokinase gene of Escherichia coli, the last (?) gene of the gal operon

We present the nucleotide sequence of the galactokinase gene (galK) of Escherichia coli including its 5' and 3' flanking regions. This DNA sequence derives from the lambda gal8 transducing phage and is identical to the sequence present in the galK gene fusion vectors, pKO and pKG, commonly used to study transcriptional regulatory elements. We define the precise 3' junction between the bacterial and phage sequences in lambda gal8 and demonstrate that this junction probably results from a homologous recombination event between identical 9 bp sequences common to the gal operon and phage lambda. Moreover, we examine the 300 bp region located immediately beyond galK for transcription termination function and find no gal operon terminator. Lastly, we compare the galK genes of E. coli and the yeast S. cerevisiae and find several regions of strong homology among which is a potential ATP-binding site homology shared by a variety of ATP-binding proteins including protein kinases encoded by mammalian oncogenes.

CII-dependent activation of the pRE promoter of coliphage lambda fused to the Escherichia coli galK gene

Using a cloning vector designed for the study of prokaryotic promoters by fusion to the Escherichia coli galactokinase gene (galK), we have constructed a plasmid in which the lambda pRE promoter controls galactokinase expression. A galK- host containing this plasmid has a Gal- phenotype since transcription from pRE requires activation by the lambda CII protein. When CII protein is provided by a prophage, galactokinase is synthesized at a rate dependent on the concentration of CII protein. A second plasmid was constructed in which the pRE promoter from phage 21 controls galactokinase expression. Transcription of the galK gene in this plasmid requires the phage 21 CII protein. Using this system, we demonstrate that the lambda and 21 pRE promoters are highly selective for their corresponding CII proteins. However, a cross-reaction between 21 pRE and the lambda CII protein was observed. In addition, we transferred the pRE-galK fusion unit from the plasmid to a phage, and then to the host chromosome in single copy. Galactokinase expression in this single copy pRE-galK system is also dependent on CII protein, which may be provided from a multicopy plasmid. The high concentration of CII protein provided by the plasmid results in maximal expression of the pRE-galK transcription unit. In this second system low levels of CII activity from CII- mutants are amplified and can be readily detected.

Removal of a terminator structure by RNA processing regulates int gene expression

The int gene of phage lambda encodes a protein involved in site-specific recombination. Its expression is regulated differentially during successive phases of the lambda infective cycle. The gene is transcribed early after infection from one promoter, pL, and later from a second promoter pI. Each transcription event requires different positive activation factors, lambda N and cII proteins, respectively. Transcription from the pI promoter, located adjacent to int, passes through int and terminates 277 nucleotides beyond int at tI. Polymerases initiating at pL transcribe through tI and into the b segment of lambda DNA. The read-through pL transcript is sensitive to cleavage by the endonuclease, RNase III, both in vivo and in vitro. Two specific cuts are made by RNase III in a double-stranded structure about 260 nucleotides beyond int in the location of the tI terminator. Functionally, the processed pL transcript is unable to synthesize the int gene product, whereas the terminated and unprocessed pI transcript expresses int. Interestingly, unprocessed pL transcripts made in hosts defective in RNase III (rnc-) can express int. Thus a correlation exists between processing and negative control of int expression. The place where processing occurs, some 260 nucleotides beyond int, is called sib, and the control of int expression from this site is called retroregulation. Retroregulation by sib is not restricted just to the int gene; we show that if the sib site is cloned beyond a bacterial gene, the gene is controlled by sib and RNase III. Specific models are discussed with respect to control of gene expression by RNase III from a site beyond the controlled gene.

Transcription terminator involved in the expression of the int gene of phage lambda

The phage lambda int gene is transcribed from two different promoters, pI and pL. Transcription from pI results in efficient synthesis of Int protein whereas transcription originating from pL results in poor int expression. The differential expression of Int from these two transcripts is dependent upon a site (sib) located distal to the int gene [Guarneros and Galindo, Virology 95 (1979) 119-126; Guarneros et al., Proc. Natl. Acad. Sci. USA 79 (1982) 238-242]. We have examined pI-promoted transcription in the region beyond the int coding sequence. The int mRNA extends to a site designated tI, which is located 277 nucleotides beyond int. Characterization of transcription at tI indicates that tI terminates with 75% efficiency in vitro, and that its efficiency is over 95% in vivo. The region between int and tI contains the regulatory signals needed for phage lamba integration and appears to be untranslated. The termination site overlaps with the sib control region that reduces Int synthesis from pL transcripts.

Studying promoters and terminators by gene fusion

Prokaryotic gene control signals can be isolated, compared, and characterized by precise fusion in vitro to the Escherichia coli galactokinase gene (galK), which provides both a simple assay and genetic selection. This recombinant galK fusion vector system was applied to the study of promoters and terminators recognized by the Escherichia coli RNA polymerase. Three promoters created by mutation from DNA sequences having no promoter function were characterized. Mutations that inactivate promoter function were selected, structurally defined, and functionally analyzed. Similarly, transcription termination was examined, and mutations affecting terminator function were isolated and characterized.

Translational coupling at an intercistronic boundary of the Escherichia coli galactose operon

Precise frameshift and nonsense mutations were introduced into the region preceding the galactokinase gene (galK) of Escherichia coli. These mutations after the position at which upstream translation terminates relative to the galK translation initiation signal. Constructions were characterized that allow ribosomes to stop selectively before, within or downstream from the galK initiation signal. The effects of these mutations on galK expression were monitored. Galactokinase levels are highest when upstream translation terminates within the galK initiation region. In contrast, when translation stops either upstream or down stream from the galK start site, galK expression is drastically reduced. These results demonstrate that the galK gene is translationally coupled to the gene immediately preceding galK in the gal operon (that is, galT), and that the coupling effect depends primarily on the position at which upstream translation terminates relative to the galK start site. Possible mechanisms and implications of this translational coupling phenomenon are discussed.

Base insertion and deletion mutations induced in an Escherichia coli plasmid by benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide

Mutations induced by (+/-)trans-benzo-[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BaP-diol epoxide-1) were selected by using a recombinant plasmid vector system designed for the study of transcription termination signals. The plasmid contains a transcription terminator positioned between a promotor signal and the Escherichia coli galactokinase structural gene (galK). By selections for the expression of galK (i.e., galK- to galK+), mutations are obtained in the terminator region that allow transcription from the promotor to read the galK gene. These mutations were characterized by direct DNA sequence of the terminator region. The DNA sequence changes caused by BaP-diol epoxide-1 were demonstrated for three different mutants. Two were found to be single-base-pair insertions of T.A into a cluster of consecutive T.A base pairs and the other change was a single-base-pair deletion of G.C from a cluster of consecutive G.C base pairs.