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M Salas

Publications and source records attributed to M Salas.

At least 163 records · Page 9Linked to original sources
PubMed1992

Site-directed mutagenesis at the Exo III motif of phi 29 DNA polymerase; overlapping structural domains for the 3'-5' exonuclease and strand-displacement activities.

In this report we present the alignment of one of the most conserved segments (Exo III) of the 3'-5' exonuclease domain in 39 DNA polymerase sequences, including prokaryotic and eukaryotic enzymes. Site-directed substitutions of the two most conserved residues, which form the Exo III motif Tyr-(X)3-Asp of phi 29 DNA polymerase, did not affect single-stranded DNA binding, DNA polymerization, processivity or protein-primed initiation. In contrast, substitution of the highly conserved Tyr residue by Phe or Cys decreased the 3'-5' exonuclease activity to 7.5 and 4.1%, respectively, of the wild-type activity. Change of the highly conserved Asp residue into Ala resulted in almost complete inactivation (0.1%) of the 3'-5' exonuclease. In accordance with the contribution of the 3'-5' exonuclease to the fidelity of DNA replication, the three mutations in the Exo III motif (Y165F, Y165C and D169A) produced enzymes with an increased frequency of misinsertion and extension of DNA polymerization errors. Surprisingly, the three mutations in the Exo III motif strongly decreased (80- to 220-fold) the ability to replicate phi 29 DNA, this behaviour being due to a defect in the strand displacement activity, an intrinsic property of phi 29 DNA polymerase required for this process. Taking these results into account, we propose that the strand displacement activity of phi 29 DNA polymerase resides in the N-terminal domain, probably overlapping with the 3'-5' exonuclease active site.

Amino Acid Sequence↗
PubMed1992

Structural and functional studies on phi 29 DNA polymerase.

The Bacillus subtilis phage phi 29 DNA polymerase, involved in protein-primed viral DNA replication, contains several amino acid consensus sequences common to other eukaryotic-type DNA polymerases. Using site-directed mutagenesis, we have studied the functional significance of a C-terminal conserved region, represented by the Lys-X-Tyr ("K-Y") motif. Single point mutants have been constructed and the corresponding proteins have been overproduced and characterized. Measurements of the activity of the mutant proteins indicated that the invariant Lys and Tyr residues play a critical role in DNA polymerization. Interestingly, substitution of the invariant Lys either by Arg or Thr, produced enzymes with an increased or a largely reduced, respectively, capability to use a protein as primer, an intrinsic property of TP-priming DNA polymerases. On the other hand, the viral protein p6, which stimulates initiation of phi 29 DNA replication by formation of a nucleoprotein complex at both DNA replication origins, increased (about 5-fold) the insertion fidelity of phi 29 DNA polymerase during the formation of the TP-dAMP initiation complex. We propose a model in which the special strategy to maintain the integrity of the phi 29 DNA ends, by means of a "sliding-back" mechanism, could also contribute to increase the fidelity of phi 29 DNA replication.

Amino Acid Sequence↗
PubMed1992

Health assessments of youngsters with insulin-dependent diabetes.

In this study with youngsters with insulin-dependent diabetes, there were a number of significant correlations among psychological variables. However, with two exceptions, metabolic indices were not correlated with psychological variables or symptom reporting. Correlations involving aspects of symptom reporting suggest relationships with psychological factors. Implications for treatment decisions are presented. Additionally, theoretical, psychometric, and methodological considerations are discussed.

Adaptation, Psychological↗
PubMed1992

Horseshoe kidney: the impact of percutaneous surgery.

Six patients with a stone disease and/or ureteropelvic junction obstruction in a horseshoe kidney underwent percutaneous surgery. No major complications were observed and only 1 patient presented residual fragments in the lower calyx 3 months after treatment. The special features of the use of percutaneous nephrolithotomy and endopyelotomy for this anomaly are described.

Adult↗
PubMed1991

Analysis of replicative intermediates produced during bacteriophage phi 29 DNA replication in vitro.

Replication of bacteriophage phi 29 DNA initiates at either end of its linear double-stranded DNA molecule and proceeds by a strand-displacement mechanism. In the present paper we have used an in vitro phi 29 DNA replication system to analyse by electron microscopy the replicative intermediates produced at different reaction times. Two types of replicative intermediates were observed: type I (full-length double-stranded phi 29 DNA molecules with one or more single-stranded DNA branches) and type II (full-length phi 29 DNA molecules formed by a double-stranded DNA portion of variable length from one end plus a single-stranded DNA portion spanning to the other end). Thus, the types of replicative intermediates produced in vivo were also formed in the in vitro phi 29 DNA replication system. Analysis of type I intermediates indicated that initiation of DNA replication occurs preferentially at both ends of the same DNA template, in a non-simultaneous manner. Type II intermediates appeared as early as two minutes after the reaction started, well before unit-length single-stranded phi 29 DNA molecules were synthesized. In addition, replication of recombinant phi 29 DNA templates lacking terminal protein at one end did not produce type II intermediates and led to an accumulation of full-length single-stranded phi 29 DNA molecules. These two observations strongly suggest that type II intermediates appear when two growing DNA chains, running from opposite ends, merge.

Bacillus subtilis↗
PubMed1991

Transcription activation at a distance by phage phi 29 protein p4. Effect of bent and non-bent intervening DNA sequences.

Protein p4 of the Bacillus subtilis phage phi 29 switches on the transcription of the viral late genes by binding to the viral late promoter at a region close to the RNA polymerase binding site. Gel retardation and DNase I footprinting assays show that the presence of protein p4 is required for RNA polymerase recognition of the late promoter. The protein p4 and RNA polymerase DNA binding sites have been separated by the insertion of bent and non-bent DNA sequences of different lengths. These mutant promoters were used to study in vitro their protein p4-dependent transcriptional activity and their interaction with both protein p4 and RNA polymerase. The results indicate that protein p4 is able to function at longer DNA distances from the RNA polymerase binding site than in the natural promoter. The extent of protein p4 activity depended on the length and conformation of the inserted DNA. Activation of transcription and RNA polymerase binding was favoured when the relative orientation of protein p4 and RNA polymerase was conserved and when the intervening DNA had a bent conformation. These data, together with the DNase I footprints, suggest that activation at distance by protein p4 involves a DNA loop held by the interaction of protein p4 and RNA polymerase.

Bacillus subtilis↗
PubMed1991

Identification of the sequences recognized by phage phi 29 transcriptional activator: possible interaction between the activator and the RNA polymerase.

Expression of Bacillus subtilis phage phi 29 late genes requires the transcriptional activator protein p4. This activator binds to a region of the late A3 promoter spanning nucleotides -56 to -102 relative to the transcription start site, generating a strong bending Tin the DNA. In this work the target sequences recognized by protein p4 in the phage phi 29 late A3 promoter have been characterized. The binding of protein p4 to derivatives of the late A3 promoter harbouring deletions in the protein p4 binding site has been studied. When protein p4 recognition sequences were altered, the activator could only bind to the promoter in the presence of RNA polymerase. This strong cooperativity in the binding of protein p4 and RNA polymerase to the promoter suggests the presence of direct protein-protein contacts between them.

Bacillus subtilis↗
PubMed1991

Characterization and mapping of the pyrophosphorolytic activity of the phage phi 29 DNA polymerase. Involvement of amino acid motifs highly conserved in alpha-like DNA polymerases.

The phi 29 DNA polymerase, an alpha-like DNA polymerase, shows an inorganic pyrophosphate-dependent degradative activity with similar requirements to the corresponding one of Escherichia coli DNA polymerase I: (a) it requires a high concentration of inorganic pyrophosphate and is reversed by polymerization; (b) like DNA polymerization, it needs a duplex DNA with protruding 5' single-strand; (c) it acts in the 3' to 5' direction releasing free dNTPs, thus, it can be considered as the reversal of polymerization; (d) although a correctly base-paired 3' primer terminus is the preferred substrate, the pyrophosphorolytic activity is able to remove mismatched 3' ends. In agreement with the structural and functional model previously proposed for the phi 29 DNA polymerase, the analysis of point mutations has revealed that the pyrophosphorolytic activity, like the polymerization activity, is located at the C-terminal portion of the molecule, involving the amino acid motif YCDTD, highly conserved in alpha-like DNA polymerases. Furthermore, the analysis of phi 29 DNA polymerase mutants indicates that pyrophosphorolysis, like DNA polymerization, also requires an efficient translocation of the enzyme along the template.

Bacteriophages↗
PubMed1991

Mechanism of stimulation of DNA replication by bacteriophage phi 29 single-stranded DNA-binding protein p5.

Protein p5 is a Bacillus subtilis phage phi 29-encoded protein required for phi 29 DNA replication in vivo. Protein p5 has single-stranded DNA binding (SSB) capacity and stimulates in vitro DNA replication severalfold when phi 29 DNA polymerase is used to replicate either the natural phi 29 DNA template or primed M13 single-stranded DNA (ssDNA). Furthermore, other SSB proteins, including Escherichia coli SSB, T4 gp32, adenovirus DNA-binding protein, and human replication factor A, can functionally substitute for protein p5. The stimulatory effect of phi 29 protein p5 is not due to an increase of the DNA replication rate. When both phi 29 DNA template and M13 competitor ssDNA are added simultaneously to the replication reaction, phi 29 DNA replication is strongly inhibited. This inhibition is fully overcome by adding protein p5, suggesting that protein p5-coated M13 ssDNA is no longer able to compete for replication factors, probably phi 29 DNA polymerase, which has a strong affinity for ssDNA. Electron microscopy demonstrates that protein p5 binds to M13 ssDNA forming saturated complexes with a smoothly contoured appearance and producing a 2-fold reduction of the DNA length. Protein p5 also binds to ssDNA in the phi 29 replicative intermediates produced in vitro, which are similar in structure to those observed in vivo. Our results strongly suggest that phi 29 protein p5 is the phi 29 SSB protein active during phi 29 DNA replication.

Bacillus subtilis↗
PubMed1991

A DNA curvature can substitute phage phi 29 regulatory protein p4 when acting as a transcriptional repressor.

Binding of phage phi 29 regulatory protein p4 to its target sequences produces a strong bend in the DNA that is important for activation of the late A3 promoter (PA3). Protein p4 binding site in PA3 overlaps with the divergently transcribed main early promoter. PA2b, which suggested that p4 could also act as a repressor. We show that protein p4 both excludes Bacillus subtilis sigma A-RNA polymerase from PA2b and directs it to the divergently transcribed A3 promoter. Although steric hindrance is likely to be involved in the repression process, we have also analysed the effect on PA2b activity of a sequence-dependent curvature that simulates that induced by protein p4. A progressive increase in the DNA curvature of protein p4 binding region, performed by site-directed mutagenesis, has indicated that a static DNA curvature by itself can inhibit transcription from PA2b, both by impairing the binding of sigma A-RNA polymerase to the promoter and by reducing its ability to form transcriptionally active open complexes. These results indicate that bending promoter sequences in a direction unfavourable for RNA polymerase binding can repress transcription. Protein p4-induced DNA bending could therefore participate in PA2b repression by producing a DNA structure not recognized as a promoter by sigma A-RNA polymerase.

Bacteriophages↗
PubMed1991

Treatment of chemically induced autochthonous rat mammary and colorectal carcinomas with interleukin-2.

The antineoplastic efficacy of human interleukin-2 (IL-2) in autochthonous methylnitrosourea-induced mammary carcinoma and in acetoxymethyl-methyl-nitrosamine-induced colorectal carcinoma of Sprague Dawley rats has been investigated. Under the conditions applied, IL-2 was non-toxic. In the mammary carcinoma IL-2 was therapeutically inactive. In the colorectal carcinoma, 1200 U IL-2/day exhibited significant antitumour activity in established tumours as well as in tumours treated "prophylactically" before their manifestation (P less than 0.05). The effect of IL-2 seemed to be more pronounced when given before manifestation of colorectal tumours (T/C = 8.7% vs 17.8% in established tumours). The differential sensitivity of the autochthonous mammary and colorectal carcinoma may be explained by differences in their proliferation rates and differences in volumes at the beginning of IL-2 therapy. IL-2 seems to be preferentially active in small tumours with a low proliferation rate, a feature typical of colon tumours.

Animals↗
PubMed1991

Neonatal undernutrition and self-grooming development in the rat: long-term effects.

The effect of neonatal undernutrition on six different self-grooming components was examined in male rats during the pre- and postweaning periods. Rats underfed by the maternal nipple-ligation procedure before weaning did not exhibit significant score differences in the various self-grooming measurements. In contrast, after weaning they showed a significant increment in the duration of face-washing, head-washing, fur licking and body-scratching. In all cases, the total postweaning self-grooming activity was significantly increased in the formerly underfed rats. Present data suggest that neonatal undernutrition may presumably interfere with the sequential maturational processes of central and/or peripheral mechanisms underlying some components of self-grooming behavior.

Aging↗
PubMed1991

Thrombin-like activity in snake venoms from Peruvian Bothrops and Lachesis genera.

Venoms from Lachesis muta muta, Bothrops pictus, B. barnetti, B. atrox and B. hyoprorus coagulate in vitro canine fibrinogen, and both bovine fibrinogen and bovine plasma. B. barnetti and L. muta muta venoms have greater activity on canine fibrinogen and B. atrox and B. hyoprorus venoms, a greater activity on bovine fibrinogen. Gel filtration showed one peak of coagulant activity in all venoms except B. atrox venom which possessed two peaks. The apparent mol. wt of these enzymes ranged from 45,000 to 69,000.

Animals↗
PubMed1991

A general structure for DNA-dependent DNA polymerases.

In addition to the general 3'-5' exonuclease domain described by Bernad et al. [Cell 59 (1989) 219-228] significant amino acid (aa) sequence similarity has been found in the C-terminal portion of 27 DNA-dependent DNA polymerases belonging to the two main superfamilies: (i) Escherichia coli DNA polymerase I (PolI)-like prokaryotic DNA polymerases, and (ii) DNA polymerase alpha-like prokaryotic and eukaryotic (viral and cellular) DNA polymerases. The six most conserved C-terminal regions, spanning approx. 340 aa, are located in the same linear arrangement and contain highly conserved motifs and critical residues involved in the polymerization function. According to the three-dimensional model of PolIk (Klenow fragment), these six conserved regions are located in the proposed polymerization domain, forming the metal and dNTP binding sites and the cleft for holding the DNA template. Site-directed mutagenesis in the phi 29 DNA polymerase supports some of these structural predictions. Therefore, it is likely that a 'Klenow-like core', containing the DNA polymerase and 3'-5' exonuclease activities, has evolved from a common ancestor, giving rise to the present-day prokaryotic and eukaryotic DNA polymerases.

Amino Acid Sequence↗
PubMed1991

Cystine stones: the impact of new treatment.

The hardness and frequent recurrence of cystine stones present a special challenge to the urologist. In this study, 15 cystinuric patients (11 males, 4 females; mean age 36 years, range 17-54) were treated and followed up over a period of 30 months (range 2-40). Most patients had previous history of open surgery. The diagnosis of cystinuria was confirmed by metabolic studies and infrared spectrometry of stones. Over the follow-up period recurrence was observed in 23 instances in 11 patients, leading to 38 "stone treatments" on 74 cystine stones. The percutaneous approach was used alone in 9 cases and in association with extracorporeal shock wave lithotripsy (ESWL) in 9 cases. ESWL was used alone in 18 cases. Medical treatment included high fluid intake, alkalinisation and Thiola (tiopronin, N-(2-mercaptopropionyl)glycine) in 6 patients. The overall stone-free rate assessed 3 months after treatment was 44.7%, which compares poorly with the rate for non-cystine stones. The recurrence rate is very high and instrumental treatment should not therefore be used excessively; it is indicated only for stones that are symptomatic or refractory to intensive medical therapy.

Adolescent↗