EVOLUTIONARY IMPLICATIONS OF DIVERGENT CLINES IN AN AVIAN (MANACUS: AVES) HYBRID ZONE

Abstract A previous study of the hybrid zone in western Panama between white‐collared (Manacus candei) and golden‐collared manakins (M. vitellinus) documented the unidirectional introgression of vitellinus male secondary sexual traits across the zone. Here, we examine the hybrid zone in greater genetic and morphological detail. Statistical comparisons of clines are performed using maximum‐likelihood and nonparametric bootstrap methods. Our results demonstrate that an array of six molecular and two morphometric markers agree in cline position and width. Clines for male collar and belly color are similar in width to the first eight clines, but are shifted in position by at least five cline widths. The result is that birds in intervening populations are genetically and morphometrically very like parental candei, but males have the plumage color of parental vitellinus. Neither neutral diffusion nor nonlinearity of color scales appear to be viable explanations for the large cline shifts. Genetic dominance of vitellinus plumage traits is another potential explanation that will require breeding experiments to test. Sexual selection remains a plausible explanation for the observed introgression of vitellinus color traits in these highly dimorphic, polygynous, lek‐mating birds. Two other clines, including a nondiagnostic isozyme locus, are similar in position to the main cluster of clines, but are broader in width. Thus, introgression at some loci is greater than that detected with diagnostic markers. Assuming that narrow clines are maintained by selection, variation in cline width indicates that selection is not uniform throughout the genome and that diagnostic markers are under more intense selective pressure. The traditional focus on diagnostic markers in studies of hybrid zones may therefore lead to underestimates of average introgression. This effect may be more pronounced in organisms with low levels of genetic divergence between hybridizing taxa.     

Constructing optimal backbone segments for joining fixed DNA base pairs.

A method is presented to link a sequence of space-fixed base pairs by the sugar-phosphate segments of single nucleotides and to evaluate the effects in the backbone caused by this positioning of the bases. The entire computational unit comprises several nucleotides that are energy-minimized, subject to constraints imposed by the sugar-phosphate backbone segments being anchored to space-fixed base pairs. The minimization schemes are based on two stages, a conjugate gradient method followed by a Newton-Raphson algorithm. Because our purpose is to examine the response, or relaxation, of an artificially stressed backbone, it is essential to be able to obtain, as closely as possible, a lowest minimum energy conformation of the backbone segment in conformational space. For this purpose, an algorithm is developed that leads to the generation of an assembly of many local energy minima. From these sets of local minima, one conformation corresponding to the one with the lowest minimum is then selected and designated to represent the backbone segment at its minimum. The effective electrostatic potential of mean force is expressed in terms of adjustable parameters that incorporate solvent screening action in the Coulombic interactions between charged backbone atoms; these parameters are adjusted to obtain the best fit of the nearest-neighbor phosphorous atoms in an x-ray structure.     

Conformational feasibility of a hairpin with two purines in the loop. 5'-d-GGTACIAGTACC-3'

Structural feasibility and conformational requirements for the sequence 5'-d-GGTACIAGTACC-3' to adopt a hairpin loop with I6 and A7 in the loop are studied. It is shown that a hairpin loop containing only two nucleotides can readily be formed without any unusual torsional angles. Stacking is continued on the 5'-side of the loop, with the I6 stacked upon C5. The base A7, on the 3'-side of the loop, can either be partially stacked with I6 or stick outside without stacking. Loop closure can be achieved for both syn and anti conformations of the glycosidic torsions for G8 while maintaining the normal Watson-Crick base pairing with the opposite C5. All torsional angles in the stem fall within the standard B-family of DNA helical structures. The phosphodiesters of the loop have trans,trans conformations. Loop formation might require the torsion about the C4'-C5' bond of G8 to be trans as opposed to the gauche+ observed in B-DNA. These results are discussed in relation to melting temperature studies [Howard et al. (1991) Biochemistry (preceding paper in this issue)] that suggest the formation of very stable hairpin structures for this sequence.     

A model of the strain-induced B-Z transition

The B-to-Z transition in supercoiled circular DNA is modeled as a strain-induced nonlinear excitation process. Using a model, in which DNA is regarded as a chain of units with a bistable energy function along the twisting coordinate together with a harmonic inter-unit interaction, we show that a Z region and the accompanying two B-Z junctions of finite width appear naturally as a solution of nonlinear equations, when the strain exceeds a critical value. We examine the B-Z transition behaviour as a function of twist under various situations. We also analyse available experimental results on B-Z transition in supercoiled plasmid with G-C insertions by this mechanistic model in order to estimate the magnitude of model parameters. The energy barrier of the B-Z transition is estimated to be of the order of 1 kcal/mole per base pair. The analysis shows that if the length of the insertion is less than a certain value, the entire insertion converts to Z form at a transition point, but if the insertion is much longer, the B-Z transition exhibits a different behavior, in which part of the insertion flips to Z form and the Z region expands linearly upon changing linking number.     

Prediction of β-sheets in immunoglobulin chains. Comparison of various methods and an expanded 20 × 20 table for evaluation of the effects of nearest-neighbors on conformations of middle amino acids in proteins

The extraordinarily large number of immunoglobulins renders them an intriguing class of molecules for attempts to predict their conformations. The predictive method applied, using a 20 × 20 table of the observed effects of nearest-neighboring amino acids on the conformation (Φ,Ψ angles) of the middle residue in known proteins, indicates positions of tri-peptides that tend to break α-helices or regular β-sheets. This 20 × 20 table is derived from data on 19 proteins, as compared with the earlier version based on 12 proteins, and includes a separate listing of residues of β-turns that have helical Φ,Ψ values. Secondary conformations predicted by methods of Chou and Fasman, Lim and Burgess, Ponnuswamy, and Scheraga have also been compared; for all three methods, wrong predicitons of residues in β-sheet conformation exceed correct ones. Better predictions are obtained when there is agreement with two or three of the methods. If there is consistent overprediction of β-structure, as with the Chou and Fasman method, the use of the β-sheet-breaking tripeptides can improve pre-dictability somewhat.     

Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching

Information readout in the DNA minor groove is accompanied by substantial DNA deformations, such as sugar switching between the two conformational domains, B-like C2'-endo and A-like C3'-endo. The effect of sugar puckering on the sequence-dependent protein-DNA interactions has not been studied systematically, however. Here, we analyzed the structural role of A-like nucleotides in 156 protein-DNA complexes solved by X-ray crystallography and NMR. To this end, a new algorithm was developed to distinguish interactions in the minor groove from those in the major groove, and to calculate the solvent-accessible surface areas in each groove separately. Based on this approach, we found a striking difference between the sets of amino acids interacting with B-like and A-like nucleotides in the minor groove. Polar amino acids mostly interact with B-nucleotides, while hydrophobic amino acids interact extensively with A-nucleotides (a hydrophobicity-structure correlation). This tendency is consistent with the larger exposure of hydrophobic surfaces in the case of A-like sugars. Overall, the A-like nucleotides aid in achieving protein-induced fit in two major ways. First, hydrophobic clusters formed by several consecutive A-like sugars interact cooperatively with the non-polar surfaces in proteins. Second, the sugar switching occurs in large kinks promoted by direct protein contact, predominantly at the pyrimidine-purine dimeric steps. The sequence preference for the B-to-A sugar repuckering, observed for pyrimidines, suggests that the described DNA deformations contribute to specificity of the protein-DNA recognition in the minor groove.     

A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design.

The interface between protein receptor-ligand complexes has been studied with respect to their binary interatomic interactions. Crystal structure data have been used to catalogue surfaces buried by atoms from each member of a bound complex and determine a statistical preference for pairs of amino-acid atoms. A simple free energy model of the receptor-ligand system is constructed from these atom-atom preferences and used to assess the energetic importance of interfacial interactions. The free energy approximation of binding strength in this model has a reliability of about +/- 1.5 kcal/mol, despite limited knowledge of the unbound states. The main utility of such a scheme lies in the identification of important stabilizing atomic interactions across the receptor-ligand interface. Thus, apart from an overall hydrophobic attraction (Young L, Jernigan RL, Covell DG, 1994, Protein Sci 3:717-729), a rich variety of specific interactions is observed. An analysis of 10 HIV-1 protease inhibitor complexes is presented that reveals a common binding motif comprised of energetically important contacts with a rather limited set of atoms. Design improvements to existing HIV-1 protease inhibitors are explored based on a detailed analysis of this binding motif.     

Molecular diagnostics and chemical analysis for assessing biodegradation of polychlorinated biphenyls in contaminated soils

Summary The microbial populations in PCB-contaminated electric power substation capacitor bank soil (TVA soil) and from another PCB-contaminated site (New England soil) were compared to determine their potential to degrade PCB. Known biphenyl operon genes were used as gene probes in colony hybridizations and in dot blots of DNA extracted from the soil to monitor the presence of PCB-degrading organisms in the soils. The microbial populations in the two soils differed in that the population in New England soil was enriched by the addition of 1000 p.p.m. 2-chlorobiphenyl (2-CB) whereas the population in the TVA capacitor bank soil was not affected. PCB degradative activity in the New England soil was indicated by a 50% PCB disappearance (gas chromatography), accumulation of chlorobenzoates (HPLC), and¹⁴CO₂ evolution from¹⁴C-2CB. The PCB-degrading bacteria in the New England soil could be identified by their positive hybridization to thebph gene probes, their ability to produce the yellowmeta-cleavage product from 2,3-dihydroxybiphenyl (2,3-DHB), and the degradation of specific PCB congeners by individual isolates in resting cell assays. Although the TVA capacitor bank soil lacked effective PCB-degrading populations, addition of a PCB-degrading organism and 10 000 p.p.m. biphenyl resulted in a >50% reduction of PCB levels. Molecular characterization of soil microbial populations in laboratory scale treatments is expected to be valuable in the design of process monitoring and performance verification approaches for full scale bioremediation.     

Radiation carcinogenesis: time-dose relationships

The present studies were undertaken to examine the time-dose relationships for the induction of lung adenocarcinomas and mammary adenocarcinomas in female BALB/c mice following gamma irradiation. Twelve-week-old female BALB/c/An NBd mice were irradiated with 137Cs gamma rays, and lifetime tumor incidences following high-dose-rate, low-dose-rate, or fractionated exposure regimens were compared. Analysis of the results indicated that the data could be fitted by linear-quadratic dose-response models for the induction of both tumors following acute doses and a linear model with a slope similar to that for the linear portion of the linear quadratic following low-dose-rate exposure regimens. When doses were fractionated the response was dependent upon the dose per fraction. If the dose per fraction was a dose which was predominantly on the linear portion of the acute dose response curve, then the response was linear and similar to that after low-dose-rate exposures. If the dose per fraction was in a region where the quadratic portion of the acute dose-response was significant, then the tumor incidence was higher than that following low-dose-rate exposures.     

Strong patterns in homooligomer tracts occurrences in non-coding and in potential regulatory sites in eukaryotic genomes

Previous studies of the dinucleotides flanking both the 5' and 3' ends of homooligomer tracts have shown that some flanks are consistently preferred over others (1,2). In the first preferred group, the homooligomer tracts are flanked by the same nucleotide and/or the complementary nucleotides, e.g.,ATAn,TTAn,CCGn, where n = 2-5. Runs flanked by nucleotides with which they cannot base pair are distinctly disfavored. (In this group An/Tn are flanked by C and/or G; Gn/Cn are flanked by A/T, e.g.,CGAn,TnGG,GnAT). The frequencies of runs flanked by A or T, and G or C ("mixed"group) are as expected. Here we seek the origin of this effect and its relevance to protein-DNA interactions. Surprisingly, within the first group, runs flanked by their complements with a pyrimidine-purine junction (e.g.,TTAn,CnGG) are greatly preferred. The frequencies of their purine-pyrimidine junction mirror-images is just as expected. This effect, as well as additional ones enumerated below, is seen universally in eukaryotes and in prokaryotes, although it is stronger in the former. Detailed analysis of regulatory regions shows these strong trends, particularly in GC sequences. The potential relationship to DNA conformation and DNA-protein interaction is discussed.