Analysis of the Primary Sequence and Secondary Structure of the Unusually Long SSU rRNA of the Soil Bug, Armadillidium vulgare

The complete nucleotide sequence of the SSU rRNA gene from the soil bug, Armadillidium vulgare (Crustacea, Isopoda), was determined. It is 3214 bp long, with a GC content of 56.3%. It is not only the longest SSU rRNA gene among Crustacea but also longer than any other SSU rRNA gene except that of the strepsipteran insect, Xenos vesparum (3316 bp). The unusually long sequence of this species is explained by the long sequences of variable regions V4 and V7, which make up more than half of the total length. RT-PCR analysis of these two regions showed that the long sequences also exist in the mature rRNA and sequence simplicity analysis revealed the presence of slippage motifs in these two regions. The putative secondary structure of the rRNA is typical for eukaryotes except for the length and shape variations of the V2, V4, V7, and V9 regions. Each of the V2, V4, and V7 regions was elongated, while the V9 region was shortened. In V2, two bulges, located between helix 8 and helix 9 and between helix 9 and helix 10, were elongated. In V4, stem E23-3 was dramatically expanded, with several small branched stems. In V7, stem 43 was branched and expanded. Comparisons with the unusually long SSU rRNAs of other organisms imply that the increase in total length of SSU rRNA is due mainly to expansion in the V4 and V7 regions. Received: 2 March 1999 / Accepted: 22 July 1999     

A Probabilistic Treatment of Phylogeny and Sequence Alignment

Carrying out simultaneous tree-building and alignment of sequence data is a difficult computational task, and the methods currently available are either limited to a few sequences or restricted to highly simplified models of alignment and phylogeny. A method is given here for overcoming these limitations by Bayesian sampling of trees and alignments simultaneously. The method uses a standard substitution matrix model for residues together with a hidden Markov model structure that allows affine gap penalties. It escapes the heavy computational burdens of other models by using an approximation called the ``*' rule, which replaces missing data by a sum over all possible values of variables. The behavior of the model is demonstrated on test sets of globins. Received: 25 May 1998 / Accepted: 8 December 1998     

Characteristics of the Quenching of 9-Aminoacridine Fluorescence by Liposomes Made from Plant Lipids

Several laboratories have determined the surface charge density of membranes utilizing methods based on vesicle-induced quenching of the fluorescence of 9-aminoacridine and its relief by other cations. However, the computational methods by which surface charge density were calculated have not been verified in a model system. In this study, the quenching of 9-aminoacridine fluorescence by liposomes made from varying amounts of digalactosyldiacylglyceride and phosphatidic acid and relief of quenching by salts was examined. Quenching of 9-aminoacridine fluorescence increased with increasing amounts of phosphatidic acid added, independent of the composition of the added liposomes. In certain instances, the computational methods did not yield the surface charge density of the liposomes expected from their composition. However, when the effects of background ionic strength on surface potential were considered, there was a positive correlation between expected and calculated values. Therefore, the data support the contention that changes in the fluorescence of 9-aminoacridine can be used to calculate surface charge density of membranes. Received: 29 November 1999/Revised: 31 July 2000     

Intron Length and Codon Usage

The correlation was shown between the length of introns and the codon usage of the coding sequences of the corresponding genes, which in some cases can be related to the level of gene expression. The link is positive in the unicellular organisms, i.e., genes with the longer introns show the higher bias of codon usage. It is most pronounced in baker's yeast, where it is definitely related to the level of gene expression—genes with the higher level of expression have the longer introns. The correlation is inverted in multicellular organisms as compared to unicellular ones. Some organisms, however, do not show the link. The presence or absence of the link does not seem to be related to the GC percent of the coding sequences. Received: 7 December 1999 / Accepted: 10 May 2000     

Temperature Sensing by Plants: Calcium-Permeable Channels as Primary Sensors—A Model

Recently the properties of temperature sensing in plants have been demonstrated experimentally by Plieth et al. (The Plant Journal 1999. 18:491–497). The relevant biophysical parameters are established here by mathematical modeling in order to understand the experimental findings in quantitative terms. A simple one-compartment model is presented, as a preliminary approach to explain how the input signal (i.e., temperature T) is perceived and how the information is translated into an output signal in the plant cell (i.e., [Ca²⁺] _c ). The model is based on the fact that calcium influx into the cytoplasm is mediated by calcium-permeable channels which are assumed to be solely dependent on cooling rate (dT/dt) and calcium efflux is mediated by calcium pumps which have been shown to be dependent on absolute temperature (T). Firstly, it is demonstrated that this model is able to meet the demand for a satisfactory interpretation of the experimental data, and secondly that it reproduces the experimentally observed features of the cooling induced [Ca²⁺] _c changes well. This suggests that the primary temperature sensor in plants might be a Ca²⁺-permeable channel. Received: 4 June 1999/Revised: 26 July 1999     

Sensitivity of Patterns of Molecular Evolution to Alterations in Methodology: A Critique of Hughes and Yeager

Employing a set of 43 othologous mouse and rat genes, Hughes and Yeager (J. Mol. Evol. 45:125–130, 1997) reported (1) no correlation between synonymous and nonsynonymous rates of nucleotide substitution, (2) a positive correlation between intronic GC contents (GC _i) and intronic substitution rates (K _i), (3) that the average K _i value was very similar to the average K _s value, and (4) that the compositional correlation between the rat and the mouse genes is stronger at the third codon position (GC₃) than at the first and second codon positions (GC₁₂). We have examined the robustness of these results to alterations in substitution rate estimation protocol, alignment protocol, and statistical procedure. We find that a significant correlation between K _a and K _s is observed either if a rank correlation statistic is used instead of regression analysis, if one outlier is excluded from the analysis, or if a regression weighted by gene size is employed. The correlation between K _i and GC _i we find to be sensitive to changes in alignment protocol and disappears on the use of weighted means. The finding that K _s and K _i are approximately the same is dependent on the method for estimating K _s values. Finally, the variance around the regression line of rat GC₃ versus mouse GC₃ we find to be significantly higher than that in GC₁₂. The source of the discrepancy between this and Hughes and Yeager's result is unclear. The variance around the line for GC₄ is higher still, as might be expected. Using a methodology that may be considered preferable to that of Hughes and Yeager, we find that all four of their results are contradicted. More importantly this analysis reinforces the need for caution in assembling and analyzing data sets, as the degree of sensitivity to what many might consider minor methodological alterations is unexpected. Received: 2 February 1998 / Accepted: 23 March 1998     

Assessing Variability by Joint Sampling of Alignments and Mutation Rates

When two sequences are aligned with a single set of alignment parameters, or when mutation parameters are estimated on the basis of a single ``optimal' sequence alignment, the variability of both the alignment and the estimated parameters can be seriously underestimated. To obtain a more realistic impression of the actual uncertainty, we propose sampling sequence alignments and mutation parameters simultaneously from their joint posterior distribution given the two original sequences. We illustrate our method with human and orangutan sequences from the hyper variable region I and with gene–pseudogene pairs. Received: 16 November 2000 / Accepted: 15 May 2001     

A New Structural Model for P-Glycoprotein

Multidrug resistance to anti-cancer drugs is a major medical problem. Resistance is manifested largely by the product of the human MDR1 gene, P-glycoprotein, an ABC transporter that is an integral membrane protein of 1280 amino acids arranged into two homologous halves, each comprising 6 putative transmembrane α-helices and an ATP binding domain. Despite the plethora of data from site-directed, scanning and domain replacement mutagenesis, epitope mapping and photoaffinity labeling, a clear structural model for P-glycoprotein remains largely elusive. In this report, we propose a new model for P-glycoprotein that is supported by the vast body of previous data. The model comprises 2 membrane-embedded 16-strand β-barrels, attached by short loops to two 6-helix bundles beneath each barrel. Each ATP binding domain contributes 2 β-strands and 1 α-helix to the structure. This model, together with an analysis of the amino acid sequence alignment of P-glycoprotein isoforms, is used to delineate drug binding and translocation sites. We show that the locations of these sites are consistent with mutational, kinetic and labeling data. Received: 18 February 1998/Revised: 2 September 1998     

Classification and Phylogenetic Analysis of the cAMP-Dependent Protein Kinase Regulatory Subunit Family

The members of the PKA regulatory subunit family (PKA-R family) were analyzed by multiple sequence alignment and clustering based on phylogenetic tree construction. According to the phylogenetic trees generated from multiple sequence alignment of the complete sequences, the PKA-R family was divided into four subfamilies (types I to IV). Members of each subfamily were exclusively from animals (types I and II), fungi (type III), and alveolates (type IV). Application of the same methodology to the cAMP-binding domains, and subsequently to the region delimited by β-strands 6 and 7 of the crystal structures of bovine RIα and rat RIIβ (the phosphate-binding cassette; PBC), proved that this highly conserved region was enough to classify unequivocally the members of the PKA-R family. A single signature sequence, F–G–E–[LIV]–A–L–[LIMV]–x(3)–[PV]–R–[ANQV]–A, corresponding to the PBC was identified which is characteristic of the PKA-R family and is sufficient to distinguish it from other members of the cyclic nucleotide-binding protein superfamily. Specific determinants for the A and B domains of each R-subunit type were also identified. Conserved residues defining the signature motif are important for interaction with cAMP or for positioning the residues that directly interact with cAMP. Conversely, residues that define subfamilies or domain types are not conserved and are mostly located on the loop that connects α-helix B′ and β strand 7. Received: 2 November 2000/Accepted: 14 June 2001     

Are Noncoding Sequences of Rickettsia prowazekii Remnants of ``Neutralized' Genes?

It has been hypothesized that a large fraction of 24% noncoding DNA in R. prowazekii consists of degraded genes. This hypothesis has been based on the relatively high G+C content of noncoding DNA. However, a comparison with other genomes also having a low overall G+C content shows that this argument would also apply to other bacteria. To test this hypothesis, we study the coding potential in sets of genes, pseudogenes, and intergenic regions. We find that the correlation function and the χ²-measure are clearly indicative of the coding function of genes and pseudogenes. However, both coding potentials make almost no indication of a preexisting reading frame in the remaining 23% of noncoding DNA. We simulate the degradation of genes due to single-nucleotide substitutions and insertions/deletions and quantify the number of mutations required to remove indications of the reading frame. We discuss a reduced selection pressure as another possible origin of this comparatively large fraction of noncoding sequences. Received: 27 December 1999 / Accepted: 5 July 2000     

Branch Length Heterogeneity Leads to Nonindependent Branch Length Estimates and Can Decrease the Efficiency of Methods of Phylogenetic Inference

Branch length estimates play a central role in maximum-likelihood (ML) and minimum-evolution (ME) methods of phylogenetic inference. For various reasons, branch length estimates are not statistically independent under ML or ME. We studied the response of correlations among branch length estimates to the degree of among-branch length heterogeneity (BLH) in the model (true) tree. The frequency and magnitude of (especially negative) correlations among branch length estimates were both shown to increase as BLH increases under simulation and analytically. For ML, we used the correct model (Jukes–Cantor). For ME, we employed ordinary least-squares (OLS) branch lengths estimated under both simple p-distances and Jukes–Cantor distances, analyzed with and without an among-site rate heterogeneity parameter. The efficiency of ME and ML was also shown to decrease in response to increased BLH. We note that the shape of the true tree will in part determine BLH and represents a critical factor in the probability of recovering the correct topology. An important finding suggests that researchers cannot expect that different branches that were in fact the same length will have the same probability of being accurately reconstructed when BLH exists in the overall tree. We conclude that methods designed to minimize the interdependencies of branch length estimates (BLEs) may (1) reduce both the variance and the covariance associated with the estimates and (2) increase the efficiency of model-based optimality criteria. We speculate on possible ways to reduce the nonindependence of BLEs under OLS and ML. Received: 9 March 1999 / Accepted: 4 May 1999     

Thermal Stability of the Plasma Membrane Calcium Pump. Quantitative Analysis of Its Dependence on Lipid-Protein Interactions

Thermal stability of plasma membrane Ca²⁺ pump was systematically studied in three micellar systems of different composition, and related with the interactions amphiphile-protein measured by fluorescence resonance energy transfer. Thermal denaturation was characterized as an irreversible process that is well described by a first order kinetic with an activation energy of 222 ± 12 kJ/mol in the range 33–45°C. Upon increasing the mole fraction of phospholipid in the mixed micelles where the Ca²⁺ pump was reconstituted, the kinetic coefficient for the inactivation process diminished until it reached a constant value, different for each phospholipid species. We propose a model in which thermal stability of the pump depends on the composition of the amphiphile monolayer directly in contact with the transmembrane protein surface. Application of this model shows that the maximal pump stability is attained when 80% of this surface is covered by phospholipids. This analysis provides an indirect measure of the relative affinity phospholipid/detergent for the hydrophobic transmembrane surface of the protein (K _LD ) showing that those phospholipids with higher affinity provide greater stability to the Ca²⁺ pump. We developed a method for directly measure K _LD by using fluorescence resonance energy transfer from the membrane protein tryptophan residues to a pyrene-labeled phospholipid. K _LD values obtained by this procedure agree with those obtained from the model, providing a strong evidence to support its validity. Received: 5 August 1999/Revised: 20 October 1999     

Concurrent Neutral Evolution of mRNA Secondary Structures and Encoded Proteins

Messenger RNA sequences often have to preserve functional secondary structure elements in addition to coding for proteins. We present a statistical analysis of retroviral mRNA which supports the hypothesis that the natural genetic code is adapted to such complementary coding. These sequences are still able to explore efficiently the space of possible proteins by point mutations. This is borne out by the observation that, in stem regions of retroviral mRNA foldings, silent mutations on one strand are preferentially accompanied by conservative mutations on the other. Distances between amino acids based on physicochemical properties are used to quantify the conservation of protein function under the constraint of maintained RNA secondary structure. We find that preservation of RNA secondary structure by compensatory mutations is evolutionary compatible with the efficient search for new variants on the protein level. Received: 4 June 1999 / Accepted: 12 October 1999     

The Codon-Degeneracy Model of Molecular Evolution

Mitochondrial genetic codons can be categorized by four patterns of nucleotide-site degeneracy based on varying combinations of twofold- or nondegenerate sites at first codon positions and twofold- or fourfold-degenerate sites at third codon positions. Herein, a model of molecular evolution is introduced that uses these patterns to calculate expected substitution frequencies for each codon position and substitution type relative to overall number of synonymous or nonsynonymous substitutions. Regions of the pocket gopher cytochrome oxidase subunit I (COI) and cytochrome b (cyt-b) genes are analyzed using this model. Chi-square distributions are used to produce relative goodness-of-fit (GF) scores for measuring the difference between substitution frequencies predicted by the codon-degeneracy model (CDM), and frequencies inferred using a well-supported phylogenetic tree of closely related species. The GF scores for expected and observed synonymous (GF_syn= 0.429, p= 0.807) and nonsynonymous (GF_ns= 2.309, p= 0.679) substitution frequencies resulted in a failure to reject the CDM as a null hypothesis for the molecular evolution of COI and cyt-b in pocket gophers. Alternative tree topologies and calculations of transition bias for these data result in higher GF scores. Received: 25 March 1999 / Accepted: 17 September 1999     

Molecular Evolution in a Multisite Nearly Neutral Mutation Model

A simple nearly neutral mutation model of protein evolution was studied using computer simulation assuming a constant population size. In this model, a gene consists of a finite number of codons and there is no recombination within a gene. Each codon has two replacement and one silent sites. The fitness of a gene was determined multiplicatively by amino acids specified by codons (the independent multicodon model). Nucleotide diversity at replacement sites decreases as selection becomes stronger. A reduction of nucleotide diversity at silent sites also occurs as selection intensifies but the magnitude of the reduction is not a monotone function of the intensity of selection. The dispersion index is close to one. The average value of Tajima's and Fu and Li's statistics are negative and their absolute values increases as selection intensifies. However, their powers of detecting selection under the present model were not high unless the number of sites is large or mutation rate is high. The MK test was shown to detect intermediate selection fairly well. For comparison, the house-of-cards model was also investigated and its behavior was shown to be more sensitive to changes of population size than that of the independent multicodon model. The relevance of the present model for explaining protein evolution was discussed comparing its prediction and recent DNA data. Received: 24 May 1999 / Accepted: 17 August 1999     

The Molecular Evolutionary History of a Winged Bean α-Chymotrypsin Inhibitor and Modeling of Its Mutations Through Structural Analyses

A serine protease inhibitor of the Kunitz-STI (soybean trypsin inhibitor) family, isolated from the legume seeds of winged bean, was found to inhibit chymotrypsin at a 1:2 stoichiometric ratio. When the structure was determined in our laboratory, it was found to form a characteristic β-trefoil fold, which is also seen in other proteins from distant families and sources. The folding organization divides the protein into three approximately equal subdomains related by a pseudo-threefold axis of symmetry passing parallel to the barrel axis of the trefoil. Following the now established idea that the present-day genes originated from ancestral minigenes through evolution, the origin of the proteins having this β-trefoil organization is scrutinized using its subdomain motif as the search probe. The results, based mainly on structural analyses, indicate the independent existence of such a motif, mimicking the unknown ancestral protein(s) that might have been distributed in nature, not only by gene duplication, but also by insertion and permutation in other folds. The understanding led to a hypothesis for the possible origin of the Kunitz-STI family. On the basis of this model of evolution, structurally hypervariable regions were located on the protein where mutations could be designed and a broad range of engineering of the protein's activity could be conceived. Received: 20 January 1999 / Accepted: 6 October 1999     

Micromechanics and anatomical changes during early ontogeny of two lianescent Aristolochia species

 The mechanical properties of young stems of Aristolochia macrophylla Lam. and Aristolochia brasiliensis Mart. et Zucc. were studied during elongation growth and primary differentiation. Data for the modulus of elasticity, for the viscoelastic behaviour caused by longitudinal tension and for the shear modulus resulting from torsion around a longitudinal axis were related to the underlying structural changes by quantitative analysis of stem anatomy, tissue distribution, ultrastructure, and cell wall biochemistry. The orientation of cellulose microfibrils was determined by light microscopy and small-angle X-ray diffraction, and the lignin content was determined by thioglycolic acid derivatization and spectroscopic quantification. It was demonstrated that the increase in stability during early development is due to the complementary effects of increase in cell wall material, lignification, and cellulose microfibril alignment. A detailed micromechanical model, considering internal prestresses, is proposed to explain the characteristic biphasic stress-strain behaviour as well as the strain-hardening observed. Received: 22 March 1999 / Accepted 9 September 1999     

Identification of Two Essential Arginine Residues in UhpT, the Sugar Phosphate Antiporter of Escherichia coli

Three lines of evidence indicate that arginine-46 (R46) and arginine-275 (R275) are essential to the function of UhpT, the Pi-linked antiport protein of Escherichia coli. A role for arginine was initially suggested by the sensitivity of UhpT to inhibition by 2,3-butanedione, an arginine-directed probe. Since the presence of substrate protected against this inhibition, this work further suggested that arginine(s) may lie at or near the UhpT active site. In other work, each UhpT arginine was examined individually by using site-directed mutagenesis to generate a cysteine or a lysine derivative. With two exceptions (R46, R275), all arginines could be replaced by either cysteine (10 of 14 residues) or lysine (12 of 14) without loss of function, implicating R46 and R275 as essential to UhpT function. This idea was strengthened by examining a multiple alignment of the eleven known UhpT-related proteins (≥30% identity). That alignment showed R46 and R275 were two of the only three arginines strongly conserved in this group of proteins. Considered together, these different approaches lead us to conclude that UhpT and its relatives have only two arginine residues (R46, R275) whose presence is essential to function. Prior biochemical work had placed R275 at the external entrance to the translocation pathway, and a symmetry argument emerging from the multiple alignment suggests a similar position for R46. Accordingly, by virtue of their locations at the entrance to this pathway, we speculate that R46 and R275 function in establishing substrate specificity. Received: 29 January 1998/Revised: 13 April 1998     

Compositional Correlations in the Chicken Genome

This paper analyses the compositional correlations that hold in the chicken genome. Significant linear correlations were found among the regions studied—coding sequences (and their first, second, and third codon positions), flanking regions (5′ and 3′), and introns—as is the case in the human genome. We found that these compositional correlations are not limited to global GC levels but even extend to individual bases. Furthermore, an analysis of 1037 coding sequences has confirmed a correlation among GC₃, GC₂, and GC₁. The implications of these results are discussed. Received: 9 December 1998 / Accepted: 18 April 1999