Near Homogeneity of PR2-Bias Fingerprints in the Human Genome and Their Implications in Phylogenetic Analyses

Genes of a multicellular organism are heterogeneous in the G+C content, which is particularly true in the third codon position. The extent of deviation from intra-strand equality rule of A = T and G = C (Parity Rule 2, or PR2) is specific for individual amino acids and has been expressed as the PR2-bias fingerprint. Previous results suggested that the PR2-bias fingerprints tend to be similar among the genes of an organism, and the fingerprint of the organism is specific for different taxa, reflecting phylogenetic relationships of organisms. In this study, using coding sequences of a large number of human genes, we examined the intragenomic heterogeneity of their PR2-bias fingerprints in relation to the G+C content of the third codon position (P ₃ ). Result shows that the PR2-bias fingerprint is similar in the wide range of the G+C content at the third codon position (0.30–0.80). This range covers approximately 89% of the genes, and further analysis of the high G+C range (0.80–1.00), where genes with normal PR2-bias fingerprints and those with anomalous fingerprints are mixed, shows that the total of 95% of genes have the similar finger prints. The result indicates that the PR2-bias fingerprint is a unique property of an organism and represents the overall characteristics of the genome. Combined with the previous results that the evolutionary change of the PR2-bias fingerprint is a slow process, PR2-bias fingerprints may be used for the phylogenetic analyses to supplement and augment the conventional methods that use the differences of the sequences of orthologous proteins and nucleic acids. Potential advantages and disadvantages of the PR2-bias fingerprint analysis are discussed. Received: 21 December 2000 / Accepted: 16 February 2001     

Sociality and the Rate of rDNA Sequence Evolution in Wasps (Vespidae) and Honeybees (Apis)

Sequence data of mitochondrial 16S ribosomal DNA (mt-rDNA) and nuclear 28S ribosomal DNA (nuc-rDNA) were compared in two honeybee species (Apis mellifera and Apis dorsata) and a selection of 22 wasp species (Vespidae) with different levels of sociality. The averge substitution rates in mt-rDNA and nuc-rDNA were almost-equal in solitary species. In species with larger nests, however, the difference between the nuclear and the mitochondrial substitution rate significantly increased. The average substitution ratio, ψ (nucleotide substitutions in mt-rDNA/nucleotide substitutions in nuc-rDNA) was 1.48 ± 0.12 (SE) among the solitary Eumeninae, 3.70 ± 0.15 among five primitive social Stenogastrinae species, 3.24 ± 0.20 among five Polistinae species, 5.76 ± 0.33 among nine highly eusocial Vespinae, and 12.7 in the two Apis species. The high egg-laying rate and the effective population size skew between the sexes may contribute to the rise of the substitution ratio in the highly eusocial species. Drift and bottleneck effects in the mitochondrial DNA pool during speciation events as well as polyandry may further enhance this phenomenon. Received: 12 January 1998 / Accepted: 28 April 1998     

Problems with Parsimony in Sequences of Biased Base Composition

Parsimony is commonly used to infer the direction of substitution and mutation. However, it is known that parsimony is biased when the base composition of the DNA sequence is skewed. Here I quantify this effect for several simple cases. The analysis demonstrates that parsimony can be misleading even when levels of sequence divergence are as low as 10%; parsimony incorrectly infers an excess of common to rare changes. Caution must therefore be excercised in the use of parsimony. Received: 13 November 1997 / Accepted: 18 June 1998     

Limitations of compositional approach to identifying horizontally transferred genes

Genes with atypical G+C content and pattern of codon usage in a certain genome are possibly of exotic origin, and this idea has been applied to identify horizontal events. In this way, it was postulated that a total of 755 genes in the E. coli genome are relics of horizontal events after the divergence of E. coli from the Salmonella lineage 100 million years ago (Lawrence and Ochman, 1998). In this paper we propose a new way to study sequence composition more thoroughly. We found that although the 755 genes differ in composition from other genes in the E. coli genome, the difference is minor. If we accepted that these genes are horizontally transferred, then (1) it would be more likely that they were transferred from genomes evolutionarily closely related to E. coli; but (2) the dating method used by Lawrence and Ochman (1997, 1998) largely underestimated the average age of introduced sequences in the E. coli genome, in particular, most of the 755 genes should be introduced into E. coli before, instead of after, the divergence of E. coli from the Salmonella lineage. Our study reveals that atypical G+C content and pattern of codon usage are not reliable indicators of horizontal gene transfer events. Received: 27 September 2000 / Accepted: 9 April 2001     

Early Detection of G + C Differences in Bacterial Species Inferred from the Comparative Analysis of the Two Completely Sequenced Helicobacter pylori Strains

Identifying the G + C difference between closely related bacterial species or between different strains of the same species is one of the first steps in understanding the evolutionary mechanisms accounting for the differences observed among bacterial species. The G + C content can be one of the most important factors in the evolution of genomic structures. In this paper, we describe a new method for detecting an initial stage of differentiation of the G + C content at the third codon base position between two strains of the same bacterial species. We apply this method to the two strains of Helicobacter pylori. A group of genes is detected with large variations of G + C in the third positions—apparently genes of early response to pressures of changing G + C. We discuss our findings from the viewpoint of genomic evolution. Received: 26 February 2001 / Accepted: 16 May 2001     

Coding in the Noncoding DNA Strand: A Novel Mechanism of Gene Evolution?

The question whether the noncoding DNA strand had or still has the capability for encoding functional polypeptides has been addressed in several articles. The theoretical background of the views advocating this idea arose from two groups of findings. One of them was based on various observations implying that the genetic code was adapted for double-strand coding. The other group of theories arose from the observation of gene-length overlapping open reading frames (O-ORFs) on the antisense DNA strand in a number of genes. In fact, the above theories, which I term selectionist, conceive a novel conception of gene evolution, proposing that new genes can be created by the utilization of antisense DNA strand. In contrast, neutralist theory claims that the O-ORFs are mere by-products of evolutionary processes acting to create special codon usage and base distribution patterns in the coding sequences. Received: 16 June 2000 / Accepted: 31 August 2000     

Evolution of Base Composition and Codon Usage Bias in the Genus Flavivirus

The extent to which base composition and codon usage vary among RNA viruses, and the possible causes of this bias, is undetermined in most cases. A maximum-likelihood statistical method was used to test whether base composition and codon usage bias covary with arthropod association in the genus Flavivirus, a major source of disease in humans and animals. Flaviviruses are transmitted by mosquitoes, by ticks, or directly between vertebrate hosts. Those viruses associated with ticks were found to have a significantly lower G+C content than non-vector-borne flaviviruses and this difference was present throughout the genome at all amino acids and codon positions. In contrast, mosquito-borne viruses had an intermediate G+C content which was not significantly different from those of the other two groups. In addition, biases in dinucleotide and codon usage that were independent of base composition were detected in all flaviviruses, but these did not covary with arthropod association. However, the overall effect of these biases was slight, suggesting only weak selection at synonymous sites. A preliminary analysis of base composition, codon usage, and vector specificity in other RNA virus families also revealed a possible association between base composition and vector specificity, although with biases different from those seen in the Flavivirus genus. Received: 29 August 2000 / Accepted: 19 December 2000     

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     

Nucleotide Composition Bias Affects Amino Acid Content in Proteins Coded by Animal Mitochondria

We show that in animal mitochondria homologous genes that differ in guanine plus cytosine (G + C) content code for proteins differing in amino acid content in a manner that relates to the G + C content of the codons. DNA sequences were analyzed using square plots, a new method that combines graphical visualization and statistical analysis of compositional differences in both DNA and protein. Square plots divide codons into four groups based on first and second position A + T (adenine plus thymine) and G + C content and indicate differences in amino acid content when comparing sequences that differ in G + C content. When sequences are compared using these plots, the amino acid content is shown to correlate with the nucleotide bias of the genes. This amino acid effect is shown in all protein-coding genes in the mitochondrial genome, including cox I, cox II, and cyt b, mitochondrial genes which are commonly used for phylogenetic studies. Furthermore, nucleotide content differences are shown to affect the content of all amino acids with A + T- and G + C-rich codons. We speculate that phylogenetic analysis of genes so affected may tend erroneously to indicate relatedness (or lack thereof) based only on amino acid content. Received: 3 July 1996 / Accepted: 6 November 1996     

Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA

The most generally applicable procedure for obtaining estimates of the symmetrical, or strand-nonspecific, directional mutation pressure (μ_D) on protein-coding DNA sequences is to determine the G+C content at synonymous codon sites (P _syn), and to divide P _syn by twice the arithmetic mean of the G+C content at synonymous codon sites of a large number of randomly generated, synonymously coding DNA sequences (P _syn). Unfortunately, the original procedure yields biased estimates of P _syn and μ_D and is computationally expensive. We here present a fast procedure for estimating unbiased μ_D values. The procedure employs direct calculation of P _syn (≈P _syn) and two normalization procedures, one for P _syn≤P _syn and another for P _syn≥P _syn. The normalization removes a bias sometimes caused by codons specifying arginine, asparagine, isoleucine, and leucine. Consequently, comparison of protein-coding genes that are translated using different genetic codes is facilitated. Received: 5 May 1995 / Accepted: 30 November 1995     

Two Aspects of DNA Base Composition: G+C Content and Translation-Coupled Deviation from Intra-Strand Rule of A=T and G=C

The relative contribution of mutation and selection to the G+C content of DNA was analyzed in bacterial species having widely different G+C contents. The analysis used two methods that were developed previously. The first method was to plot the average G+C content of a set of nucleotides against the G+C content of the third codon position for each gene. This method was used to present the G+C distribution of the third codon position and to assess the relative neutrality of a set of nucleotides to that of the G+C content of the third codon position. The second method was to plot the intrastrand bias of the third codon position from Parity Rule 2 (PR2), where A=T and G=C. It was found that whereas intragenomic distributions of the DNA G+C content of these bacteria are narrow in the majority of species, in some species the G+C content of the minor class of genes distributes over wider ranges than the major class of genes. On the other hand, ubiquitous PR2 biases are amino acid specific and independent of the G+C content of DNA, so that when averaged over the amino acids, the biases are small and not correlated with the DNA G+C content. Therefore, translation coupled PR2-biases are unlikely to explain the wide range of G+C contents among different species. Considering all data available, it was concluded that the amino acid-specific PR2 bias has only a minor effect, if any, on the average G+C content. In addition, PR2 bias patterns of different species show phylogenetic relationships, and the pattern can be as a taxal fingerprint. Received: 5 November 1998 / Accepted: 1 March 1999     

Relationships Between Genomic G+C Content,RNA Secondary Structures,and Optimal Growth Temperature in Prokaryotes

G:C pairs are more stable than A:T pairs because they have an additional hydrogen bond. This has led to many studies on the correlation between the guanine+cytosine (G+C) content of nucleic acids and temperature over the last 20 years. We collected the optimal growth temperatures (T_opt) and the G+C contents of genomic DNA; 23S, 16S, and 5S ribosomal RNAs; and transfer RNAs for 764 prokaryotic species. No correlation was found between genomic G+C content and T_opt, but there were striking correlations between the G+C content of ribosomal and transfer RNA stems and T_opt. Two explanations have been proposed—neutral evolution and selection pressure—for the approximate equalities of G and C (respectively, A and T) contents within each strand of DNA molecules. Our results do not support the notion that selection pressure induces complementary oligonucleotides in close proximity and therefore numerous secondary structures in prokaryotic DNA, as the genomic G+C content does not behave in the same way as that of folded RNA with respect to optimal growth temperature. Received: 25 September 1996 / Accepted: 21 January 1997     

The Impermeant Ion Methylammonium Blocks K+ and NH+ 4 Currents through KAT1 Channel Differently: Evidence for Ion Interaction in Channel Permeation

The permeation properties of KAT1, an inward rectifying potassium channel from plant cells, were investigated with different ions in the external medium. With either K⁺, NH⁺ ₄ or methylammonium (MA) in the external solution, the channel, expressed in Xenopus oocytes, appeared permeable to K⁺ and, to a lesser extent, to NH⁺ ₄ but not to the slightly bigger, methylated analogue of NH⁺ ₄, MA. Substituting NH⁺ ₄ for K⁺ shifted the voltage dependency of channel activation further negative and hastened activation kinetics. This suggests that channel operation depends on the transported substrate. In mixed solution (50 mm K⁺, 50 mm MA) MA inhibited K⁺ current in a voltage-independent manner. The maximum block did not exceed 50% of the K⁺ current. In contrast, when NH⁺ ₄ was the permeant ion (50 mm NH⁺ ₄, 50 mm MA) MA caused a voltage-dependent, slowly developing open channel block, achieving complete inhibition at very negative voltages. The latter block could be partially overcome by the addition of K⁺ in the external solution. The data support a model in which ions, after entering the channel pore, compete with different affinities for binding sites on their permeation pathway. Received: 6 October 1997/Revised: 28 January 1998     

Leukotriene D4-induced Ca2+ Mobilization in Ehrlich Ascites Tumor Cells

Stimulation of Ehrlich ascites tumor cells with leukotriene D₄ (LTD₄) within the concentration range 1–100 nm leads to a concentration-dependent, transient increase in the intracellular, free Ca²⁺ concentration, [Ca²⁺] _i . The Ca²⁺ peak time, i.e., the time between addition of LTD₄ and the highest measured [Ca²⁺] _i value, is in the range 0.20 to 0.21 min in ten out of fourteen independent experiments. After addition of a saturating concentration of LTD₄ (100 nm), the highest measured increase in [Ca²⁺] _i in Ehrlich cells suspended in Ca²⁺-containing medium is 260 ± 14 nm and the EC₅₀ value for LTD₄-induced Ca²⁺ mobilization is estimated at 10 nm. Neither the peptido-leukotrienes LTC₄ and LTE₄ nor LTB₄ are able to mimic or block the LTD₄-induced Ca²⁺ mobilization, hence the receptor is specific for LTD₄. Removal of Ca²⁺ from the experimental buffer significantly reduces the size of the LTD₄-induced increase in [Ca²⁺] _i . Furthermore, depletion of the intracellular Ins(1,4,5)P₃-sensitive Ca²⁺ stores by addition of the ER-Ca²⁺-ATPase inhibitor thapsigargin also reduces the size of the LTD₄-induced increase in [Ca²⁺] _i in Ehrlich cells suspended in Ca²⁺-containing medium, and completely abolishes the LTD₄-induced increase in [Ca²⁺] _i in Ehrlich cells suspended in Ca²⁺-free medium containing EGTA. Thus, the LTD₄-induced increase in [Ca²⁺] _i in Ehrlich cells involves an influx of Ca²⁺ from the extracellular compartment as well as a release of Ca²⁺ from intracellular Ins(1,4,5)P₃-sensitive stores. The Ca²⁺ peak times for the LTD₄-induced Ca²⁺ influx and for the LTD₄-induced Ca²⁺ release are recorded in the time range 0.20 to 0.21 min in four out of five experiments and in the time range 0.34 to 0.35 min in six out of eight experiments, respectively. Stimulation with LTD₄ also induces a transient increase in Ins(1,4,5)P₃ generation in the Ehrlich cells, and the Ins(1,4,5)P₃ peak time is recorded in the time range 0.27 to 0.30 min. Thus, the Ins(1,4,5)P₃ content seems to increase before the LTD₄-induced Ca²⁺ release from the intracellular stores but after the LTD₄-induced Ca²⁺ influx. Inhibition of phospholipase C by preincubation with U73122 abolishes the LTD₄-induced increase in Ins(1,4,5)P₃ as well as the LTD₄-induced increase in [Ca²⁺] _i , indicating that a U73122-sensitive phospholipase C is involved in the LTD₄-induced Ca²⁺ mobilization in Ehrlich cells. The LTD₄-induced Ca²⁺ influx is insensitive to verapamil, gadolinium and SK&F 96365, suggesting that the LTD₄-activated Ca²⁺ channel in Ehrlich cells is neither voltage gated nor stretch activated and most probably not receptor operated. In conclusion, LTD₄ acts in the Ehrlich cells via a specific receptor for LTD₄, which upon stimulation initiates an influx of Ca²⁺, through yet unidentified Ca²⁺ channels, and an activation of a U73122-sensitive phospholipase C, Ins(1,4,5)P₃ formation and finally release of Ca²⁺ from the intracellular Ins(1,4,5)P₃-sensitive stores. Received: 9 February 1996/Revised: 15 August 1996     

The Permeation of Ammonium through a Voltage-independent K+ Channel in the Plasma Membrane of Rye Roots

Nitrogen is available to the plant in the form of NH⁺ ₄ in the soil solution. Here it is shown that a voltage-independent K⁺ channel in the plasma membrane of rye (Secale cereale L.) roots is permeable to NH⁺ ₄. The channel was studied following its incorporation into planar 1-palmitoyl-2-oleoyl phosphatidyl ethanolamine bilayers. The unitary conductance of the channel was greater when assayed in the presence of 100 mm NH₄Cl than 100 mm KCl. However, the probability of finding the channel open (P _o ) was lower in the presence of 100 mm NH₄Cl (P _o = 0.63) than in 100 mm KCl (P _o = 0.8), suggesting that P _o can be regulated by the (permeant) ions present in solution. When assayed in equimolar concentrations of NH₄Cl (cis) and KCl (trans), the zero-current (reversal) potential for the channel (E _rev) exhibited a complex concentration dependence. At low cation concentrations, the apparent permeability of NH⁺ ₄ relative to K⁺ (P_NH4/P_K) was greater than 1.0. However, as the cation concentration was increased, P_NH4/P_K initially decreased to a minimum of 0.95 at 3 mm before increasing again to a maximum of 1.89 at 300 mm. At cation concentrations above 300 mm, P_NH4/P_K decreased slightly. This implies that the pore of the channel can be occupied by more than one cation simultaneously. Ammonium permeation through the pore was simulated using a model which is composed of three energy barriers and two energy wells (the ion-binding sites). The model (3B2S) allowed for single-file permeation, double cation occupancy, ion-ion repulsion within the pore and surface potential effects. Results indicated that energy peaks and energy wells were situated asymmetrically within the electrical distance of the pore, that cations repel each other within the pore and that the vestibules to the pore contain negligible surface charge. The energy profile obtained for NH⁺ ₄ is compared with ones obtained for K⁺ and Na⁺. This information allows the fluxes through the K⁺ channel of the three major monovalent cations present in the soil solution to be predicted. Received: 16 October 1995/Revised 12 March 1996     

A Collagen Substrate Enhances the Sealing Capacity of Tight Junctions of A6 Cell Monolayers

A6 cells, a kidney derived epithelial cell line, when cultured either on a collagen-coated substrate or on polycarbonate substrate without collagen form confluent monolayers that are similar in cell density and overall morphology. However, the transepithelial electrical resistance (TER) of monolayers grown on the collagen-coated substrate is ninefold higher than that of monolayers grown without collagen. A comparative freeze-fracture study showed that this large difference in TER is not related to the length or number of tight junction strands but to differences in the specific conductance of individual strands. This conductance was obtained considering the TER, the linear junctional density and the mean number of tight junction strands. We estimated the specific linear conductance of the tight junction strands to be 2.56 × 10⁻⁷ S/cm for cells grown on collagen and 30.3 × 10⁻⁷ S/cm for the cells grown without collagen. We also examined changes in distribution and phosphorylation states of the zonula occludens associated protein, ZO-1, during monolayer formation. Immunocytochemistry reveals that the distribution of ZO-1 follows a similar time course and pattern independent of the presence or absence of collagen. While the amount of ZO-1 expression is identical in cells grown on both substrates, this protein is phosphorylated to a greater extent during the initial stages of confluence in cells cultured on collagen. We suggest that the phosphorylation levels of ZO-1 in A6 cells at the early stages of monolayer formation may determine the final molecular structure and specific conductance of the tight junctions strands. Received: 18 September 1996/Revised: 17 June 1997